Configuration

Badge acquisition function on an MLP surrogate (Roohani et al. 2025)

Badge acquisition function on an MLP surrogate, a configuration of Badge acquisition function (MLP surrogate); no settings beyond its name are recorded.

6 evaluations · 12 results

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Evaluations and results

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

Protocol: BioDiscoveryAgent 1-gene perturbation design: hit ratio after 5 rounds of 128 genes

Sorted by Recall (hit ratio after round 5, all genes; mean of 10 runs) (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	Recall (hit ratio after round 5, all genes; mean of 10 runs)	Recall (hit ratio after round 5, non-essential genes only; mean of 10 runs)
Badge acquisition function on an MLP surrogate (Roohani et al. 2025)Evaluation	Scharenberg et al. 2023 screen, lysosomal choline recycling in pancreatic cells	0.258 (best in column)	0.211 (best in column)
Badge acquisition function on an MLP surrogate (Roohani et al. 2025)Evaluation	Schmidt et al. 2022 screen, interleukin-2 production in primary human T cells	0.077	0.058
Badge acquisition function on an MLP surrogate (Roohani et al. 2025)Evaluation	Schmidt et al. 2022 screen, interferon-gamma production in primary human T cells	0.06	0.05
Badge acquisition function on an MLP surrogate (Roohani et al. 2025)Evaluation	Carnevale et al. 2022 screen, T-cell resistance to tumour-microenvironment inhibitory signals	0.044	0.036
Badge acquisition function on an MLP surrogate (Roohani et al. 2025)Evaluation	CAR-T proliferation screen (unpublished dataset used by Roohani et al. 2025)	0.042	0.038
Badge acquisition function on an MLP surrogate (Roohani et al. 2025)Evaluation	Sanchez et al. 2021 screen, endogenous tau protein level in neurons	0.039	0.035

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Badge 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	0.044 Recall (hit ratio after round 5, all genes; mean of 10 runs) 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 Badge 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 'Badge', column 'All' under 'Carnev.'
Configuration: Badge 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 (hit ratio after round 5, non-essential genes only; mean of 10 runs) 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 Badge 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 'Badge', column 'N/E' under 'Carnev.'
Configuration: Badge 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)	0.042 Recall (hit ratio after round 5, all genes; mean of 10 runs) 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 Badge 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 'Badge', column 'All' under 'CAR-T'
Configuration: Badge 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)	0.038 Recall (hit ratio after round 5, non-essential genes only; mean of 10 runs) 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 Badge 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 'Badge', column 'N/E' under 'CAR-T'
Configuration: Badge 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	0.039 Recall (hit ratio after round 5, all genes; mean of 10 runs) 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 Badge 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 'Badge', column 'All' under 'Sanchez'
Configuration: Badge 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	0.035 Recall (hit ratio after round 5, non-essential genes only; mean of 10 runs) 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 Badge 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 'Badge', column 'N/E' under 'Sanchez'
Configuration: Badge 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	0.258 Recall (hit ratio after round 5, all genes; mean of 10 runs) 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 Badge 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 'Badge', column 'All' under 'Scharen.'
Configuration: Badge 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	0.211 Recall (hit ratio after round 5, non-essential genes only; mean of 10 runs) 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 Badge 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 'Badge', column 'N/E' under 'Scharen.'
Configuration: Badge 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	0.06 Recall (hit ratio after round 5, all genes; mean of 10 runs) 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 Badge 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 'Badge', column 'All' under 'Schmidt1'
Configuration: Badge 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	0.05 Recall (hit ratio after round 5, non-essential genes only; mean of 10 runs) 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 Badge 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 'Badge', column 'N/E' under 'Schmidt1'
Configuration: Badge 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	0.077 Recall (hit ratio after round 5, all genes; mean of 10 runs) 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 Badge 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 'Badge', column 'All' under 'Schmidt2'
Configuration: Badge 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	0.058 Recall (hit ratio after round 5, non-essential genes only; mean of 10 runs) 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 Badge 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 'Badge', 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-badge

areas: cells-tissues
contexts: research
method types: supervised_machine_learning
reported name: Badge
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
provenance note: Configuration as run in the cited comparison.

Related records

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

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