Configuration

Embedding kNN (AssayBench)

Configuration as run in the cited comparison.

Overview

Configuration as run in the cited comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

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

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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 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 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 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 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 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 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 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 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 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'

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Sources and history

Release 2026-10-10-6e93f504adfc · 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

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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