| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 3.83 Hit enrichment factor (hits found divided by hits expected under random selection, after 10 rounds of 100 genes; hallucinated genes and unfilled slots count in the denominator, valid genes outside the screen library do not; mean over the 20 AssayBench-Loop test screens) unitless · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "EF (↑)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 18.3 Effective number of groups (EP-B: Hill number of order 1 at batch scope, rarefied to 30 annotated genes per batch, one random group per gene per draw, 400 Monte Carlo draws, averaged within each screen then across the 20 test screens; not comparable with EP-S or EP-D) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (Appendix H excludes batches or screens with fewer annotated genes than the rarefaction size; how many were excluded is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "EP-B" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 56.9 Effective number of groups (EP-D: Hill number of order 1 at dataset scope, rarefied to 6,000 annotated genes across the complete test set, one random group per gene per draw, 300 Monte Carlo draws; not comparable with EP-B or EP-S) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (One value pooled over the 20 test screens (Appendix H), not a per-screen mean as the Table 1 caption says of all metrics. Appendix H also excludes sample sets with fewer annotated genes than the rarefaction size; how many is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "EP-D" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 42.7 Effective number of groups (EP-S: Hill number of order 1 at screen scope, rarefied to 200 annotated genes per screen, one random group per gene per draw, 400 Monte Carlo draws, averaged across the 20 test screens; not comparable with EP-B or EP-D) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (Appendix H excludes batches or screens with fewer annotated genes than the rarefaction size; how many were excluded is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "EP-S" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 37.5% Proportion (share of acquired hits that are DepMap common-essential genes (1,827 genes); mean over the 20 AssayBench-Loop test screens) percent · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "%ess (%)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 18.3% Recall (fraction of the screen's hits acquired within 10 rounds of 100 genes (FH); mean over the 20 AssayBench-Loop test screens) percent · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "FH (%)(↑)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 13.2 Normalized cumulative hits AUC (area under the fraction-of-hits against fraction-of-library-queried curve over 10 rounds, divided by an oracle's area over the same effective budget; mean over the 20 AssayBench-Loop test screens) unitless · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "nAUC (%)(↑)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 3.82 Hit enrichment factor (hits found divided by hits expected under random selection, after 10 rounds of 100 genes; hallucinated genes and unfilled slots count in the denominator, valid genes outside the screen library do not; mean over the 20 AssayBench-Loop test screens) unitless · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "EF" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 18.8 Effective number of groups (EP-B: Hill number of order 1 at batch scope, rarefied to 30 annotated genes per batch, one random group per gene per draw, 400 Monte Carlo draws, averaged within each screen then across the 20 test screens; not comparable with EP-S or EP-D) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (Appendix H excludes batches or screens with fewer annotated genes than the rarefaction size; how many were excluded is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "EP-B" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 56.5 Effective number of groups (EP-D: Hill number of order 1 at dataset scope, rarefied to 6,000 annotated genes across the complete test set, one random group per gene per draw, 300 Monte Carlo draws; not comparable with EP-B or EP-S) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (One value pooled over the 20 test screens (Appendix H), not a per-screen mean as the Table 1 caption says of all metrics. Appendix H also excludes sample sets with fewer annotated genes than the rarefaction size; how many is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "EP-D" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 43.2 Effective number of groups (EP-S: Hill number of order 1 at screen scope, rarefied to 200 annotated genes per screen, one random group per gene per draw, 400 Monte Carlo draws, averaged across the 20 test screens; not comparable with EP-B or EP-D) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (Appendix H excludes batches or screens with fewer annotated genes than the rarefaction size; how many were excluded is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "EP-S" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 62.6% Proportion (share of acquired hits that are DepMap common-essential genes (1,827 genes); mean over the 20 AssayBench-Loop test screens) percent · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "Ess. (%)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 19.1% Recall (fraction of the screen's hits acquired within 10 rounds of 100 genes (FH); mean over the 20 AssayBench-Loop test screens) percent · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "Frac. hits (%)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 13.1 Normalized cumulative hits AUC (area under the fraction-of-hits against fraction-of-library-queried curve over 10 rounds, divided by an oracle's area over the same effective budget; mean over the 20 AssayBench-Loop test screens) unitless · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "nAUC (%)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 2.68 Annotation overlap ratio (mean pairwise Jaccard overlap of GO biological-process annotations within a batch, divided by that of an equal-size random batch from the screen library, averaged over batches; mean over the 20 AssayBench-Loop test screens) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "Path. Ov." |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 5.1% Proportion (shortfall: share of acquired genes outside the screen library, including hallucinated gene names; mean over the 20 AssayBench-Loop test screens) percent · lower Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "Shortfall (%)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 56.7 Vendi ratio (Vendi score of each batch under a cosine kernel on GenePT embeddings, divided by batch size and averaged over batches; mean over the 20 AssayBench-Loop test screens) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only, no screen description on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "- screen desc." (group 'Ablations'), column "Vendi (%)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 2.54 Annotation overlap ratio (mean pairwise Jaccard overlap of GO biological-process annotations within a batch, divided by that of an equal-size random batch from the screen library, averaged over batches; mean over the 20 AssayBench-Loop test screens) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "Path. Ov." |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 10.2% Proportion (shortfall: share of acquired genes outside the screen library, including hallucinated gene names; mean over the 20 AssayBench-Loop test screens) percent · lower Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "SF (%)(↓)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 52.5 Vendi ratio (Vendi score of each batch under a cosine kernel on GenePT embeddings, divided by batch size and averaged over batches; mean over the 20 AssayBench-Loop test screens) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "+ BPMF Embeddings" (group 'AssayFormer (Ours)'), column "Vendi (%)" |
|---|
| Configuration: AssayFormer (BPMF embeddings, supervised then GRPO) (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 4.83 Hit enrichment factor (hits found divided by hits expected under random selection, after 10 rounds of 100 genes; hallucinated genes and unfilled slots count in the denominator, valid genes outside the screen library do not; mean over the 20 AssayBench-Loop test screens) unitless · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer (BPMF embeddings, supervised then GRPO) on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Table 1, row "+ GRPO (= AssayFormer)" (group 'AssayFormer (Ours)'), column "EF (↑)" |
|---|
| Configuration: AssayFormer, BPMF embeddings, GRPO with terminal-EF reward (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 4.29 Hit enrichment factor (hits found divided by hits expected under random selection, after 10 rounds of 100 genes; hallucinated genes and unfilled slots count in the denominator, valid genes outside the screen library do not; mean over the 20 AssayBench-Loop test screens) unitless · higher Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, GRPO with terminal-EF reward on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "BPMF + GRPO (EFterminal )" (group 'Ablations'), column "EF" |
|---|
| Configuration: AssayFormer, BPMF embeddings, GRPO with terminal-EF reward (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 19 Effective number of groups (EP-B: Hill number of order 1 at batch scope, rarefied to 30 annotated genes per batch, one random group per gene per draw, 400 Monte Carlo draws, averaged within each screen then across the 20 test screens; not comparable with EP-S or EP-D) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (Appendix H excludes batches or screens with fewer annotated genes than the rarefaction size; how many were excluded is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, GRPO with terminal-EF reward on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "BPMF + GRPO (EFterminal )" (group 'Ablations'), column "EP-B" |
|---|
| Configuration: AssayFormer, BPMF embeddings, GRPO with terminal-EF reward (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 62.7 Effective number of groups (EP-D: Hill number of order 1 at dataset scope, rarefied to 6,000 annotated genes across the complete test set, one random group per gene per draw, 300 Monte Carlo draws; not comparable with EP-B or EP-S) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (One value pooled over the 20 test screens (Appendix H), not a per-screen mean as the Table 1 caption says of all metrics. Appendix H also excludes sample sets with fewer annotated genes than the rarefaction size; how many is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, GRPO with terminal-EF reward on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "BPMF + GRPO (EFterminal )" (group 'Ablations'), column "EP-D" |
|---|
| Configuration: AssayFormer, BPMF embeddings, GRPO with terminal-EF reward (AssayBench-Loop) | Protocol: AssayBench-Loop adaptive hit discovery: 10 rounds of 100 genes on 20 held-out CRISPR screens
Dataset subset: AssayBench-Loop test split (20 genome-wide CRISPR screens published after 2021) | 45 Effective number of groups (EP-S: Hill number of order 1 at screen scope, rarefied to 200 annotated genes per screen, one random group per gene per draw, 400 Monte Carlo draws, averaged across the 20 test screens; not comparable with EP-B or EP-D) unitless · unknown Uncertainty: Not reported by the source: Table 1 and Supplementary Table 4 print means without spread. Coverage: 20 test screens scored (Appendix H excludes batches or screens with fewer annotated genes than the rarefaction size; how many were excluded is not reported.) | Author-reported evaluation · Source checkedMethods, coverage and sourceAssayFormer, BPMF embeddings, GRPO with terminal-EF reward on AssayBench-Loop test (Edwards et al. 2026) ucpheno-20261022-protocol-edwards2026-assaybench-loop-test-10x100 Aggregation: Not reported Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Supplementary Table 4, row "BPMF + GRPO (EFterminal )" (group 'Ablations'), column "EP-S" |
|---|