Evidence claim

Relevance of tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 to "Which targets should I test to change a defined disease-relevant phenotype?"

Use case: Select therapeutic targets for validation
Assessed by: Independent replication of 1-gene perturbation design: cumulative hits after 5 rounds of 128 genes
Relevance: Proxy evidence
Endpoint: Cumulative hits after 5 rounds of 128 selected genes on five of the same screens, for the agent, the agent given randomly permuted feedback, linear bandits and Gaussian process optimisation, alongside the originally reported numbers

An independent replication of the same selection task, which adds the control the original lacks: the same agent given permuted feedback. It is proxy evidence for the same reasons as the original, and it bears on how the original numbers should be read rather than on target usefulness.

55 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-gupta2025 locator Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Comparison group gupta2025-perturbation-replication Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Comparison title Independent replication: cumulative hits on five CRISPR screens Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` 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	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Endpoint Cumulative hits after 5 rounds of 128 selected genes on five of the same screens, for the agent, the agent given randomly permuted feedback, linear bandits and Gaussian process optimisation, alongside the originally reported numbers Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Claimed field links:assessed_by:tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Headline metric true-positive-count Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Limitations 5 values Offline replay of five of the same screens; untested genes are absent from the candidate pool rather than negative. Cumulative hits is a count, so values are comparable only within a screen. The Claude 3.5 Sonnet 'Reported Numbers' row is converted from Roohani et al. 2025, not re-run here; the source's own replication of that setting is lower on three of the four screens with a reported value (interleukin-2, interferon-gamma, tau) and higher on one (Carnevale). The source does not print the hit threshold; it prints its own ground-truth hit counts per screen. No linked benchmark here runs a prospective validation batch or measures target usefulness, dependency, tractability, therapeutic window or patient benefit. Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
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attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 c9e83e7bd2abc7f51bee0f1626f9ce4a676f1a35e2dd608fdc22bb3dcfec6b75 record id tgtval-20261009-source-gupta2025 fields status attributes.artifact_sha256 sha256 6f5ca86baa095c19fc137331fb00935d89468ace1de74510fee46e8dba5971a7 record id use-case-therapeutic-target-validation fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 3b7601f2decfe5a3304ea2c8ccaa89929148f2d443b05bd6c9e92f1844c0a578 Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` Hash scope: pdftotext -layout text layer, parsed by extract/extract_target_validation.py Inspected artifact
Rationale An independent replication of the same selection task, which adds the control the original lacks: the same agent given permuted feedback. It is proxy evidence for the same reasons as the original, and it bears on how the original numbers should be read rather than on target usefulness. Negatives are genes the screen assayed whose measured response did not meet its significance criterion. Genes the screen did not assay are excluded from the candidate pool, so the benchmark never treats an untested gene as a negative; it also never tests whether a method would have found a target outside that pool. Context-only references	LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? Original source ↗ tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1 Version: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510 Retrieved: 2026-10-09T20:55:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `7dda0b590f2736b7d30e48b97167a0868a2b4bde253589d8aff7929d01506ff9` 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

1 source record and release history

LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Original source · Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-target-validation-20261009-gupta2025-cumulative-hits

field: links:assessed_by:tgtval-20261009-protocol-gupta2025-cumulative-hits-round5
value: tgtval-20261009-protocol-gupta2025-cumulative-hits-round5
relevance: proxy
endpoint: Cumulative hits after 5 rounds of 128 selected genes on five of the same screens, for the agent, the agent given randomly permuted feedback, linear bandits and Gaussian process optimisation, alongside the originally reported numbers
rationale: An independent replication of the same selection task, which adds the control the original lacks: the same agent given permuted feedback. It is proxy evidence for the same reasons as the original, and it bears on how the original numbers should be read rather than on target usefulness. Negatives are genes the screen assayed whose measured response did not meet its significance criterion. Genes the screen did not assay are excluded from the candidate pool, so the benchmark never treats an untested gene as a negative; it also never tests whether a method would have found a target outside that pool.
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: Offline replay of five of the same screens; untested genes are absent from the candidate pool rather than negative.; Cumulative hits is a count, so values are comparable only within a screen.; The Claude 3.5 Sonnet 'Reported Numbers' row is converted from Roohani et al. 2025, not re-run here; the source's own replication of that setting is lower on three of the four screens with a reported value (interleukin-2, interferon-gamma, tau) and higher on one (Carnevale).; The source does not print the hit threshold; it prints its own ground-truth hit counts per screen.; 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-gupta2025; locator: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1
source locator: tgtval-20261009-source-gupta2025: Sections 4.1, 5 and 6; Tables 1 and 2; appendix B.1.1
revision: 1
reason: Add primary-source target-prioritisation comparisons from the therapeutic target validation use-case pass 2026-10-09.
comparison group: gupta2025-perturbation-replication
comparison title: Independent replication: cumulative hits on five CRISPR screens
headline metric: true-positive-count
reviewed evaluations: tgtval-20261009-eval-gupta2025-bda-llama-3-1-8b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-llama-3-1-8b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-llama-3-1-8b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-llama-3-1-8b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-llama-3-1-8b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-bda-qwen-2-7b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-qwen-2-7b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-qwen-2-7b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-qwen-2-7b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-qwen-2-7b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-bda-rand-claude-3-5-sonnet-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-rand-claude-3-5-sonnet-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-rand-claude-3-5-sonnet-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-rand-claude-3-5-sonnet-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-rand-claude-3-5-sonnet-schmidt2022-il2; tgtval-20261009-eval-gupta2025-bda-rand-llama-3-1-8b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-rand-llama-3-1-8b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-rand-llama-3-1-8b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-rand-llama-3-1-8b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-rand-llama-3-1-8b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-bda-rand-qwen-2-7b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-rand-qwen-2-7b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-rand-qwen-2-7b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-rand-qwen-2-7b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-rand-qwen-2-7b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-bda-replicated-claude-3-5-sonnet-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-replicated-claude-3-5-sonnet-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-replicated-claude-3-5-sonnet-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-replicated-claude-3-5-sonnet-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-replicated-claude-3-5-sonnet-schmidt2022-il2; tgtval-20261009-eval-gupta2025-bda-reported-numbers-claude-3-5-sonnet-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-bda-reported-numbers-claude-3-5-sonnet-sanchez2021-tau; tgtval-20261009-eval-gupta2025-bda-reported-numbers-claude-3-5-sonnet-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-bda-reported-numbers-claude-3-5-sonnet-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-bda-reported-numbers-claude-3-5-sonnet-schmidt2022-il2; tgtval-20261009-eval-gupta2025-gp-llama-3-1-8b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-gp-llama-3-1-8b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-gp-llama-3-1-8b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-gp-llama-3-1-8b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-gp-llama-3-1-8b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-gp-qwen-2-7b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-gp-qwen-2-7b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-gp-qwen-2-7b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-gp-qwen-2-7b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-gp-qwen-2-7b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-linear-ucb-llama-3-1-8b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-linear-ucb-llama-3-1-8b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-linear-ucb-llama-3-1-8b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-linear-ucb-llama-3-1-8b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-linear-ucb-llama-3-1-8b-schmidt2022-il2; tgtval-20261009-eval-gupta2025-linear-ucb-qwen-2-7b-carnevale2022-tcell; tgtval-20261009-eval-gupta2025-linear-ucb-qwen-2-7b-sanchez2021-tau; tgtval-20261009-eval-gupta2025-linear-ucb-qwen-2-7b-sanchez2021-tau-down; tgtval-20261009-eval-gupta2025-linear-ucb-qwen-2-7b-schmidt2022-ifng; tgtval-20261009-eval-gupta2025-linear-ucb-qwen-2-7b-schmidt2022-il2
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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