The validation cohort of the AssayBench temporal split.
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16 evaluations · 48 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Biomni A1 (Claude 4) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.141 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiomni A1 (Claude 4) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Biomni A1 (Claude 4)' cohort 'val', column 'AnDCG@100' |
| Configuration: Biomni A1 (Claude 4) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0164 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiomni A1 (Claude 4) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Biomni A1 (Claude 4)' cohort 'val', column 'dFDR@100' |
| Configuration: Biomni A1 (Claude 4) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.247 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiomni A1 (Claude 4) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Biomni A1 (Claude 4)' cohort 'val', column 'Precision@100' |
| Configuration: C2S (Gemma-2B) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0842 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceC2S (Gemma-2B) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'C2S (Gemma-2B)' cohort 'val', column 'AnDCG@100' |
| Configuration: C2S (Gemma-2B) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0429 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceC2S (Gemma-2B) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'C2S (Gemma-2B)' cohort 'val', column 'dFDR@100' |
| Configuration: C2S (Gemma-2B) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.12 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceC2S (Gemma-2B) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'C2S (Gemma-2B)' cohort 'val', column 'Precision@100' |
| Configuration: Embedding kNN (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0697 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbedding kNN on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Embedding kNN' cohort 'val', column 'AnDCG@100' |
| Configuration: Embedding kNN (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0321 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbedding kNN on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Embedding kNN' cohort 'val', column 'dFDR@100' |
| Configuration: Embedding kNN (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.103 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbedding kNN on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Embedding kNN' cohort 'val', column 'Precision@100' |
| Configuration: Gemini 3 Flash (GEPA) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.192 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGemini 3 Flash (GEPA) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Flash (GEPA)' cohort 'val', column 'AnDCG@100' |
| Configuration: Gemini 3 Flash (GEPA) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0102 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGemini 3 Flash (GEPA) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Flash (GEPA)' cohort 'val', column 'dFDR@100' |
| Configuration: Gemini 3 Flash (GEPA) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.344 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGemini 3 Flash (GEPA) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Flash (GEPA)' cohort 'val', column 'Precision@100' |
| Configuration: Gemini 3 Flash (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.156 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Flash on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Flash' cohort 'val', column 'AnDCG@100' |
| Configuration: Gemini 3 Flash (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.026 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Flash on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Flash' cohort 'val', column 'dFDR@100' |
| Configuration: Gemini 3 Flash (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.249 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Flash on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Flash' cohort 'val', column 'Precision@100' |
| Configuration: Gemini 3 Pro (Few-shot) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.169 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Pro (Few-shot) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Pro (Few-shot)' cohort 'val', column 'AnDCG@100' |
| Configuration: Gemini 3 Pro (Few-shot) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0155 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Pro (Few-shot) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Pro (Few-shot)' cohort 'val', column 'dFDR@100' |
| Configuration: Gemini 3 Pro (Few-shot) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.288 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Pro (Few-shot) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Pro (Few-shot)' cohort 'val', column 'Precision@100' |
| Configuration: Gemini 3 Pro (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.172 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Pro on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Pro' cohort 'val', column 'AnDCG@100' |
| Configuration: Gemini 3 Pro (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0208 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Pro on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Pro' cohort 'val', column 'dFDR@100' |
| Configuration: Gemini 3 Pro (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.371 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGemini 3 Pro on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gemini 3 Pro' cohort 'val', column 'Precision@100' |
| Configuration: Gene-frequency (by phenotype) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.169 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGene-frequency (by phenotype) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gene-frequency (by phenotype)' cohort 'val', column 'AnDCG@100' |
| Configuration: Gene-frequency (by phenotype) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.0606 directional-false-discovery-rate-at-100 fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGene-frequency (by phenotype) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gene-frequency (by phenotype)' cohort 'val', column 'dFDR@100' |
| Configuration: Gene-frequency (by phenotype) (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.41 precision-at-100 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGene-frequency (by phenotype) on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gene-frequency (by phenotype)' cohort 'val', column 'Precision@100' |
| Configuration: Gene-relevance predictor (AssayBench) | Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens | 0.141 adjusted-ndcg-at-100 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGene-relevance predictor on the AssayBench validation cohort tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Aggregation: Not reported AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Table 3, row 'Gene-relevance predictor' cohort 'val', column 'AnDCG@100' |
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7 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.assay Pooled human CRISPR screens with the screen's own significance criterion Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
| attributes.population 218 benchmark entries from screens published in 2021 Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
| attributes.scope_note Each entry is one screen cast as a gene-ranking task. Hits are the genes meeting that screen's significance criterion; non-hits are assayed genes that do not meet it and are given relevance 0; for AnDCG@100, genes the screen did not assay are removed from the ranked list rather than counted as false positives; the printed Precision@100 and dFDR@100 formulas do not state that step. In screens with a bidirectional criterion, genes significant in the opposite direction get negative relevance. Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
| attributes.source_locator Sections 2.1 to 2.3; Table 1 (split statistics) Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
| attributes.version AssayBench, arXiv:2605.10876v1; built from the 2025 BioGRID ORCS release and 19 recent publications Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
| description The validation cohort of the AssayBench temporal split. Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
| name AssayBench validation cohort of human CRISPR screens Context-only references | AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Sections 2.1 to 2.3; Table 1 (split statistics) Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py |
Release 2026-10-10-7fcc3e48a123 · Record review: source checked
Stable ID: tgtval-20261009-data-assaybench-validation