Configuration

BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.032 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'All' under 'Carnev.'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.034 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'N/E' under 'Carnev.'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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)	0.064 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'All' under 'CAR-T'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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)	0.066 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'N/E' under 'CAR-T'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.039 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'All' under 'Sanchez'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.038 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'N/E' under 'Sanchez'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.23 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'All' under 'Scharen.'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.188 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'N/E' under 'Scharen.'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.044 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'All' under 'Schmidt1'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.048 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'N/E' under 'Schmidt1'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.061 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'All' under 'Schmidt2'
Configuration: BioDiscoveryAgent (No-Tools), GPT-3.5-Turbo (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	0.073 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	Author-reported evaluation · Source checked Methods, coverage and source GPT-3.5-Turbo 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 'GPT-3.5-Turbo', column 'N/E' under 'Schmidt2'

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Sources and history

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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-gpt-3-5-turbo

areas: cells-tissues
contexts: research
method types: foundation_model
reported name: GPT-3.5-Turbo
foundation model eligible: true
source locator: Table 1, BioDiscoveryAgent (No-Tools) block
missing metadata: version: reason: unreported; note: No release or commit is printed for this configuration
parameters: No-Tools variant: no literature search, gene search or critic tool

Related records

configuration of: BioDiscoveryAgent
uses model: GPT-3.5-Turbo
system: GPT-3.5-Turbo on Carnev. (Roohani et al. 2025)
system: GPT-3.5-Turbo on CAR-T (Roohani et al. 2025)
system: GPT-3.5-Turbo on Sanchez (Roohani et al. 2025)
system: GPT-3.5-Turbo on Scharen. (Roohani et al. 2025)
system: GPT-3.5-Turbo on Schmidt1 (Roohani et al. 2025)
system: GPT-3.5-Turbo on Schmidt2 (Roohani et al. 2025)

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