Configuration

Gene-relevance predictor (AssayBench)

Configuration of Gene-relevance predictor: neural predictor trained on the AssayBench training split from screen-text and gene embeddings.

3 evaluations · 9 results

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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))
Gene-relevance predictor (AssayBench)Evaluation	AssayBench post-cutoff cohort of human CRISPR screens	0.066	Not reported	Not reported	NA	Not reported	Not reported	0.154	Not reported	Not reported
Gene-relevance predictor (AssayBench)Evaluation	AssayBench test cohort of human CRISPR screens	Not reported	0.0565	Not reported	Not reported	0.0306	Not reported	Not reported	0.158	Not reported
Gene-relevance predictor (AssayBench)Evaluation	AssayBench validation cohort of human CRISPR screens	Not reported	Not reported	0.141	Not reported	Not reported	0.0316	Not reported	Not reported	0.215

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Gene-relevance predictor (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	0.066 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-relevance predictor 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 'Gene-relevance predictor' cohort 'LaTest', column 'AnDCG@100'
Configuration: Gene-relevance predictor (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	Author-reported evaluation · Source checked Methods, coverage and source Gene-relevance predictor 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 'Gene-relevance predictor' cohort 'LaTest', column 'dFDR@100'
Configuration: Gene-relevance predictor (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	0.154 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-relevance predictor 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 'Gene-relevance predictor' cohort 'LaTest', column 'Precision@100'
Configuration: Gene-relevance predictor (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.0565 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-relevance predictor 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 'Gene-relevance predictor' cohort 'test', column 'AnDCG@100'
Configuration: Gene-relevance predictor (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.0306 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-relevance predictor 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 'Gene-relevance predictor' cohort 'test', column 'dFDR@100'
Configuration: Gene-relevance predictor (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.158 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-relevance predictor 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 'Gene-relevance predictor' cohort 'test', 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 (validation cohort; mean over benchmark entries) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Gene-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'
Configuration: Gene-relevance predictor (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench validation cohort of human CRISPR screens	0.0316 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-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 'dFDR@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	0.215 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	Author-reported evaluation · Source checked Methods, coverage and source Gene-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 'Precision@100'

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

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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: tgtval-20261009-config-debrouwer2026-gene-relevance-predictor

areas: cells-tissues
contexts: research
method types: supervised_machine_learning
reported name: Gene-relevance predictor
foundation model eligible: false
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: neural predictor trained on the AssayBench training split from screen-text and gene embeddings
provenance note: Configuration as run in the cited comparison.

Related records

configuration of: Gene-relevance predictor
system: Gene-relevance predictor on the AssayBench post-cutoff cohort
system: Gene-relevance predictor on the AssayBench test cohort
system: Gene-relevance predictor on the AssayBench validation cohort

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