Configuration

AssayFormer, K562-PCA embeddings, supervised only (AssayBench-Loop)

Configuration of AssayFormer, K562-PCA embeddings, supervised only: K562 Perturb-seq embeddings reduced by PCA; supervised training only.

1 evaluation · 10 results

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1 evaluation · 10 results. Different protocols are not a single leaderboard.

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)

Sorted by 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) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	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)	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)	Proportion (shortfall: share of acquired genes outside the screen library, including hallucinated gene names; mean over the 20 AssayBench-Loop test screens)	Recall (fraction of the screen's hits acquired within 10 rounds of 100 genes (FH); mean over the 20 AssayBench-Loop test screens)	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)	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)	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)	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)	Proportion (share of acquired hits that are DepMap common-essential genes (1,827 genes); mean over the 20 AssayBench-Loop test screens)	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)
AssayFormer, K562-PCA embeddings, supervised only (AssayBench-Loop)Evaluation	2.95	10.2	10.6%	14%	2.16	19.8	64.5	48.4	55.3%	58.7

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AssayFormer, K562-PCA 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)	2.95 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "EF"
Configuration: AssayFormer, K562-PCA 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)	19.8 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "EP-B"
Configuration: AssayFormer, K562-PCA 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)	64.5 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "EP-D"
Configuration: AssayFormer, K562-PCA 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)	48.4 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "EP-S"
Configuration: AssayFormer, K562-PCA 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)	55.3% 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "Ess. (%)"
Configuration: AssayFormer, K562-PCA 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)	14% 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "Frac. hits (%)"
Configuration: AssayFormer, K562-PCA 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 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "nAUC (%)"
Configuration: AssayFormer, K562-PCA 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)	2.16 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "Path. Ov."
Configuration: AssayFormer, K562-PCA 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)	10.6% 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "Shortfall (%)"
Configuration: AssayFormer, K562-PCA 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)	58.7 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 checked Methods, coverage and source AssayFormer, K562-PCA 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 "AssayFormer (K562-PCA)" (group 'Ablations'), column "Vendi (%)"

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Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Original source · arXiv:2609.11877 version 1, submitted 2026-09-10; not peer reviewed

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Stable ID: ucpheno-20261022-config-edwards2026-assayformer-k562-pca-sft

areas: cells-tissues
contexts: research
method types: specialist
reported name: AssayFormer (K562-PCA)
foundation model eligible: false
parameters: K562 Perturb-seq embeddings reduced by PCA; supervised training only
source locator: Table 1 and Supplementary Table 4 row labels; Methods 4.6-4.9
missing metadata: access reuse: reason: unextracted; note: Page 1 shows Website, GitHub, PyPI and Models & Data link labels; their URLs were not resolved from the text layer; version: reason: unreported; note: No release, commit or checkpoint is printed for this configuration
provenance note: Configuration as run in the AssayLoop comparison (arXiv:2609.11877v1).

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configuration of: AssayFormer
system: AssayFormer, K562-PCA embeddings, supervised only on AssayBench-Loop test (Edwards et al. 2026)

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