Evaluation

RECOVER (gene adaptation) with MPE acquisition on Horlbeck K562 (Table 4, NAIAD against RECOVER by acquisition function)

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Evaluation results

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: RECOVER (gene adaptation) with MPE acquisition	Protocol: Retrospective active learning on a fully measured two-gene CRISPR viability screen: top-200 gene pairs found by round 4 Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025)	53.7 (23.7) True positives (the screen's 200 strongest measured gene pairs found among the 200 strongest measured-plus-predicted values, round 4 of active learning) count · higher Uncertainty: SE 23.7. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RECOVER (gene adaptation) with MPE acquisition on Horlbeck K562 (Table 4, NAIAD against RECOVER by acquisition function) pheno-20261022-qin2025-protocol-al-top200 Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 4, row "RECOVER MPE", column "Horlbeck K562"

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Evaluation procedure

Retrospective active learning on a fully measured two-gene CRISPR viability screen: top-200 gene pairs found by round 4

Configuration: RECOVER (gene adaptation) with MPE acquisition
Protocol: Retrospective active learning on a fully measured two-gene CRISPR viability screen: top-200 gene pairs found by round 4
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025)

origin: Independent external evaluation
configuration: Qin et al. 2025, PMLR 267 proceedings PDF
protocol id: pheno-20261022-qin2025-protocol-al-top200
dataset version: Gene-level viability as processed in Qin et al. 2025 Appendix A.1
split: No held-out split; the whole screen is both the candidate pool and the ground truth
population: 100,576 two-gene combinations of 448 genes
inputs: Single-gene viability effects of every gene, plus the measured viability of pairs acquired so far
adaptation: RECOVER ensemble; MPE acquisition
metric implementation: P_i = |X_i,P ∩ Y_i,P| at P = 200 (Appendix D)
aggregation: Three cross-fold replicates with standard error printed; the caption does not name the point statistic
budget: 500 uniformly sampled seed pairs, then 500 acquired pairs in each of 4 rounds (2,500 measured pairs at round 4)

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No held-out split; the whole screen is both the candidate pool and the ground truth
Adaptation: RECOVER ensemble; MPE acquisition
Scoring implementation: P_i = |X_i,P ∩ Y_i,P| at P = 200 (Appendix D)

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Evidence table

Inspect claims, sources and review details

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22 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Comparison: adaptation RECOVER ensemble; MPE acquisition Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: aggregation Three cross-fold replicates with standard error printed; the caption does not name the point statistic Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: budget 500 uniformly sampled seed pairs, then 500 acquired pairs in each of 4 rounds (2,500 measured pairs at round 4) Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: dataset version Gene-level viability as processed in Qin et al. 2025 Appendix A.1 Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: inputs Single-gene viability effects of every gene, plus the measured viability of pairs acquired so far Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: metric implementation P_i = \|X_i,P ∩ Y_i,P\| at P = 200 (Appendix D) Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: population 100,576 two-gene combinations of 448 genes Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: protocol id pheno-20261022-qin2025-protocol-al-top200 Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Comparison: split No held-out split; the whole screen is both the candidate pool and the ground truth Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact
Evaluation group id qin2025-table4 Context-only references	Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) Original source ↗ Table 4, row 'RECOVER MPE', column 'Horlbeck K562' Version: Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read. Retrieved: 2026-10-22T13:57:27Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.evaluation_group_id` Source artifact SHA-256: `983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb` Hash scope: pdftotext -layout text layer, parsed by extract/qin2025naiad.py Inspected artifact

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Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release history

Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Original source · Proceedings of the 42nd ICML, PMLR 267:50363-50383, 2025; proceedings PDF qin25g.pdf. The arXiv preprint 2411.12010 was not read.

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Technical metadata and extraction receipts

Stable ID: pheno-20261022-qin2025-eval-table4-recover-mpe-horlbeck2018-k562

areas: cells-tissues
contexts: research
origin: independent_paper
protocol: pheno-20261022-qin2025-protocol-al-top200
version: Qin et al. 2025, PMLR 267 proceedings PDF
comparison: protocol id: pheno-20261022-qin2025-protocol-al-top200; dataset version: Gene-level viability as processed in Qin et al. 2025 Appendix A.1; split: No held-out split; the whole screen is both the candidate pool and the ground truth; population: 100,576 two-gene combinations of 448 genes; inputs: Single-gene viability effects of every gene, plus the measured viability of pairs acquired so far; adaptation: RECOVER ensemble; MPE acquisition; metric implementation: P_i = |X_i,P ∩ Y_i,P| at P = 200 (Appendix D); aggregation: Three cross-fold replicates with standard error printed; the caption does not name the point statistic; budget: 500 uniformly sampled seed pairs, then 500 acquired pairs in each of 4 rounds (2,500 measured pairs at round 4)
evaluation group id: qin2025-table4
evaluation group name: Table 4, NAIAD against RECOVER by acquisition function
retrospective: true
source locator: Table 4, row 'RECOVER MPE', column 'Horlbeck K562'
review: method: source-hash-verification; scope-review; independent-cell-check; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; artifact sha256: 983b2da8aed78f0aced27053301c15f0f67ebd0fac706435bb6800e309dd64eb; retrieval url: https://raw.githubusercontent.com/mlresearch/v267/main/assets/qin25g/qin25g.pdf; method note: Re-hashed the PDF in the scratchpad (SHA-256 matches the source record). Read the captions and methods text in the pdftotext layer and on the rendered pages.; note: Origin, comparison fields, group, locator and links checked against the table caption, Sections 4.2, 4.3 and 5.3 and Appendices B to D.
limitations: Run by the NAIAD authors on their own adaptation of this method, not by its developers.

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