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Embedding kNN (AssayBench)

Configuration of Embedding kNN: top genes of the most similar training screen by description embedding.

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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))
Embedding kNN (AssayBench)Evaluation	AssayBench post-cutoff cohort of human CRISPR screens	0.0271	Not reported	Not reported	NA	Not reported	Not reported	0.113	Not reported	Not reported
Embedding kNN (AssayBench)Evaluation	AssayBench test cohort of human CRISPR screens	Not reported	0.0646	Not reported	Not reported	0.0226	Not reported	Not reported	0.106	Not reported
Embedding kNN (AssayBench)Evaluation	AssayBench validation cohort of human CRISPR screens	Not reported	Not reported	0.0697	Not reported	Not reported	0.0321	Not reported	Not reported	0.103

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Embedding kNN (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	0.0271 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 Embedding kNN 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 'Embedding kNN' cohort 'LaTest', column 'AnDCG@100'
Configuration: Embedding kNN (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 Embedding kNN 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 'Embedding kNN' cohort 'LaTest', column 'dFDR@100'
Configuration: Embedding kNN (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench post-cutoff cohort of human CRISPR screens	0.113 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 Embedding kNN 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 'Embedding kNN' cohort 'LaTest', column 'Precision@100'
Configuration: Embedding kNN (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.0646 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 Embedding kNN 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 'Embedding kNN' cohort 'test', column 'AnDCG@100'
Configuration: Embedding kNN (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.0226 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 Embedding kNN 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 'Embedding kNN' cohort 'test', column 'dFDR@100'
Configuration: Embedding kNN (AssayBench)	Protocol: AssayBench: rank 100 candidate genes for a described CRISPR screen Dataset: AssayBench test cohort of human CRISPR screens	0.106 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 Embedding kNN 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 'Embedding kNN' cohort 'test', 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 (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 Embedding 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 (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 Embedding 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 (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 Embedding 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'

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-embedding-knn

areas: cells-tissues
contexts: research
method types: conventional_pipeline
reported name: Embedding kNN
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: top genes of the most similar training screen by description embedding
provenance note: Configuration as run in the cited comparison.

Related records

configuration of: Embedding kNN
system: Embedding kNN on the AssayBench post-cutoff cohort
system: Embedding kNN on the AssayBench test cohort
system: Embedding kNN on the AssayBench validation cohort

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