Configuration

GPT-5.4 (AssayBench)

Configuration of GPT-5.4: zero-shot.

Overview

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Evaluations and results

3 evaluations · 9 results. Different protocols are not a single leaderboard.

Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen

Sorted by Adjusted NDCG at 100 (post-cutoff cohort; mean over benchmark entries) (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	Protocol and dataset	Adjusted NDCG at 100 (post-cutoff cohort; mean over benchmark entries)	Adjusted NDCG at 100 (test cohort; mean over benchmark entries)	Adjusted NDCG at 100 (validation cohort; mean over benchmark entries)	Directional false discovery rate at 100 (post-cutoff cohort; mean over benchmark entries)	Directional false discovery rate at 100 (test cohort; mean over benchmark entries)	Directional false discovery rate at 100 (validation cohort; mean over benchmark entries)	Precision at 100 (post-cutoff cohort; mean over benchmark entries; denominator min(100, positive-relevance genes))	Precision at 100 (test cohort; mean over benchmark entries; denominator min(100, positive-relevance genes))	Precision at 100 (validation cohort; mean over benchmark entries; denominator min(100, positive-relevance genes))
GPT-5.4 (AssayBench)Evaluation	AssayBench post-cutoff cohort of human CRISPR screens	0.0982	Not reported	Not reported	NA	Not reported	Not reported	0.222	Not reported	Not reported
GPT-5.4 (AssayBench)Evaluation	AssayBench test cohort of human CRISPR screens	Not reported	0.147	Not reported	Not reported	0.0206	Not reported	Not reported	0.198	Not reported
GPT-5.4 (AssayBench)Evaluation	AssayBench validation cohort of human CRISPR screens	Not reported	Not reported	0.166	Not reported	Not reported	0.0162	Not reported	Not reported	0.326

All 9 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	0.0982 Adjusted NDCG at 100 (post-cutoff cohort; mean over benchmark entries) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 on the AssayBench post-cutoff 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 'GPT-5.4' cohort 'LaTest', column 'AnDCG@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	NA Directional false discovery rate at 100 (post-cutoff cohort; mean over benchmark entries) fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 on the AssayBench post-cutoff 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 'GPT-5.4' cohort 'LaTest', column 'dFDR@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	0.222 Precision at 100 (post-cutoff cohort; mean over benchmark entries; denominator min(100, positive-relevance genes)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 on the AssayBench post-cutoff 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 'GPT-5.4' cohort 'LaTest', column 'Precision@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.147 Adjusted NDCG at 100 (test cohort; mean over benchmark entries) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 on the AssayBench test 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 'GPT-5.4' cohort 'test', column 'AnDCG@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.0206 Directional false discovery rate at 100 (test cohort; mean over benchmark entries) fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 on the AssayBench test 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 'GPT-5.4' cohort 'test', column 'dFDR@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.198 Precision at 100 (test cohort; mean over benchmark entries; denominator min(100, positive-relevance genes)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 on the AssayBench test 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 'GPT-5.4' cohort 'test', column 'Precision@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens	0.166 Adjusted NDCG at 100 (validation cohort; mean over benchmark entries) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 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 'GPT-5.4' cohort 'val', column 'AnDCG@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens	0.0162 Directional false discovery rate at 100 (validation cohort; mean over benchmark entries) fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 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 'GPT-5.4' cohort 'val', column 'dFDR@100'
Configuration: GPT-5.4 (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens	0.326 Precision at 100 (validation cohort; mean over benchmark entries; denominator min(100, positive-relevance genes)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPT-5.4 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 'GPT-5.4' cohort 'val', column 'Precision@100'

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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Sources and history

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

1 source record and release history

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: tgtval-20261009-config-debrouwer2026-gpt-5-4

areas: cells-tissues
contexts: research
method types: foundation_model
reported name: GPT-5.4
foundation model eligible: true
source locator: Tables 2-3 row labels; section 4
missing metadata: version: reason: unreported; note: No release or commit is printed for this configuration
parameters: zero-shot
provenance note: Configuration as run in the cited comparison.

Related records

configuration of: GPT-5.4
system: GPT-5.4 on the AssayBench post-cutoff cohort
system: GPT-5.4 on the AssayBench test cohort
system: GPT-5.4 on the AssayBench validation cohort

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