Collection coverage

Benchmark results and remaining gaps

See which pages have checked results and charts, and which still need their published evidence collected.

Release 2026-09-30-e37e3ab1284d. Counts include results reached through source-backed membership links. A metric row is not an independent experiment. Charts keep a source, protocol, dataset and metric together.

Pages without results indicate gaps in this collection. A paper may contain experiments we have not yet transcribed. We do not substitute unrelated results or zero scores for missing evidence.

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Benchmarks

51 pages · 50 with results · 38 with charts.

Page	Evaluations / metric rows	Charts	Collection status
ATOM3D	57 / 57	14 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
BEACON	221 / 221	13 source-scoped figures	Checked result tables available. Scope and remaining work Multi-task suite; model adaptation and metric differ by task. Full comparison table extraction remains pending; no composite RNA score inferred.
BEELINE	384 / 588	71 source-scoped figures	Checked result tables available. Scope and remaining work Primary XML has no numeric table-wrap results; comparisons are figures and supplementary data. Exact full model-by-dataset scores require supplemental/source-data extraction, not digitizing figure heights.
BEND	105 / 105	7 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
CAFA	438 / 438	6 source-scoped figures	Checked result tables available. Scope and remaining work Main tables describe participation and benchmark construction; numerical performance is mainly in figures/supplementary files. CAFA versions, ontology branch, full/partial mode and no/limited-knowledge cohorts must remain separate. No scores estimated from plot pixels.
CAMI	16 / 256	16 source-scoped figures	Checked result tables available. Scope and remaining work Main Table 1 gives best-ranked software, not a complete numerical score table. Assembly, genome binning, taxonomic binning and taxonomic profiling are separate tasks; strain diversity and sample cohorts must be separated. Further source-data extraction remains before new score publication.
Cancer Immunotherapy Data Science Challenge	54 / 54	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAPRI	100 / 400	16 source-scoped figures	Checked result tables available. Scope and remaining work Round 54 has 37 targets and 38 assessment units; round 57 has 34 targets and 47 units. These are different denominators. Official page says data may change; pin each round CSV before numerical ingestion. Freshly discovered Rosetta CAPRI rounds 47–55 paper (PMC12462888) was blocked: Europe PMC HTTP 500 and PMC browser challenge. It is not a universal all-participant assessment.
CASP	90 / 270	6 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
CIViC MCP 2026 evidence-retrieval evaluation	3 / 162	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro Protein Docking Benchmark 5.0 study	16 / 111	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval	316 / 316	23 source-scoped figures	Checked result tables available. Scope and remaining work Regulatory sequence detection, TF motifs, cell-type activity and variant effects are distinct protocols. Enhancer broad-task record must link concrete tasks, not inherit every DART result. Existing DART observations require source-cell identity reuse.
ENIGMA 2024 BRCA evidence-calibration and curation study	5 / 39	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ESMFold2 Runs N’ Poses comparison	11 / 11	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP	155 / 155	15 source-scoped figures	Checked result tables available. Scope and remaining work No suite-wide raw score. Random splits and biologically motivated splits are distinct. Thermostability NA entries are not zeros; Table 4 includes negative Spearman correlations. No new numeric extraction in this scoped release; full tables identified.
FLIP2	149 / 293	33 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
FoldBench	45 / 175	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FramePool translation-prediction study	30 / 30	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB	80 / 80	16 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GENEB	22 / 22	2 source-scoped figures	Checked result tables available. Scope and remaining work Broad benchmark suite with task-specific cohorts and adaptations. Main artifact acquired; complete per-task table and supplement extraction remains pending.
Genie 3 unconditional short monomer comparison	13 / 65	5 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks	18 / 36	18 source-scoped figures	Checked result tables available. Scope and remaining work The two implementations are not distinct foundation-model families. Dataset totals in Table 1 are not test-set denominators. Table 2 does not enumerate dataset-version numbers, split file hashes or replicate uncertainty.
GlycanML	323 / 323	50 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
GUE	280 / 280	28 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
HEST-Benchmark	100 / 100	10 source-scoped figures	Checked result tables available. Scope and remaining work New web search finds updated official benchmark inventory; current README values cannot be assigned to original v 1 paper configurations. Fresh PDF retrieval failed; cached pinned v 1 PDF preserved. Complete table extraction remains pending.
Jores plant promoter prediction study	4 / 4	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MassSpecGym	24 / 116	28 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MIST CANOPUS molecular retrieval	6 / 45	8 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MPRabc K562 enhancer–gene evaluation	6 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench	696 / 700	26 source-scoped figures	Checked result tables available. Scope and remaining work Table 5 labels localization columns Pearson R while Table 2 labels them AUPRC; quarantine those metric identities pending reconciliation. Appendix C claims ten splits but enumerates nine seeds. Record ten as reported, with discrepancy, not an inferred tenth seed. Tables 5–6 uncertainties are 95% confidence intervals, not standard deviations. Task/subtask pooling and transformed aggregate rankings must not be conflated with printed raw metrics.
MSAlign molecular retrieval evaluations	63 / 189	24 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench	1101 / 1101	43 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
OncoVI 2026 oncogenicity evaluation study	5 / 27	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems	384 / 384	24 source-scoped figures	Checked result tables available. Scope and remaining work Task release, dataset, preprocessing and metric must be fixed before charting. The page lists multiple releases; a downloaded release artifact is needed to pin exact numerical leaderboard observations. No values estimated from chart coordinates.
PerturBench	76 / 76	8 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
PEtab benchmark collection	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Collection of parameter-estimation problems, not one universal biological accuracy benchmark. Model/dataset identifiers, objective, solver and restart budget are necessary before comparing runs. No universal score generated.
PFMBench	141 / 141	12 source-scoped figures	Checked result tables available. Scope and remaining work Core-model filtering and excluded poorly performing tasks make Table 3 a selected subset, not all 17 models across every task. Task metrics and 30% sequence-identity splits vary; Table 1 maps each. Full values staged only after task-specific extraction; no overall family ranking inferred.
Plant Genomic Benchmark (PGB)	24 / 24	12 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PLINDER	7 / 33	5 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
ProteinBench	556 / 556	95 source-scoped figures	Checked result tables available. Scope and remaining work Mean/median slash pairs in Table 7 are not uncertainty. EigenFold removes unknown amino acids and lacks a peptide-bond metric; preserve applicability caveats. Do not transfer Table 8 bootstrap uncertainty to Table 7.
ProteinGym	187 / 328	17 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
RhoFold+ CASP15 natural RNA comparison	56 / 112	12 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoMax original wavelength-prediction comparison	15 / 60	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scFoundation cell-type annotation comparison	14 / 14	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scIB	69 / 821	13 source-scoped figures	Checked result tables available. Scope and remaining work Bio-conservation and batch-removal components depend on datasets and preprocessing. Figures do not justify new exact numerical scores; official source-data matrix extraction remains pending. Broad batch integration is not identical to scIB or Open Problems.
scTab published annotation evaluation	21 / 26	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation	294 / 588	28 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos 2026 evaluation and reanalysis study	14 / 82	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TAPE	50 / 50	5 source-scoped figures	Checked result tables available.
TDC molecular tasks	66 / 66	22 source-scoped figures	Checked result tables available. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows. Fresh arXiv v1 retrieval was incomplete and primary NSF v2 retrieval timed out; cached v1 bytes were hash-verified. The v2 full text is not claimed to have been reviewed.
Virtual Cell Challenge 2026	1048 / 1048	14 source-scoped figures	Checked result tables available. Scope and remaining work Challenge scope found; this pass does not establish a final published 2026 result table. Do not copy 2025 rankings into 2026 challenge.

Tasks

495 pages · 473 with results · 389 with charts.

Page	Evaluations / metric rows	Charts	Collection status
A-to-I RNA editing site prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work This is validation-set reporting, not a cleanly identified untouched test set. Table 2 calls it the '15% liver validation set', while methods describe held-out 20% validation; retain wording and resolve data partition before external ranking. No uncertainty in the table.
antibody deamidation-site prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Antibody loop structure prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. Antibodyloops cannot be pooled withnanobody/TCR cohorts orframeworkRMSD; sixloopregions separate. LowerÅRMSD; nanobodylight-chain N/A retained. Structured extraction pending.
Antibody–antigen interaction prediction using folded complexes	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Original structure 0.89 ± 0.05 spans columns and is one reference result, not three independent results. Table 3 XML merges three RMSD cells using ampersands; numeric normalization needs explicit splitting/visual check. Confidence pTM/ipTM is not experimental interaction accuracy.
antigen-antibody HIV neutralization prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Keep the three held-out-entity regimes separate. Section S1 contains detailed split/hyperparameter information; no sequence-design or biological optimization material is part of this extraction.
ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D LEP-AUROC: Ligand efficacy prediction	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D MSP: Mutation stability prediction	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D PIP: Protein interface prediction	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D RES: Residue identity	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D SMP-MU: Small molecule properties, dipole moment	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ATOM3D SMP-U0AT: Small molecule properties, atomization energy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Bacterial promoter prediction	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Broad bacterial promoter prediction includes other organisms and dataset constructions; one E. coli table is not a universal ranking.
Batch integration	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Bio-conservation and batch-removal components depend on datasets and preprocessing. Figures do not justify new exact numerical scores; official source-data matrix extraction remains pending. Broad batch integration is not identical to scIB or Open Problems.
BEACON APA: Alternative polyadenylation isoform prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON CMP: Contact map prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON CRI-Off: CRISPR off-target effect prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON CRI-On: CRISPR on-target efficiency prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON DMP: Distance map prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON Modif: RNA modification site prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON MRL: Mean ribosome loading prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON ncRNA: Non-coding RNA family classification	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON PRS: Programmable RNA switch prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON SPL: Splice site prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON SSI: Structure score imputation	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON SSP: Secondary structure prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEACON VDP: Vaccine degradation prediction	17 / 17	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND CHROMATIN: Chromatin accessibility	15 / 15	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND CPG: CpG methylation	15 / 15	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND ENHANCER: Enhancer annotation	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND GENE-FINDING: Gene finding	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND HISTONE: Histone modification	15 / 15	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND VARIANT-DISEASE: Noncoding variant effects on disease	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEND VARIANT-EXPRESSION: Noncoding variant effects on expression	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Biomolecular complex structure	0 / 0	Not yet available	Published results still to collect. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
CAMI genome binning	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Main Table 1 gives best-ranked software, not a complete numerical score table. Assembly, genome binning, taxonomic binning and taxonomic profiling are separate tasks; strain diversity and sample cohorts must be separated. Further source-data extraction remains before new score publication.
CAMI II phylum read classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table 5 prints NCD only. Narrative compares Kraken2 but supplies no paired numerical Kraken2 row; do not manufacture a two-model chart. Do not attach five-fold Human DNA results from Table 3 to CAMI II.
CAMI II superkingdom read classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table 5 prints NCD only. Narrative compares Kraken2 but supplies no paired numerical Kraken2 row; do not manufacture a two-model chart. Do not attach five-fold Human DNA results from Table 3 to CAMI II.
CAMI metagenome assembly	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Main Table 1 gives best-ranked software, not a complete numerical score table. Assembly, genome binning, taxonomic binning and taxonomic profiling are separate tasks; strain diversity and sample cohorts must be separated. Further source-data extraction remains before new score publication.
CAMI taxonomic binning	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Main Table 1 gives best-ranked software, not a complete numerical score table. Assembly, genome binning, taxonomic binning and taxonomic profiling are separate tasks; strain diversity and sample cohorts must be separated. Further source-data extraction remains before new score publication.
CAMI taxonomic profiling	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Main Table 1 gives best-ranked software, not a complete numerical score table. Assembly, genome binning, taxonomic binning and taxonomic profiling are separate tasks; strain diversity and sample cohorts must be separated. Further source-data extraction remains before new score publication.
CATH superfamily annotation	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
cell-type annotation	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Cell-type annotation	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Cell-type identification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Cell-type structure in frozen embeddings	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
clathrin protein classification	14 / 79	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
ClinVar 3-prime UTR variant classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw matrix acquired. Five methods for assignedUTRrow; othervariantclasses remain separate. Alignment-aware versus sequence-only inputs explicit; no architecture equivalence inferred. Structured extraction pending.
Combinatorial cell-label classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Partial-credit and full-label metrics cannot share a ranking; keep dataset and label regime explicit. Version is the archived preprint, not a later model family release.
Community profiling	0 / 0	Not yet available	Published results still to collect. Scope and remaining work OPAL is an evaluator rather than a single dataset. Numerical comparisons require selected community dataset, taxonomic rank and profiling output version. No complete main-text score matrix; source data remains pending.
Cross-dataset single-cell drug response transfer	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Keep bulk and single-cell settings explicit; do not call this feature-unseen inductive transfer. Standard deviations are printed; resolve exact aggregation population from scenario-level source data before attaching seed-count error bars.
Cross-platform scATAC cell-type annotation	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Reference-to-query direction is part of protocol identity; reversed pairs are not replicates. Inputs and adaptation differ across baselines; scJoint uses scATAC at both stages and Cellcano follows its original target-size-dependent rounds. No uncertainty in tables; F1 and accuracy printed separately, including slash-joined Table 3 cells.
cross-species conservation prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table 1 is not a complete baseline comparison: named full-baseline scores are in Fig. 2/source workbook. Do not invent model identities from 'best benchmark'. Keep lower PlantCAD2 non-TIS score as printed.
DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval CTS-K562: Cell-type-specific element classification, K562	14 / 14	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval REI-ABS: Regulatory element identification, absolute accuracy	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval REI-PAIR: Regulatory element identification, paired accuracy	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC	22 / 22	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC	22 / 22	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
differentially expressed gene identification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Do not pool cell types or recall thresholds; table gives no uncertainty for these cells.
DNA-binding residue prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. Assigned benchmark is DNA-binding; RNA cohorts need distinct protocols. PCC-to-MegSite agreement and associatedPvalues are not predictive performance. Structured extraction pending.
Donor-aware age-class prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw comparison acquired. Best-scFM is a selected pipeline, not a named family by inference. PCA, permutation mean/p 95 and chance 1/K remain separate reference types. Structured extraction pending.
Donor-held-out reference mapping	0 / 0	Not yet available	Published results still to collect. Scope and remaining work A split by batch/reference is not automatically a donor-held-out split. A chart needs the exact dataset donor manifest. Open Problems controls and normalization choices must remain separate from raw label accuracy/F1.
E. coli sigma70 promoter prediction	15 / 60	4 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
E. coli sigma70 promoter prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Enhancer / MPRA effects	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Regulatory sequence detection, TF motifs, cell-type activity and variant effects are distinct protocols. Enhancer broad-task record must link concrete tasks, not inherit every DART result. Existing DART observations require source-cell identity reuse.
Enhancer classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
enhancer prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Text S6 defines the independent test set; supplementary data is necessary for a complete dataset manifest. Table 2 does not report replicate uncertainty; other-method provenance must retain paper citations rather than imply all were rerun.
enhancer prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Published Fig. 5/6 advanced-model comparisons require figure/source-data review; do not pretend Table 3 gives scores. Avoid mixing human and mouse populations or treating source-level similarity filtering as an exact split manifest.
enhancer recognition	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Enhancer-target gene prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Enzyme functional identity prediction	5 / 40	8 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
extremely long RNA species classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work No uncertainty in Table 2; exact long-sequence window/aggregation details remain tied to this paper's downstream classifiers. Species classification scores do not measure RNA-structure accuracy.
FLIP AAV-1-VS-REST: AAV fitness prediction, 1-vs-rest split	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP AAV-2-VS-REST: AAV fitness prediction, 2-vs-rest split	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP AAV-7-VS-REST: AAV fitness prediction, 7-vs-rest split	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP AAV-DES-MUT: AAV fitness prediction, Des-Mut split	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP AAV-LOW-VS-HIGH: AAV fitness prediction, low-vs-high split	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP AAV-MUT-DES: AAV fitness prediction, Mut-Des split	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP GB1-1-VS-REST: GB1 fitness prediction, 1-vs-rest split	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP GB1-2-VS-REST: GB1 fitness prediction, 2-vs-rest split	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP GB1-3-VS-REST: GB1 fitness prediction, 3-vs-rest split	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP GB1-LOW-VS-HIGH: GB1 fitness prediction, low-vs-high split	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP RANDOM-SAMPLED-SPLITS-AAV: Random sampled splits fitness prediction, AAV split	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP RANDOM-SAMPLED-SPLITS-GB1: Random sampled splits fitness prediction, GB1 split	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP THERMOSTABILITY-HUMAN-CELL: Thermostability fitness prediction, Human-Cell split	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP THERMOSTABILITY-HUMAN: Thermostability fitness prediction, Human split	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP THERMOSTABILITY-MIXED: Thermostability fitness prediction, Mixed split	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
flu-vaccine mRNA property prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
G-quadruplex classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw tables acquired. Positive/negative construction, sequence lengths and train/test splits remain part of each G4 protocol; existing observations preserved. Structured extraction pending.
gene fusion breakpoint classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Counts are approximate (~36k train, ~8k validation, ~8k test) and must remain approximate. NN values are final-epoch performance; SVM is a single run. No replicate confidence bounds. Do not assign embedding-plus-classifier scores to bare foundation-model checkpoints.
Gene-regulatory link prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Raw XML stacked AUROC/AUPRC cells preserved with explicit linebreak delimiters. Two GENELink settings must not be conflated. Structured table extraction and exact uncertainty scope remain pending.
gene-regulatory signal prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Original asymmetric extraction in Table 4 is not a fair matched-input comparison; prefer Table 9 with its single-seed context. Strict leave-both-out improvements shrink near zero; do not omit this limitation. Source contains rounded deltas and intervals/significance annotations; do not recompute them from rounded absolute numbers.
GENEB LINEAR-PROBE: Average macro-MCC across the 13 representative tasks, linear probe	11 / 11	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GENEB MLP-PROBE: Average macro-MCC across the 13 representative tasks, MLP probe	11 / 11	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genome-wide prophage detection	17 / 102	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-ACCURACY: demo_coding_vs_intergenomic_seqs, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-F1: demo_coding_vs_intergenomic_seqs, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DEMO-HUMAN-OR-WORM-ACCURACY: demo_human_or_worm, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DEMO-HUMAN-OR-WORM-F1: demo_human_or_worm, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-ACCURACY: drosophila_enhancers_stark, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-F1: drosophila_enhancers_stark, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-ACCURACY: dummy_mouse_enhancers_ensembl, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-F1: dummy_mouse_enhancers_ensembl, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-ENHANCERS-COHN-ACCURACY: human_enhancers_cohn, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-ENHANCERS-COHN-F1: human_enhancers_cohn, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-ACCURACY: human_enhancers_ensembl, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-F1: human_enhancers_ensembl, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-ACCURACY: human_ensembl_regulatory, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-F1: human_ensembl_regulatory, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-ACCURACY: human_nontata_promoters, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-F1: human_nontata_promoters, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-OCR-ENSEMBL-ACCURACY: human_ocr_ensembl, Accuracy	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genomic Benchmarks HUMAN-OCR-ENSEMBL-F1: human_ocr_ensembl, F1 score	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML glycosylation type prediction	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
GlycanML immunogenicity prediction	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
GlycanML protein-glycan interaction prediction	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
GlycanML taxonomy prediction	190 / 190	26 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
GUE CORE-PROMOTER-DETECTION-ALL: Core promoter detection, dataset all	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE CORE-PROMOTER-DETECTION-NOTATA: Core promoter detection, dataset notata	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE CORE-PROMOTER-DETECTION-TATA: Core promoter detection, dataset tata	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE COVID-VARIANT-CLASSIFICATION-COVID: Covid variant classification, dataset Covid	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3: Epigenetic marks prediction, dataset H3	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K14AC: Epigenetic marks prediction, dataset H3K14ac	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K36ME3: Epigenetic marks prediction, dataset H3K36me3	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K4ME1: Epigenetic marks prediction, dataset H3K4me1	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K4ME2: Epigenetic marks prediction, dataset H3K4me2	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K4ME3: Epigenetic marks prediction, dataset H3K4me3	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K79ME3: Epigenetic marks prediction, dataset H3K79me3	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H3K9AC: Epigenetic marks prediction, dataset H3K9ac	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H4: Epigenetic marks prediction, dataset H4	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE EPIGENETIC-MARKS-PREDICTION-H4AC: Epigenetic marks prediction, dataset H4ac	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE PROMOTER-DETECTION-ALL: Promoter detection, dataset all	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE PROMOTER-DETECTION-NOTATA: Promoter detection, dataset notata	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE PROMOTER-DETECTION-TATA: Promoter detection, dataset tata	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE SPLICE-SITE-PREDICTION-RECONSTRUCT: Splice site prediction, dataset Reconstruct	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-0: Transcription factor prediction (human), dataset 0	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-1: Transcription factor prediction (human), dataset 1	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-2: Transcription factor prediction (human), dataset 2	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-3: Transcription factor prediction (human), dataset 3	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-4: Transcription factor prediction (human), dataset 4	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-0: Transcription factor prediction (mouse), dataset 0	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-1: Transcription factor prediction (mouse), dataset 1	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-2: Transcription factor prediction (mouse), dataset 2	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-4: Transcription factor prediction (mouse), dataset 4	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Held-out-clade classification	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder.
HEST-Benchmark CCRCC: Gene expression prediction from histology, Clear cell renal cell carcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark COAD: Gene expression prediction from histology, Colon adenocarcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark HCC: Gene expression prediction from histology, Hepatocellular carcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark LUNG: Gene expression prediction from histology, Lung	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark PAAD: Gene expression prediction from histology, Pancreatic adenocarcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark PRAD: Gene expression prediction from histology, Prostate adenocarcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark READ: Gene expression prediction from histology, Rectum adenocarcinoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Hierarchical metagenomic taxonomy classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work MetaPhlAn4 uses its official prebuilt database, unlike the common training database; preserve the asterisk. CAT and MetaPhlAn4 do not supply probabilities, so AveP is inapplicable, not zero. Bootstrap intervals exist in supplemental figures; main-table values lack printed intervals.
Human 5mC detection	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
human core-promoter classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
human protein-protein interaction prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. HumanPPI AUC column must be extracted separately from localization, thermostability,fluorescence andGO. Different model sizes/representation inputs remain distinct. Structured extraction pending.
human RNA 2-prime-O-methylation site prediction	12 / 84	14 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Human thymus cell-type classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only the thymus row belongs to the assigned benchmark; cortex and breast must be separate protocols. The authors' Euclidean nonidentity check is not proof that all leakage is absent; source wording must not become an independently established guarantee. No replicate uncertainty in Table 4.
human-versus-viral protein classification	8 / 32	4 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Intrinsically disordered protein ensemble docking	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Parenthesized numbers are the <5 Å success percentage, not uncertainty; main numbers use <3 Å. Each ligand and ensemble/matching definition needs its own group; do not pool them. MD-reference agreement is not experimental binding affinity.
Ligand potency prediction using generated poses	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Lipid–protein binding pose	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw tables acquired. RMSD-only versusRMSD+physicalvalidity separate;95%exactbinomialCI onLiPP, prior PoseBusters numbers quoted and notnewindependent runs. Structured extraction pending.
Long-range regulation	0 / 0	Not yet available	Published results still to collect. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
Long-read taxonomic profiling	9 / 23	3 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym De novo molecule generation	6 / 36	12 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym Molecule retrieval	10 / 40	8 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym Spectrum simulation	8 / 40	8 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Mean ribosome load from MPRA	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table 5 labels localization columns Pearson R while Table 2 labels them AUPRC; quarantine those metric identities pending reconciliation. Appendix C claims ten splits but enumerates nine seeds. Record ten as reported, with discrepancy, not an inferred tenth seed. Tables 5–6 uncertainties are 95% confidence intervals, not standard deviations. Task/subtask pooling and transformed aggregate rankings must not be conflated with printed raw metrics.
metagenomic genus classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. Dataset and k-mer row spans must be propagated; CNN/DBN/RDP/PC-mer-LR/WalkIm rows retained. Structured extraction pending; do not infer equivalent preprocessing.
Metagenomic taxonomic classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw tables acquired.19 new versusold reference experiments separate; Bray-Curtis lower-is-better unlike F1. Reference database state required before chart groups. Structured extraction pending.
MFASS splice-variant prioritisation	9 / 31	4 source-scoped figures	Checked result tables available. Scope and remaining work Primary browser text accessible but rawXML endpoint 500, PMC HTMLreCAPTCHA and mirror returned 0 bytes. Existing MFASS corrected runs must retain identities and assay-oriented window correction; no new score duplicates or revert to withdrawn v 1 conclusion.
microbiome disease-state classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Disease datasets and cohort prevalences differ; do not pool accuracy. No uncertainty in Table 3. Visualization using a 7:3 split is not the evaluation split.
miRNA-mRNA interaction prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Mock-community MAG taxonomy classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Do not pool assemblies, ranks or raw/corrected taxonomic labels. Table entries such as '9 + 33' and '8 + 35' are printed decompositions, not unambiguous single numerical observations. Total MAGs and metric confusion-matrix denominators differ; retain both.
Monomer structure	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Mean and median are separate aggregates; slash pairs are not confidence bounds. ESMFold Science publisher full-text request returned HTTP 403; its DOI was discovered but not used for uninspected full-text claims.
mRNA half-life prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
mRNA-protein interaction prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
mRNABench ECLIP: eCLIP binding site prediction	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench GO: Gene Ontology term prediction	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench HL: mRNA half life	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench MRL-MPRA: Mean ribosome load on an MPRA library	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench MRL: Mean ribosome load	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench MRNA-LOC-LR: mRNA localisation, long range	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench MRNA-LOC-SR: mRNA localisation, short range	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench PROT-LOC: Protein localisation	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench VEP: Variant effect prediction	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Multi-species prokaryotic promoter detection	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work iPro-MP's first four scores duplicate across Tables 1–2; one result with two source occurrences. Species-averaged accuracy/AUROC/AUPRC/MCC differ from pooled sample scores; retain source aggregation. Runtime is seconds, lower-is-better, and hardware-dependent.
Mutated RBD binding prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation	23 / 23	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation	24 / 24	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-CCV: Overall fitness prediction on NABench deep mutational scanning assays, Contiguous cross validation Spearman ρ	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-FS: Overall fitness prediction on NABench deep mutational scanning assays, Few-shot Spearman ρ	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-RCV: Overall fitness prediction on NABench deep mutational scanning assays, Random cross validation Spearman ρ	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-ZS-AUC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot AUC	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-ZS-CORR: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot Spearman ρ	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench DMS-ZS-NDCG: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot NDCG	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench SELEX-FS: Overall fitness prediction on NABench SELEX assays, Few-shot Spearman ρ	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench SELEX-RCV: Overall fitness prediction on NABench SELEX assays, Random cross validation Spearman ρ	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench SELEX-ZS-AUC: Overall fitness prediction on NABench SELEX assays, Zero-shot AUC	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench SELEX-ZS-CORR: Overall fitness prediction on NABench SELEX assays, Zero-shot Spearman ρ	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench SELEX-ZS-MCC: Overall fitness prediction on NABench SELEX assays, Zero-shot MCC	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench SELEX-ZS-NDCG: Overall fitness prediction on NABench SELEX assays, Zero-shot NDCG	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-AUC-APTAMER: Fitness prediction on aptamer assays, zero-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-AUC-ENHANCER: Fitness prediction on enhancer assays, zero-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-AUC-MRNA: Fitness prediction on mRNA assays, zero-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-AUC-PROMOTER: Fitness prediction on promoter assays, zero-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-AUC-RIBOZYME: Fitness prediction on ribozyme assays, zero-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-AUC-TRNA: Fitness prediction on tRNA assays, zero-shot	24 / 24	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-CORR-APTAMER: Fitness prediction on aptamer assays, zero-shot	27 / 27	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-CORR-ENHANCER: Fitness prediction on enhancer assays, zero-shot	26 / 26	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-CORR-MRNA: Fitness prediction on mRNA assays, zero-shot	27 / 27	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-CORR-PROMOTER: Fitness prediction on promoter assays, zero-shot	27 / 27	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, zero-shot	27 / 27	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
NABench ZS-CORR-TRNA: Fitness prediction on tRNA assays, zero-shot	25 / 25	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Natural vs artificial microbial genome sequence	3 / 9	3 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
non-coding RNA pairwise interaction prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Interaction-pair splitting does not guarantee unseen RNA identities across partitions. Random baseline AUPRC reflects class prevalence; do not treat it as a fitted model run. CUPID variants are distinct adaptations; no uncertainty printed.
Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection CENGEN-BATCH-F1-MACRO: Label projection on CeNGEN (split by batch), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection CENGEN-BATCH-F1: Label projection on CeNGEN (split by batch), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection CENGEN-RANDOM-ACCURACY: Label projection on CeNGEN (random split), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-ACCURACY: Label projection on Pancreas (random split with label noise), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1-MACRO: Label projection on Pancreas (random split with label noise), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1: Label projection on Pancreas (random split with label noise), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-ACCURACY: Label projection on Tabula Muris Senis Lung (random split), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1-MACRO: Label projection on Tabula Muris Senis Lung (random split), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1: Label projection on Tabula Muris Senis Lung (random split), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score	16 / 16	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
pathogen detection	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Comparison blocked: Section 4.3 lacks exact sample/split manifest and reference-label construction. Section 4.2 five-fold procedure concerns other datasets and cannot be assigned to Table 3. Do not claim the genomic experiment is absent: Section 4.3 explicitly describes it.
PBMC cell-type classification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. Celltype accuracy is distinct from cellstate and time/memory. Time formatting and hardware need review before efficiency comparisons; no new timing claim accepted. Structured extraction pending.
Perturbation response	0 / 0	Not yet available	Published results still to collect. Scope and remaining work A task guide cannot merge perturbation identities, context holdouts, gene subsets or DEG metrics into one leaderboard. Primary figures/source data must be extracted before adding new numerical comparisons.
PerturBench CB-COSINE-RANK: combination prediction on Norman19, Cosine LogFC rank	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CB-COSINE: combination prediction on Norman19, Cosine similarity of log fold change	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CB-RMSE-RANK: combination prediction on Norman19, RMSE mean rank	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CB-RMSE: combination prediction on Norman19, RMSE of the mean	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CT-COSINE-RANK: covariate transfer on Srivatsan20, Cosine LogFC rank	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CT-COSINE: covariate transfer on Srivatsan20, Cosine similarity of log fold change	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CT-RMSE-RANK: covariate transfer on Srivatsan20, RMSE mean rank	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PerturBench CT-RMSE: covariate transfer on Srivatsan20, RMSE of the mean	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench ANTI-RES: Antibiotic resistance	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench BINDING-DB: BindingDB	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench CLONING-CLF: Cloning CLF	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench DEEPLOC2: DeepLoc2 Multi	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench DEEPSOL: DeepSol	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench EC: Enzyme Commission	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench MAT-PROD: Material production	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench METAL-ION: Metal ion binding	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench PDB-BIND: PDBbind	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench SEC-STRUCT: Secondary structure	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PFMBench STABILITY: TAPE_Stability	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Phage / pathogen reads	0 / 0	Not yet available	Published results still to collect. Scope and remaining work The broad guide has no single common test population. No sequence-design instructions or pathogen enhancement content is needed for detection benchmarking. Full paired numerical figure data remain unextracted; no estimated graph heights.
Physically valid protein–ligand pose selection	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. Source compares selected algorithm versusSBS percohort; gap is derived difference, not new model score. Five-fold means and paired-significance stars do not imply confidence intervals. Structured extraction pending.
polyadenylation site detection	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Raw complete comparison acquired. Few-shot versus fine-tuning and Gene-Gene versus Intergenic-Gene conditions cannot share a chart group; NT100M and 500M are different configurations. Structured extraction pending.
Protein design / inverse folding	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Protein design is a broad task. ProteinMPNN reports native sequence recovery on 402 backbones and separate noisy-backbone/experimental design evaluations; no general protein-design ranking. New primary paper pinned, concrete protocol extraction required.
protein function annotation	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
protein localization classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table 2 architectures and pretraining datasets differ; HPA-FoV and HPA-SC are separate protocols. Do not attach Cell Painting MoA AUPRC to protein localization. Table 6 ensembling is five MLPs with threshold/prediction averaging; not the base frozen model alone.
protein variant fitness prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Pinned source PDF retained; source-specific assay aggregation and substitution/indel scope require full table mapping. Existing result preserved; structured extraction pending.
protein variant-effect classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Artifact returned HTML rather than XML, so XML table parser intentionally rejected it. Prior reviewed observation retained. Complete table extraction and source-version comparison remain pending.
protein-ligand binding affinity prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
protein-protein binding-site prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
protein-protein interaction prediction	7 / 34	11 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
protein-protein interaction prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw tables acquired. Tables 3/4 matched four-method experiments;Table 5 combines different datasets and cannot form a common ranking. Units mix percentaccuracy and fractionalmetrics. Structured extraction pending.
protein-small molecule binding-site prediction	12 / 45	12 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Protein–ligand binding affinity prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw tables acquired. Table 1PCC footnote sayspercentcorrectclassification whileTable 2 labelsPearson; ambiguity quarantined. Literature comparison rows have different training histories. Structured extraction pending.
Protein–ligand binding affinity scoring	37 / 82	9 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Protein–ligand binding energy prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work RMSE is lower-is-better; do not mix correlation and energy errors. Conventional-function rows must retain software suffixes and scoring settings; exact common test/context needs methods review before merging Tables 1–2 into one chart.
Protein–ligand pose	0 / 0	Not yet available	Published results still to collect. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
Protein–ligand pose prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Protein–ligand pose prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Pose benchmark values are mainly in figures; Table 1 reports ablation/cycling conditions and cannot substitute for complete competitor pose matrix. Source artifacts acquired; no scores estimated from pixels.
Protein–ligand virtual screening	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Target-level EF, mean EF and counts above EF cutoffs are separate metrics. Do not describe pKd-score or pKd-screen as experimentally calibrated affinity from the EF metric. All table scores are conditional on the stated docked poses.
ProteinBench AB-ACCURACY-AAR: Accuracy AAR	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-RATIONALITY-SCRMSD: Rationality scRMSD	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-SPECIFICITY-PHR: Specificity PHR	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust.	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust.	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-50-DIVERSITY-MAX-CLUST: length 50, Diversity Max Clust.	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-50-DIVERSITY-PAIRWISE-TM: length 50, Diversity pairwise TM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-50-NOVELTY-MAX-TM: length 50, Novelty Max TM	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-50-QUALITY-SCRMSD: length 50, Quality scRMSD	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-50-QUALITY-SCTM: length 50, Quality scTM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust.	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-500-QUALITY-SCRMSD: length 500, Quality scRMSD	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench BB-LENGTH-500-QUALITY-SCTM: length 500, Quality scTM	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-200-NOVELTY-MAX-TM: length 200, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-200-QUALITY-SCRMSD: length 200, Quality scRMSD	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-200-QUALITY-SCTM: length 200, Quality scTM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-500-QUALITY-SCRMSD: length 500, Quality scRMSD	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench CO-LENGTH-500-QUALITY-SCTM: length 500, Quality scTM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-GDT-TS-MEAN: Accuracy GDT-TS (mean)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-GDT-TS-MEDIAN: Accuracy GDT-TS (median)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-LDDT-MEAN: Accuracy lDDT (mean)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-LDDT-MEDIAN: Accuracy lDDT (median)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-RMSD-MEAN: Accuracy RMSD (mean)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-RMSD-MEDIAN: Accuracy RMSD (median)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-TM-SCORE-MEAN: Accuracy TM-score (mean)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-ACCURACY-TM-SCORE-MEDIAN: Accuracy TM-score (median)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-QUALITY-CA-BREAK-MEAN: Quality CA break (%) (mean)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-QUALITY-CA-BREAK-MEDIAN: Quality CA break (%) (median)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-QUALITY-CA-CLASH-MEAN: Quality CA clash (%) (mean)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-QUALITY-CA-CLASH-MEDIAN: Quality CA clash (%) (median)	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEAN: Quality PepBond break (%) (mean)	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEDIAN: Quality PepBond break (%) (median)	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-PLDDT: De novo backbones based sequence design, length 100 pLDDT	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-200-PLDDT: De novo backbones based sequence design, length 200 pLDDT	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-200-SCTM: De novo backbones based sequence design, length 200 scTM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-300-PLDDT: De novo backbones based sequence design, length 300 pLDDT	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-300-SCTM: De novo backbones based sequence design, length 300 scTM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-400-PLDDT: De novo backbones based sequence design, length 400 pLDDT	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-400-SCTM: De novo backbones based sequence design, length 400 scTM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-500-PLDDT: De novo backbones based sequence design, length 500 pLDDT	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-500-SCTM: De novo backbones based sequence design, length 500 scTM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-FITTING-EVOLUTION-DISTRIBUTION-CAMEO-AAR: Fitting Evolution Distribution, CAMEO AAR	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench IF-FITTING-EVOLUTION-DISTRIBUTION-CASP-AAR: Fitting Evolution Distribution, CASP AAR	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-100-QUALITY-PLDDT: length 100, Quality pLDDT	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-100-QUALITY-PPL: length 100, Quality ppl	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-200-DIVERSITY-PAIRWISE-TM: length 200, Diversity pairwise TM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-200-NOVELTY-MAX-TM: length 200, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-200-QUALITY-PLDDT: length 200, Quality pLDDT	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-200-QUALITY-PPL: length 200, Quality ppl	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-300-QUALITY-PLDDT: length 300, Quality pLDDT	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-300-QUALITY-PPL: length 300, Quality ppl	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust.	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-500-QUALITY-PLDDT: length 500, Quality pLDDT	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinBench SEQ-LENGTH-500-QUALITY-PPL: length 500, Quality ppl	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym mutation effects	0 / 0	Not yet available	Published results still to collect. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-SPEARMAN-AVG: Supervised substitutions, average over splits, Spearman	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym SUP-SUB-SPEARMAN-RAND: Supervised substitutions, random split, Spearman	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10%	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
regulatory element identification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
regulatory sequence classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Models differ in architecture, size and pretraining as well as tokenizer, so Table 2 alone does not isolate tokenizer causality. Table 3 offers paired tokenizer comparisons; do not relabel whole-family comparisons as controlled tokenizer ablations. No per-cell uncertainty in Table 2.
regulatory-variant scoring	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work These are trained hybrid models, not zero-shot ARSENAL scores. Keep QTL cohorts and Pearson/Spearman/AUROC separate; verify printed ± definition before plotting error bars.
RNA compound-binding site prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Baselines in Table 4 are taken from Gao et al., Zhu et al. and Chen et al.; this is a literature comparison, not uniformly rerun methods. Do not assign the selected CoBRA pipeline score to RiNALMo alone; absent values are unavailable, not zero.
RNA secondary structure	40 / 160	16 source-scoped figures	Checked result tables available.
RNA secondary structure	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Full raw tables acquired. Different family-held-out cohorts and median-over-three versus median-over-two aggregates must stay distinct. Repeated DEBFold row in Table 2 is not new independent evidence; comRNA missing predictions retained. Structured extraction pending.
RNA secondary structure	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw comparison acquired,11 methods across overall and two length bands; means/SD preserved. F1/INF and precision/recall separate columns; no aggregate across different length cohorts. Structured extraction pending.
RNA secondary structure	40 / 160	16 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
RNA secondary-structure prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
RNA sequence design	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
RNA splice-site mapping	0 / 0	Not yet available	Published results still to collect. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
RNA tertiary structure	0 / 0	Not yet available	Published results still to collect. Scope and remaining work complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
RNA-small-molecule binding-site prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Most baseline values are copied from original publications; RNABind is a web-server run. T18/T3/T10 are separate protocols and cannot be pooled as one model score. Unavailable RNet AUC is a dash, not zero.
Simulated metagenome virus-taxon retrieval	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Simulated prophage-contig detection	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Performance averages over simulation conditions, not independent training seeds; do not use rank as a probability. Benchmark simulation conditions differ from real metagenomic samples.
Small-molecule affinity	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Binding probability, mixed-measure affinity regression and virtual-screening enrichment are different outcomes. Affinity head mixes biochemical quantities; values are not automatically assay-calibrated Kd. No paper-wide universal affinity score or common ligand denominator.
Strain-level abundance quantification	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Complete raw table acquired. Identified-strain counts/ratios and L1/L2 abundance errors must remain different metrics; MetaPhlAn detection bounds are not exact counts. Structured extraction pending.
TAPE Contact Prediction	10 / 10	1 source-scoped figures	Checked result tables available.
TAPE Fluorescence	10 / 10	1 source-scoped figures	Checked result tables available.
TAPE Remote Homology Detection	10 / 10	1 source-scoped figures	Checked result tables available.
TAPE Secondary Structure	10 / 10	1 source-scoped figures	Checked result tables available.
TAPE Stability	10 / 10	1 source-scoped figures	Checked result tables available.
TDC ADMET benchmark group TDC-AMES: Toxicity: TDC.AMES	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-AQSOL: Absorption: TDC.AqSol	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-BBB: Distribution: TDC.BBB	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-BIOAV: Absorption: TDC.Bioav	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CACO2: Absorption: TDC.Caco2	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CL-HEPA: Excretion: TDC.CL-Hepa	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CL-MICRO: Excretion: TDC.CL-Micro	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CYP2C9-INHIBITION: Metabolism: TDC.CYP2C9 Inhibition	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CYP2C9-SUBSTRATE: Metabolism: TDC.CYP2C9 Substrate	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CYP2D6-INHIBITION: Metabolism: TDC.CYP2D6 Inhibition	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CYP2D6-SUBSTRATE: Metabolism: TDC.CYP2D6 Substrate	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CYP3A4-INHIBITION: Metabolism: TDC.CYP3A4 Inhibition	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-CYP3A4-SUBSTRATE: Metabolism: TDC.CYP3A4 Substrate	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-DILI: Toxicity: TDC.DILI	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-HALF-LIFE: Excretion: TDC.Half Life	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-HERG: Toxicity: TDC.hERG	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-HIA: Absorption: TDC.HIA	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-LD50: Toxicity: TDC.LD50	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-LIPO: Absorption: TDC.Lipo	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-PGP: Absorption: TDC.Pgp	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-PPBR: Distribution: TDC.PPBR	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TDC ADMET benchmark group TDC-VD: Distribution: TDC.VDss	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
transcription-factor DNA binding-site prediction	6 / 12	2 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Translation / RNA stability	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Translation and stability encompass separate species, cell contexts, transcript regions and assays. Fresh primary XML pinned; concrete mRNABench protocols should be linked instead of attaching all suite results to broad task.
translation-efficiency prediction	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
unseen-species genus classification	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder.
vaccine-antigen candidate prediction	4 / 22	7 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
viral sequence detection	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone. exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Zero-shot substitution mutation effects: stability	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Other functional-category columns do not belong to the stability benchmark. This pinned 2023 paper table is not the latest ProteinGym leaderboard; do not overwrite later-version results. MSA and structure inputs differ across model categories; no universal sequence-only ranking.
Zero-shot variant effect prediction	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Table contains two zero-shot mean absolute Spearman values already in catalogue; no new independent observations warranted. Other Table 2 tasks are different benchmarks. Full raw table and source receipt retained.

Protocols

406 pages · 399 with results · 326 with charts.

Page	Evaluations / metric rows	Charts	Collection status
African-ancestry LCL caQTL classification (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
African-ancestry LCL caQTL effect-size prediction (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Alternative polyadenylation coverage ratios (AlphaGenome paper)	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Reported scores remain quarantined because the supplementary table and another source disagree; see the protocol limitations for the exact discrepancy. Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
ArchiveII (RNA secondary structure)	10 / 40	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
ATAC prediction on held-out peaks (AlphaGenome paper)	2 / 6	3 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
ATAC track prediction at 128 bp (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
ATAC track prediction at 32 bp (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Author MFASS splice-disruption prediction (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Base-resolution RNA-seq prediction (AlphaGenome paper)	2 / 4	2 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
BEELINE 2020 Figure 2 · BF · {}	12 / 24	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 2 · BFC · {}	12 / 24	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 2 · CY · {}	12 / 24	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 2 · LI · {}	12 / 24	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 2 · LL · {}	12 / 24	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 2 · TF · {}	12 / 24	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 4 · GSD · {}	12 / 48	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 4 · HSC · {}	12 / 48	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 4 · mCAD · {}	12 / 48	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 4 · VSC · {}	12 / 36	3 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hESC · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hESC · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hESC · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hESC · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hESC · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hESC · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hHep · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hHep · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hHep · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hHep · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hHep · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · hHep · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mDC · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mDC · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mDC · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mDC · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mDC · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mDC · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"log/gof","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"log/gof","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mESC · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-E · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-E · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-E · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-E · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-E · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-E · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · MHSC-GM · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · MHSC-GM · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · MHSC-GM · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · MHSC-GM · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · MHSC-GM · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · MHSC-GM · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-L · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-L · {"reference_network":"Cell-type specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-L · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-L · {"reference_network":"Non-specific ChIP-Seq","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-L · {"reference_network":"STRING","gene_selection":"TFs+1000"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BEELINE 2020 Figure 5 · mHSC-L · {"reference_network":"STRING","gene_selection":"TFs+500"}	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
bpRNA-TS0 (RNA secondary structure)	10 / 40	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
BRCA1 BayesDel evidence calibration	1 / 15	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BRCA1 generic BayesDel threshold evidence-code assignment	1 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BRCA2 BayesDel evidence calibration	1 / 15	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
BRCA2 generic BayesDel threshold evidence-code assignment	1 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAFA3 BPO all organisms; type1 no-knowledge; mode1 · CAFA3 final benchmark; BPO; all; type1; mode1	146 / 146	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAFA3 CCO all organisms; type1 no-knowledge; mode1 · CAFA3 final benchmark; CCO; all; type1; mode1	146 / 146	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAFA3 MFO all organisms; type1 no-knowledge; mode1 · CAFA3 final benchmark; MFO; all; type1; mode1	146 / 146	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAGE track prediction at 128 bp (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
CAGE track prediction at 32 bp (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
CAMI II marine genome binning; pooled short-read gold-standard assembly; circular elements excluded · marmgCAMI2_short_read_pooled_gold_standard_assembly	16 / 256	16 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAPRI round 61 predictor; submitted model 1; T312.1 · CAPRI round 61 T312.1	25 / 100	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAPRI round 61 predictor; submitted model 1; T314.1 · CAPRI round 61 T314.1	25 / 100	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAPRI round 61 predictor; submitted model 1; T315.1 · CAPRI round 61 T315.1	25 / 100	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CAPRI round 61 predictor; submitted model 1; T316.1 · CAPRI round 61 T316.1	25 / 100	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CASF-2016 docking (Protein–ligand binding affinity scoring)	9 / 27	3 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
CASF-2016 ranking (Protein–ligand binding affinity scoring)	9 / 27	3 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
CASF-2016 scoring (Protein–ligand binding affinity scoring)	9 / 9	1 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
CASP16 protein domain; first submitted model; T1201-D1 · CASP16 T1201-D1	90 / 270	6 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Cell-type difference in chromatin contact-map prediction (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
chromatin contact-map prediction (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
CIViC evidence-direction retrieval, March 2026	3 / 162	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Clathrin independent test: selected-embedding classifiers (clathrin protein classification)	13 / 78	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
ClusPro BM5 Bound antibody top10	1 / 9	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Bound antibody top30	1 / 9	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 difficult aggregate top10	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 difficult aggregate top30	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 easy aggregate top10	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 easy aggregate top30	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Enzyme top10	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Enzyme top30	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 intermediate aggregate top10	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 intermediate aggregate top30	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Others top10	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Others top30	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Total top10	1 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Total top30	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Unbound antibody top10	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ClusPro BM5 Unbound antibody top30	1 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
COACH420, trained on CHEN11 (protein-small molecule binding-site prediction)	3 / 12	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
CPPC original Challenge 1 final four-knockout prediction score	20 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CPPC original Challenge 2 prospective target ranking score	20 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CPPC prospective nomination of desired T-cell states	1 / 1	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CPPC reimplemented best-model Challenge 2 score	13 / 13	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
CPPC screen-1 held-out knockout cell-state proportions	0 / 0	Not yet available	Published results still to collect. Scope and remaining work No evaluations linked in this release; this is a catalogue gap, not a claim that no published experiments exist.
Deep intronic and synonymous variants splicing-based classification (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
DNase prediction on held-out peaks (AlphaGenome paper)	2 / 6	3 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
DNase track prediction at 128 bp (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
DNase track prediction at 32 bp (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)	15 / 60	4 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Enformer CAGE gene-expression comparison	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ENIGMA specification pilot resolution	1 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)	5 / 40	8 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
eQTL effect direction (AlphaGenome paper)	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Reported scores remain quarantined because the supplementary table and another source disagree; see the protocol limitations for the exact discrepancy. Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
eQTL effect-size ranking (AlphaGenome paper)	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Reported scores remain quarantined because the supplementary table and another source disagree; see the protocol limitations for the exact discrepancy. Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)	7 / 7	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
European-ancestry LCL caQTL classification (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
European-ancestry LCL caQTL effect-size prediction (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Exomiser rank-budget recovery in ACG trios	1 / 8	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 Amylase by-mutation; held-out test set · Amylase	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 Amylase close-to-far; held-out test set · Amylase	9 / 17	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 Amylase far-to-close; held-out test set · Amylase	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 Amylase one-to-many; held-out test set · Amylase	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 hydro low-to-high; held-out test set · hydro	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 hydro three-to-many; held-out test set · hydro	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 hydro to-P01053; held-out test set · hydro	9 / 17	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 hydro to-P06241; held-out test set · hydro	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 hydro to-P0A9X9; held-out test set · hydro	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 IRED two-to-many; held-out test set · IRED	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 NucB two-to-many; held-out test set · NucB	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 PDZ3 single-to-double; held-out test set · PDZ3	9 / 17	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 Rhomax by_wild_type	5 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 rhomax by-wild-type; held-out test set · rhomax	9 / 17	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 TrpB by-position; held-out test set · TrpB	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 TrpB one-to-many; held-out test set · TrpB	9 / 17	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FLIP2 TrpB two-to-many; held-out test set · TrpB	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench antibody-antigen published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench dna-monomer published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench protein-dna published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench protein-ligand published full-set assessment	5 / 15	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench protein-monomer published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench protein-peptide published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench protein-protein published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench protein-rna published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FoldBench rna-monomer published full-set assessment	5 / 20	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FramePool study MRL: Human 25-100nt	5 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FramePool study MRL: Human 50nt	5 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FramePool study MRL: Random 25-100nt	10 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
FramePool study MRL: Random 50nt	10 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GEARS Norman2019 CPA-control comparison	4 / 8	2 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE	4 / 4	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPD-sex: HMPD-sex genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPD-single: HMPD-single genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPD-source: HMPD-source genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPR-p2p: HMPR-p2p genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPR-s2s-align: HMPR-s2s-align genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPR-s2s-small: HMPR-s2s-small genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HMPR-s2s-tiny: HMPR-s2s-tiny genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark Human-Virus-1: Human-Virus-1 genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark Human-Virus-2: Human-Virus-2 genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark Human-Virus-3: Human-Virus-3 genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark Human-Virus-4: Human-Virus-4 genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HVR-p2p: HVR-p2p genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HVR-s2s-align: HVR-s2s-align genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HVR-s2s-small: HVR-s2s-small genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Gene-MTEB genomic embedding benchmark HVR-s2s-tiny: HVR-s2s-tiny genomic embedding evaluation	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genie 3 short monomer generation designability: Unconditional short monomer Designability	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genie 3 short monomer generation diversity-tm-05: Unconditional short monomer Diversity, TM < 0.5	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genie 3 short monomer generation diversity-tm-06: Unconditional short monomer Diversity, TM < 0.6	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB	13 / 13	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Genome-wide prophage detection (Genome-wide prophage detection)	17 / 102	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
GlycanML class Accuracy: GlycanGT study: class Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML class Macro-F1: GlycanGT study: class Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML domain Accuracy: GlycanGT study: domain Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML domain Macro-F1: GlycanGT study: domain Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML family Accuracy: GlycanGT study: family Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML family Macro-F1: GlycanGT study: family Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML genus Accuracy: GlycanGT study: genus Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML genus Macro-F1: GlycanGT study: genus Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML glycosylation Accuracy: GlycanGT study: glycosylation Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML glycosylation Macro-F1: GlycanGT study: glycosylation Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML immunogenicity Accuracy: GlycanGT study: immunogenicity Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML immunogenicity AUPRC: GlycanGT study: immunogenicity AUPRC	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML immunogenicity Macro-F1: GlycanGT study: immunogenicity Macro-F1	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML kingdom Accuracy: GlycanGT study: kingdom Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML kingdom Macro-F1: GlycanGT study: kingdom Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML order Accuracy: GlycanGT study: order Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML order Macro-F1: GlycanGT study: order Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML phylum Accuracy: GlycanGT study: phylum Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML phylum Macro-F1: GlycanGT study: phylum Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML species Accuracy: GlycanGT study: species Accuracy	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlycanML species Macro-F1: GlycanGT study: species Macro-F1	5 / 5	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction)	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
Held-out human-versus-virus protein classification (human-versus-viral protein classification)	8 / 32	4 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
histone ChIP-seq track prediction at 128 bp (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
histone ChIP-seq track prediction at 32 bp (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)	7 / 49	7 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction)	5 / 35	7 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Human splice-junction classification and count prediction (AlphaGenome paper)	2 / 4	2 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Human splice-site classification: annotation-derived (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Human splice-site classification: RNA-derived (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Human splice-site usage (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Jores 2021 promoter strength: maize-protoplasts	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Jores 2021 promoter strength: tobacco-leaves	2 / 2	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
LectinOracle interaction · Interaction (GlycanML protein-glycan interaction prediction)	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
MassSpecGym · formula (MassSpecGym De novo molecule generation)	3 / 18	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym · formula (MassSpecGym Molecule retrieval)	5 / 20	4 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym · formula (MassSpecGym Spectrum simulation)	4 / 20	3 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym · main (MassSpecGym De novo molecule generation)	3 / 18	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym · main (MassSpecGym Molecule retrieval)	5 / 20	4 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MassSpecGym · main (MassSpecGym Spectrum simulation)	4 / 20	5 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
MFASS v1 (superseded)	0 / 0	Not yet available	Superseded record, retained for history.
MFASS v2	9 / 31	4 source-scoped figures	Checked result tables available.
MFASS: matched GENCODE 44 canonical annotation	4 / 16	4 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Microglia caQTL effect-size prediction (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
MIMIC mRNABench probes eCLIP: eCLIP prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIMIC mRNABench probes GO: GO prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIMIC mRNABench probes Protein Localization: Protein Localization prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIMIC mRNABench probes RNA Localization: RNA Localization prediction	12 / 12	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Missense variants splicing-based classification (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
MIST CANOPUS retrieval Cos. similarity: MIST CANOPUS fingerprint retrieval: Cos. similarity	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 1: MIST CANOPUS fingerprint retrieval: Top 1	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 10: MIST CANOPUS fingerprint retrieval: Top 10	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 100: MIST CANOPUS fingerprint retrieval: Top 100	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 20: MIST CANOPUS fingerprint retrieval: Top 20	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 200: MIST CANOPUS fingerprint retrieval: Top 200	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 5: MIST CANOPUS fingerprint retrieval: Top 5	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MIST CANOPUS retrieval Top 50: MIST CANOPUS fingerprint retrieval: Top 50	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MPRabc K562 CRISPRi enhancer–gene evaluation	6 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench Sample designed MRL	2 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes eCLIP: eCLIP binding site prediction	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes GO: Gene Ontology term prediction	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes HL: mRNA half life	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes MRL-HL-Pair: Paired mean ribosome load and half life	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes MRL-MPRA: Mean ribosome load on an MPRA library	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes MRL: Mean ribosome load	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes Prot-Loc: Protein localisation	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
mRNABench variant probes VEP: Variant effect prediction	50 / 50	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym formula split: formula supplied, R@1: MassSpecGym formula split retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym formula split: formula supplied, R@20: MassSpecGym formula split retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym formula split: formula supplied, R@5: MassSpecGym formula split retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym formula split: no formula, R@1: MassSpecGym formula split retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym formula split: no formula, R@20: MassSpecGym formula split retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym formula split: no formula, R@5: MassSpecGym formula split retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@1: MassSpecGym MCES split retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@20: MassSpecGym MCES split retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@5: MassSpecGym MCES split retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval NPLIB1: formula supplied, R@1: NPLIB1 retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval NPLIB1: formula supplied, R@20: NPLIB1 retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval NPLIB1: formula supplied, R@5: NPLIB1 retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval NPLIB1: no formula, R@1: NPLIB1 retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval NPLIB1: no formula, R@20: NPLIB1 retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval NPLIB1: no formula, R@5: NPLIB1 retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval Spectraverse: formula supplied, R@1: Spectraverse retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval Spectraverse: formula supplied, R@20: Spectraverse retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval Spectraverse: formula supplied, R@5: Spectraverse retrieval with formula supplied	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval Spectraverse: no formula, R@1: Spectraverse retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval Spectraverse: no formula, R@20: Spectraverse retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign molecular retrieval Spectraverse: no formula, R@5: Spectraverse retrieval with no formula	6 / 6	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign v2 retrieval: massspecgym-formula-formula-free	5 / 15	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign v2 retrieval: massspecgym-formula-formula-oracle	4 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign v2 retrieval: massspecgym-mces-formula-free	5 / 15	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign v2 retrieval: massspecgym-mces-formula-oracle	4 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign v2 retrieval: spectraverse-formula-free	5 / 15	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
MSAlign v2 retrieval: spectraverse-formula-oracle	4 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence)	3 / 9	3 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
OncoVI three-class assessment: ClinVar April 2025 oncogenicity assertions	1 / 6	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
OncoVI three-class assessment: Erlangen MTB variants	1 / 8	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
OncoVI three-class assessment: Guideline SOP variants	1 / 8	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
OncoVI three-class assessment: MTB selected expert reassessment	2 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction)	3 / 15	5 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding	5 / 25	5 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · docking with ground-truth-centred search box	1 / 4	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · rigid-receptor docking	1 / 4	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PDB (RNA secondary structure)	10 / 40	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
PDBbind-2016 core set (Protein–ligand binding affinity scoring)	9 / 18	2 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB promoter strength maize protoplasts: S. bicolor: promoter strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB promoter strength maize protoplasts: Z. mays: promoter strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB promoter strength tobacco leaves: A. thaliana: promoter strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB promoter strength tobacco leaves: S. bicolor: promoter strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB promoter strength tobacco leaves: Z. mays: promoter strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB terminator strength maize protoplasts: A. thaliana: terminator strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB terminator strength maize protoplasts: randomized GC sequences: terminator strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB terminator strength maize protoplasts: Z. mays: terminator strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB terminator strength tobacco leaves: A. thaliana: terminator strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB terminator strength tobacco leaves: randomized GC sequences: terminator strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
PGB terminator strength tobacco leaves: Z. mays: terminator strength prediction	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Polyadenylation-QTL causality (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
PRO-cap prediction on held-out peaks (AlphaGenome paper)	2 / 4	2 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Project Score target-priority scoring v2.0	0 / 0	Not yet available	Published results still to collect. Scope and remaining work No evaluations linked in this release; this is a catalogue gap, not a claim that no published experiments exist.
Protective-antigen classification feature comparison (vaccine-antigen candidate prediction)	3 / 21	7 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
ProteinGym AMFR official zero-shot Spearman snapshot	97 / 97	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym v1.3 AMFR seeded-random control	1 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym v1.3 AMFR substitution assay	1 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
ProteinGym v1.3 zero-shot DMS substitutions	0 / 0	Not yet available	Published results still to collect. Scope and remaining work No evaluations linked in this release; this is a catalogue gap, not a claim that no published experiments exist.
real_test PPI held-out evaluation (protein-protein interaction prediction)	3 / 18	6 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
Rfam12.3–14.10 (RNA secondary structure)	10 / 40	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
RhoFold+ 2024 CASP15 natural RNA comparison R1107-rmsd: R1107: RMSD	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1107-sum_z_gdt_ts_tm_score: R1107: Sum of Z-scores for GDT-TS and TM-score	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1108-rmsd: R1108: RMSD	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1108-sum_z_gdt_ts_tm_score: R1108: Sum of Z-scores for GDT-TS and TM-score	8 / 8	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1116-rmsd: R1116: RMSD	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1116-sum_z_gdt_ts_tm_score: R1116: Sum of Z-scores for GDT-TS and TM-score	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1117-rmsd: R1117: RMSD	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1117-sum_z_gdt_ts_tm_score: R1117: Sum of Z-scores for GDT-TS and TM-score	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1149-rmsd: R1149: RMSD	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1149-sum_z_gdt_ts_tm_score: R1149: Sum of Z-scores for GDT-TS and TM-score	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1156-rmsd: R1156: RMSD	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoFold+ 2024 CASP15 natural RNA comparison R1156-sum_z_gdt_ts_tm_score: R1156: Sum of Z-scores for GDT-TS and TM-score	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoMax WT-background holdout mean	3 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoMax WT-background holdout split 1	3 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoMax WT-background holdout split 2	3 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoMax WT-background holdout split 3	3 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RhoMax WT-background holdout split 4	3 / 12	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
RNA expression correlation across genes (AlphaGenome paper)	2 / 4	2 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
RNA expression correlation across tracks (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
RNA-seq track prediction at 32 bp (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation	7 / 7	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation	7 / 7	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scIB official RNA metrics export · pancreas	69 / 821	13 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scTab Table 1a: seeded model fits	11 / 11	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scTab Table 1b: seeded fits plus donor bootstrap	5 / 5	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
scTab Table 2 hardware-specific resources	5 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation 3UTR auPRC: 3UTR: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation 3UTR MCC: 3UTR: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation 5UTR auPRC: 5UTR: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation 5UTR MCC: 5UTR: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation CTCF-bound auPRC: CTCF-bound: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation CTCF-bound MCC: CTCF-bound: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation enhancer tissue-invariant auPRC: enhancer tissue-invariant: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation enhancer tissue-invariant MCC: enhancer tissue-invariant: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation exon auPRC: exon: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation exon MCC: exon: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation intron auPRC: intron: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation intron MCC: intron: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation lncRNA MCC: lncRNA: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation polyA signal auPRC: polyA signal: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation polyA signal MCC: polyA signal: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation promoter tissue-specific auPRC: promoter tissue-specific: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation promoter tissue-specific MCC: promoter tissue-specific: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation protein coding gene auPRC: protein coding gene: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation protein coding gene MCC: protein coding gene: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation splice acceptor auPRC: splice acceptor: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation splice acceptor MCC: splice acceptor: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation splice donor auPRC: splice donor: per-nucleotide annotation (auPRC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SegmentNT human genome annotation splice donor MCC: splice donor: per-nucleotide annotation (MCC)	21 / 21	1 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
SJC test split (protein-small molecule binding-site prediction)	4 / 16	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Species profiling on Dilthey2019 simulated long reads (Long-read taxonomic profiling)	7 / 21	3 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
SPI1 binding QTL classification (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
SPI1 binding QTL effect-size prediction (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Splice-site-region variants splicing-based classification (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Splicing-QTL causality (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
SugarBase immunogenicity · Immuno (GlycanML immunogenicity prediction)	10 / 10	1 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Class (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Domain (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Family (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Genus (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Kingdom (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Mean Acc (GlycanML taxonomy prediction)	14 / 14	2 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Order (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Phylum (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
SugarBase taxonomy · Species (GlycanML taxonomy prediction)	22 / 22	3 source-scoped figures	Checked result tables available. Scope and remaining work Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
Supervised distance-balanced eQTL causality (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Supervised enhancer–gene linking (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Supervised GTEx splicing-outlier prediction (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Talos diagnosis recovery and workload: ACG full	2 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos diagnosis recovery and workload: ACG singleton	2 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos diagnosis recovery and workload: ACG trio	2 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos diagnosis recovery and workload: RGP full	2 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos diagnosis recovery and workload: RGP singleton	2 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos diagnosis recovery and workload: RGP trio	2 / 10	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Talos programme reanalysis yield	1 / 14	Not yet available	Results available; comparison group not yet validated. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
TF ChIP-seq track prediction at 128 bp (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
TF ChIP-seq track prediction at 32 bp (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)	6 / 12	2 source-scoped figures	Checked result tables available. Scope and remaining work Independent batch review before import; preserve existing observation identities.
UniProtSMB test split (protein-small molecule binding-site prediction)	4 / 16	4 source-scoped figures	Checked result tables available. Scope and remaining work exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
vcc2026-val-1 · 2026 validation contexts A, B and C	1048 / 1048	14 source-scoped figures	Checked result tables available. Scope and remaining work Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table.
Yoruba LCL dsQTL classification (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Yoruba LCL dsQTL effect-size prediction (AlphaGenome paper)	3 / 3	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Zero-shot CAGI5 MPRA activity-effect prediction (chrombpnet-matched comparison) (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Zero-shot distance-balanced eQTL causality (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Zero-shot enhancer–gene linking (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.
Zero-shot GTEx splicing-outlier prediction (AlphaGenome paper)	2 / 2	1 source-scoped figures	Checked result tables available. Scope and remaining work Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked. Subsequent studies use different datasets and are not pooled with this paper.

Evaluators

4 pages · 0 with results · 0 with charts.

Page	Evaluations / metric rows	Charts	Collection status
AMBER	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Do not rank AMBER as a predictor; AMBER is the scoring implementation. Gold-standard 596 is a reference ceiling, not a competing method. These are recovered-genome counts, not bin-level precision or seed-averaged means; no uncertainty in Table 1.
OPAL	0 / 0	Not yet available	Published results still to collect. Scope and remaining work OPAL is an evaluator rather than a single dataset. Numerical comparisons require selected community dataset, taxonomic rank and profiling output version. No complete main-text score matrix; source data remains pending.
PoseBusters	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Main tables define benchmark/validity tests, not a complete method score matrix. Individual docking output data at Zenodo 8278563 identified for next extraction. RMSD-only and RMSD-plus-validity must stay distinct.
scPertEval	0 / 0	Not yet available	Published results still to collect. Scope and remaining work Supplementary Figure 1 reuses a separate Wei et al. benchmark; its origin must be retained rather than attributed as newly run scPertEval model results. No universal default metric/normalization or scientific model winner is implied by the evaluator.