Configuration

K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)

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

6 evaluations · 12 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Carnevale et al. 2022 screen, T-cell resistance to tumour-microenvironment inhibitory signals	0.036 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Carnev. (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'All' under 'Carnev.'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Carnevale et al. 2022 screen, T-cell resistance to tumour-microenvironment inhibitory signals	0.029 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Carnev. (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'N/E' under 'Carnev.'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: CAR-T proliferation screen (unpublished dataset used by Roohani et al. 2025)	0.028 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on CAR-T (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'All' under 'CAR-T'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: CAR-T proliferation screen (unpublished dataset used by Roohani et al. 2025)	0.024 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on CAR-T (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'N/E' under 'CAR-T'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Sanchez et al. 2021 screen, endogenous tau protein level in neurons	0.037 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Sanchez (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'All' under 'Sanchez'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Sanchez et al. 2021 screen, endogenous tau protein level in neurons	0.032 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Sanchez (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'N/E' under 'Sanchez'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Scharenberg et al. 2023 screen, lysosomal choline recycling in pancreatic cells	0.17 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Scharen. (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'All' under 'Scharen.'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Scharenberg et al. 2023 screen, lysosomal choline recycling in pancreatic cells	0.154 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Scharen. (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'N/E' under 'Scharen.'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Schmidt et al. 2022 screen, interferon-gamma production in primary human T cells	0.045 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Schmidt1 (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'All' under 'Schmidt1'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Schmidt et al. 2022 screen, interferon-gamma production in primary human T cells	0.035 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Schmidt1 (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'N/E' under 'Schmidt1'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Schmidt et al. 2022 screen, interleukin-2 production in primary human T cells	0.064 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Schmidt2 (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'All' under 'Schmidt2'
Configuration: K-Means (E) acquisition function on an MLP surrogate (Roohani et al. 2025)	Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: Schmidt et al. 2022 screen, interleukin-2 production in primary human T cells	0.053 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs for these values; not extracted in this pass. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source K-Means (E) on Schmidt2 (Roohani et al. 2025) tgtval-20261009-protocol-roohani2025-hitratio-round5 Aggregation: Not reported BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Table 1, row 'K-Means (E)', column 'N/E' under 'Schmidt2'

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BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments · Original source · arXiv:2405.17631 version 3, updated 2025-03-09; published as a conference paper at ICLR 2025

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Technical metadata and extraction receipts

Stable ID: tgtval-20261009-config-roohani2025-k-means-e

areas: cells-tissues
contexts: research
method types: supervised_machine_learning
reported name: K-Means (E)
foundation model eligible: false
source locator: Table 1, Baseline Models block
missing metadata: version: reason: unreported; note: No release or commit is printed for this configuration

Related records

configuration of: K-Means (E) acquisition function (MLP surrogate)
system: K-Means (E) on Carnev. (Roohani et al. 2025)
system: K-Means (E) on CAR-T (Roohani et al. 2025)
system: K-Means (E) on Sanchez (Roohani et al. 2025)
system: K-Means (E) on Scharen. (Roohani et al. 2025)
system: K-Means (E) on Schmidt1 (Roohani et al. 2025)
system: K-Means (E) on Schmidt2 (Roohani et al. 2025)

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