Configuration

Soft Uncertain 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.

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Evaluations and results

6 evaluations · 12 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: Soft Uncertain 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	0.031 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 Soft Uncertain 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 'Soft Uncertain', column 'All' under 'Carnev.'
Configuration: Soft Uncertain 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	0.035 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 Soft Uncertain 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 'Soft Uncertain', column 'N/E' under 'Carnev.'
Configuration: Soft Uncertain 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1-gene perturbation design: hit ratio after 5 rounds of 128 genes Dataset: CAR-T proliferation screen (unpublished dataset used by Roohani et al. 2025)	0.034 recall fraction · higher Uncertainty: Not yet extracted: Appendix Table 7 prints one standard deviation over 10 runs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 Soft Uncertain 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 'Soft Uncertain', column 'All' under 'CAR-T'
Configuration: Soft Uncertain 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)	0.032 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 Soft Uncertain 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 'Soft Uncertain', column 'N/E' under 'CAR-T'
Configuration: Soft Uncertain 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	0.029 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 Soft Uncertain 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 'Soft Uncertain', column 'All' under 'Sanchez'
Configuration: Soft Uncertain 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	0.029 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 Soft Uncertain 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 'Soft Uncertain', column 'N/E' under 'Sanchez'
Configuration: Soft Uncertain 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	0.205 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 Soft Uncertain 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 'Soft Uncertain', column 'All' under 'Scharen.'
Configuration: Soft Uncertain 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	0.161 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 Soft Uncertain 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 'Soft Uncertain', column 'N/E' under 'Scharen.'
Configuration: Soft Uncertain 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	0.037 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 Soft Uncertain 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 'Soft Uncertain', column 'All' under 'Schmidt1'
Configuration: Soft Uncertain 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	0.037 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 Soft Uncertain 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 'Soft Uncertain', column 'N/E' under 'Schmidt1'
Configuration: Soft Uncertain 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	0.037 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 Soft Uncertain 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 'Soft Uncertain', column 'All' under 'Schmidt2'
Configuration: Soft Uncertain 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	0.035 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 Soft Uncertain 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 'Soft Uncertain', 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-soft-uncertain

areas: cells-tissues
contexts: research
method types: supervised_machine_learning
reported name: Soft Uncertain
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: Soft Uncertain acquisition function (MLP surrogate)
system: Soft Uncertain on Carnev. (Roohani et al. 2025)
system: Soft Uncertain on CAR-T (Roohani et al. 2025)
system: Soft Uncertain on Sanchez (Roohani et al. 2025)
system: Soft Uncertain on Scharen. (Roohani et al. 2025)
system: Soft Uncertain on Schmidt1 (Roohani et al. 2025)
system: Soft Uncertain on Schmidt2 (Roohani et al. 2025)

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