Evidence claim

Relevance of tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking to "Which targets should I test to change a defined disease-relevant phenotype?"

Use case: Select therapeutic targets for validation
Assessed by: AssayBench: rank 100 candidate genes for a described CRISPR screen
Relevance: Proxy evidence
Endpoint: AnDCG@100, Precision@100 and dFDR@100 for 16 systems on 571 screen-ranking entries across a validation, test and post-cutoff cohort: frontier and open-weight language models, fine-tuned and prompt-optimised variants, an agent, a single-cell language model, a trained relevance predictor and retrieval and frequency baselines

The broadest multi-system comparison of ranking genes for a described screen, with a post-cutoff cohort that probes whether apparent skill is prior exposure to the literature. It is proxy evidence: screens are replayed retrospectively, hits follow each screen's own criterion, and ranking quality is not target usefulness.

48 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Citation locations 1 values source id tgtval-20261009-source-debrouwer2026 locator Sections 2 to 4; Tables 1 to 3 Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Comparison group assaybench-screen-ranking Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Comparison title AssayBench: ranking 100 genes for described CRISPR screens (preprint) Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Constraints 3 values Inspect every linked evaluation's source locator and preserved limitations before citing a result. Do not combine this mapping's evaluations with any other protocol's results; screens, hit definitions, candidate pools and metrics differ. Genes absent from a screen's candidate pool are untested, not negative, and no result here says otherwise. Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Endpoint AnDCG@100, Precision@100 and dFDR@100 for 16 systems on 571 screen-ranking entries across a validation, test and post-cutoff cohort: frontier and open-weight language models, fine-tuned and prompt-optimised variants, an agent, a single-cell language model, a trained relevance predictor and retrieval and frequency baselines Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Claimed field links:assessed_by:tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Headline metric adjusted-ndcg-at-100 Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Limitations 8 values AnDCG@100 removes genes the screen did not assay before scoring, so for the headline metric untested genes are not negatives. The printed Precision@100 and dFDR@100 formulas sum over the top 100 predictions without that step, so an unassayed gene adds nothing to Precision@100 and counts in the dFDR@100 denominator; the text calls them measures over in-screen predictions, so whether they were condensed is unclear. Hits follow each screen's own significance criterion, so the phenotype and threshold vary between entries. Retrospective replay of published screens; no new experiment was run. Phenotype descriptions and effect directions come from an LLM-assisted curation step over BioGRID metadata. The post-cutoff cohort has 19 screens against 334 in the test cohort. Most systems score lower on it, which the source reads as partly prior exposure to the literature; the trained gene-relevance predictor (0.0660 against 0.0565) and Qwen3.5-2B (0.0324 against 0.0284) score higher. Precision@100 divides by min(100, number of positive-relevance genes), so it is not precision over a fixed 100 predictions when a screen has fewer than 100 hits. The gene-frequency baseline is competitive mainly through fitness and viability screens, where frequently recurring essential genes give a phenotype-level prior (section 5.4). No linked benchmark here runs a prospective validation batch or measures target usefulness, dependency, tractability, therapeutic window or patient benefit. Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
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attributes.setting attributes.clinical_scope attributes.intended_users sha256 3b7601f2decfe5a3304ea2c8ccaa89929148f2d443b05bd6c9e92f1844c0a578 Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Rationale The broadest multi-system comparison of ranking genes for a described screen, with a post-cutoff cohort that probes whether apparent skill is prior exposure to the literature. It is proxy evidence: screens are replayed retrospectively, hits follow each screen's own criterion, and ranking quality is not target usefulness. Negatives are genes the screen assayed whose measured response did not meet its significance criterion. A system may name any gene; for the headline AnDCG@100, genes the screen did not assay are removed before scoring, so an untested gene is never a negative there. The printed Precision@100 and dFDR@100 formulas do not state that step. Context-only references	AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents Original source ↗ tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3 Version: arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed Retrieved: 2026-10-09T20:56:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `805b402c28e0daa186415af202e04df56bf0cd7c7b1f872a6db170ee3c6c623d` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents · Original source · arXiv:2605.10876 version 1, posted 2026-05-11; not peer reviewed

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-target-validation-20261009-debrouwer2026-assaybench

field: links:assessed_by:tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking
value: tgtval-20261009-protocol-debrouwer2026-screen-gene-ranking
relevance: proxy
endpoint: AnDCG@100, Precision@100 and dFDR@100 for 16 systems on 571 screen-ranking entries across a validation, test and post-cutoff cohort: frontier and open-weight language models, fine-tuned and prompt-optimised variants, an agent, a single-cell language model, a trained relevance predictor and retrieval and frequency baselines
rationale: The broadest multi-system comparison of ranking genes for a described screen, with a post-cutoff cohort that probes whether apparent skill is prior exposure to the literature. It is proxy evidence: screens are replayed retrospectively, hits follow each screen's own criterion, and ranking quality is not target usefulness. Negatives are genes the screen assayed whose measured response did not meet its significance criterion. A system may name any gene; for the headline AnDCG@100, genes the screen did not assay are removed before scoring, so an untested gene is never a negative there. The printed Precision@100 and dFDR@100 formulas do not state that step.
constraints: Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; screens, hit definitions, candidate pools and metrics differ.; Genes absent from a screen's candidate pool are untested, not negative, and no result here says otherwise.
limitations: AnDCG@100 removes genes the screen did not assay before scoring, so for the headline metric untested genes are not negatives. The printed Precision@100 and dFDR@100 formulas sum over the top 100 predictions without that step, so an unassayed gene adds nothing to Precision@100 and counts in the dFDR@100 denominator; the text calls them measures over in-screen predictions, so whether they were condensed is unclear.; Hits follow each screen's own significance criterion, so the phenotype and threshold vary between entries.; Retrospective replay of published screens; no new experiment was run.; Phenotype descriptions and effect directions come from an LLM-assisted curation step over BioGRID metadata.; The post-cutoff cohort has 19 screens against 334 in the test cohort. Most systems score lower on it, which the source reads as partly prior exposure to the literature; the trained gene-relevance predictor (0.0660 against 0.0565) and Qwen3.5-2B (0.0324 against 0.0284) score higher.; Precision@100 divides by min(100, number of positive-relevance genes), so it is not precision over a fixed 100 predictions when a screen has fewer than 100 hits.; The gene-frequency baseline is competitive mainly through fitness and viability screens, where frequently recurring essential genes give a phenotype-level prior (section 5.4).; No linked benchmark here runs a prospective validation batch or measures target usefulness, dependency, tractability, therapeutic window or patient benefit.
citation locators: source id: tgtval-20261009-source-debrouwer2026; locator: Sections 2 to 4; Tables 1 to 3
source locator: tgtval-20261009-source-debrouwer2026: Sections 2 to 4; Tables 1 to 3
revision: 1
reason: Add primary-source target-prioritisation comparisons from the therapeutic target validation use-case pass 2026-10-09.
comparison group: assaybench-screen-ranking
comparison title: AssayBench: ranking 100 genes for described CRISPR screens (preprint)
headline metric: adjusted-ndcg-at-100
reviewed evaluations: tgtval-20261009-eval-debrouwer2026-biomni-a1-claude-4-post-cutoff; tgtval-20261009-eval-debrouwer2026-biomni-a1-claude-4-test; tgtval-20261009-eval-debrouwer2026-biomni-a1-claude-4-validation; tgtval-20261009-eval-debrouwer2026-c2s-gemma-2b-post-cutoff; tgtval-20261009-eval-debrouwer2026-c2s-gemma-2b-test; tgtval-20261009-eval-debrouwer2026-c2s-gemma-2b-validation; tgtval-20261009-eval-debrouwer2026-embedding-knn-post-cutoff; tgtval-20261009-eval-debrouwer2026-embedding-knn-test; tgtval-20261009-eval-debrouwer2026-embedding-knn-validation; tgtval-20261009-eval-debrouwer2026-gemini-3-flash-gepa-post-cutoff; tgtval-20261009-eval-debrouwer2026-gemini-3-flash-gepa-test; tgtval-20261009-eval-debrouwer2026-gemini-3-flash-gepa-validation; tgtval-20261009-eval-debrouwer2026-gemini-3-flash-post-cutoff; tgtval-20261009-eval-debrouwer2026-gemini-3-flash-test; tgtval-20261009-eval-debrouwer2026-gemini-3-flash-validation; tgtval-20261009-eval-debrouwer2026-gemini-3-pro-few-shot-post-cutoff; tgtval-20261009-eval-debrouwer2026-gemini-3-pro-few-shot-test; tgtval-20261009-eval-debrouwer2026-gemini-3-pro-few-shot-validation; tgtval-20261009-eval-debrouwer2026-gemini-3-pro-post-cutoff; tgtval-20261009-eval-debrouwer2026-gemini-3-pro-test; tgtval-20261009-eval-debrouwer2026-gemini-3-pro-validation; tgtval-20261009-eval-debrouwer2026-gene-frequency-by-phenotype-post-cutoff; tgtval-20261009-eval-debrouwer2026-gene-frequency-by-phenotype-test; tgtval-20261009-eval-debrouwer2026-gene-frequency-by-phenotype-validation; tgtval-20261009-eval-debrouwer2026-gene-relevance-predictor-post-cutoff; tgtval-20261009-eval-debrouwer2026-gene-relevance-predictor-test; tgtval-20261009-eval-debrouwer2026-gene-relevance-predictor-validation; tgtval-20261009-eval-debrouwer2026-gpt-5-4-post-cutoff; tgtval-20261009-eval-debrouwer2026-gpt-5-4-test; tgtval-20261009-eval-debrouwer2026-gpt-5-4-validation; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-post-cutoff; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-sft-grpo-post-cutoff; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-sft-grpo-test; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-sft-grpo-validation; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-sft-post-cutoff; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-sft-test; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-sft-validation; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-test; tgtval-20261009-eval-debrouwer2026-gpt-oss-120b-validation; tgtval-20261009-eval-debrouwer2026-llm-ensemble-post-cutoff; tgtval-20261009-eval-debrouwer2026-llm-ensemble-test; tgtval-20261009-eval-debrouwer2026-llm-ensemble-validation; tgtval-20261009-eval-debrouwer2026-oracle-knn-post-cutoff; tgtval-20261009-eval-debrouwer2026-oracle-knn-test; tgtval-20261009-eval-debrouwer2026-oracle-knn-validation; tgtval-20261009-eval-debrouwer2026-qwen3-5-2b-post-cutoff; tgtval-20261009-eval-debrouwer2026-qwen3-5-2b-test; tgtval-20261009-eval-debrouwer2026-qwen3-5-2b-validation
review: method: automated-source-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent extracted and judged; a separate Claude review agent checked every value and this judgement against the pinned sources (data/omics/use-case-coverage-target-validation-20261009/review.json); reviewed at: 2026-10-09T21:22:54Z; note: Bounded primary-source transcription with independent automated cell check and relevance review. No execution, reproduction, qualified human scientific review or clinical validation.
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subject: Select therapeutic targets for validation

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