BDA (Replicated), claude-3-5-sonnet backbone (Gupta et al. 2025)

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Configuration as run in the cited comparison.

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Evaluations and results

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BDA (Replicated), claude-3-5-sonnet backbone (Gupta et al. 2025)	Protocol: Independent replication of 1-gene perturbation design: cumulative hits after 5 rounds of 128 genes Dataset: Carnevale et al. 2022 screen, T-cell resistance to tumour-microenvironment inhibitory signals	43.8 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BDA (Replicated) (Claude 3.5 Sonnet backbone) on Carnevale (Gupta et al. 2025) tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 Aggregation: Not reported LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Table 1, 'Claude 3.5 Sonnet backbone' block, row 'BDA (Replicated)', column 'Carnevale'
Configuration: BDA (Replicated), claude-3-5-sonnet backbone (Gupta et al. 2025)	Protocol: Independent replication of 1-gene perturbation design: cumulative hits after 5 rounds of 128 genes Dataset: Sanchez et al. 2021 screen, decreased endogenous tau protein level in neurons	51.8 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BDA (Replicated) (Claude 3.5 Sonnet backbone) on Sanchez Down (Gupta et al. 2025) tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 Aggregation: Not reported LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Table 1, 'Claude 3.5 Sonnet backbone' block, row 'BDA (Replicated)', column 'Sanchez Down'
Configuration: BDA (Replicated), claude-3-5-sonnet backbone (Gupta et al. 2025)	Protocol: Independent replication of 1-gene perturbation design: cumulative hits after 5 rounds of 128 genes Dataset: Sanchez et al. 2021 screen, endogenous tau protein level in neurons	31.6 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BDA (Replicated) (Claude 3.5 Sonnet backbone) on Sanchez (Gupta et al. 2025) tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 Aggregation: Not reported LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Table 1, 'Claude 3.5 Sonnet backbone' block, row 'BDA (Replicated)', column 'Sanchez'
Configuration: BDA (Replicated), claude-3-5-sonnet backbone (Gupta et al. 2025)	Protocol: Independent replication of 1-gene perturbation design: cumulative hits after 5 rounds of 128 genes Dataset: Schmidt et al. 2022 screen, interferon-gamma production in primary human T cells	78.8 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BDA (Replicated) (Claude 3.5 Sonnet backbone) on IFNG (Gupta et al. 2025) tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 Aggregation: Not reported LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Table 1, 'Claude 3.5 Sonnet backbone' block, row 'BDA (Replicated)', column 'IFNG'
Configuration: BDA (Replicated), claude-3-5-sonnet backbone (Gupta et al. 2025)	Protocol: Independent replication of 1-gene perturbation design: cumulative hits after 5 rounds of 128 genes Dataset: Schmidt et al. 2022 screen, interleukin-2 production in primary human T cells	59.4 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BDA (Replicated) (Claude 3.5 Sonnet backbone) on IL2 (Gupta et al. 2025) tgtval-20261009-protocol-gupta2025-cumulative-hits-round5 Aggregation: Not reported LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Table 1, 'Claude 3.5 Sonnet backbone' block, row 'BDA (Replicated)', column 'IL2'

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Release 2026-10-10-6e93f504adfc · Record review: source checked

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LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? · Original source · Findings of the Association for Computational Linguistics: EMNLP 2025, pages 15482-15510

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Technical metadata and extraction receipts

Stable ID: tgtval-20261009-config-gupta2025-bda-replicated-claude-3-5-sonnet

areas: cells-tissues
contexts: research
method types: foundation_model
reported name: BDA (Replicated)
foundation model eligible: true
source locator: Table 1, 'Claude 3.5 Sonnet backbone' block
missing metadata: version: reason: unreported; note: No release or commit is printed for this configuration
parameters: No-Tool variant of BioDiscoveryAgent

Related records

configuration of: BioDiscoveryAgent
uses model: Claude 3.5 Sonnet
system: BDA (Replicated) (Claude 3.5 Sonnet backbone) on Carnevale (Gupta et al. 2025)
system: BDA (Replicated) (Claude 3.5 Sonnet backbone) on Sanchez (Gupta et al. 2025)
system: BDA (Replicated) (Claude 3.5 Sonnet backbone) on Sanchez Down (Gupta et al. 2025)
system: BDA (Replicated) (Claude 3.5 Sonnet backbone) on IFNG (Gupta et al. 2025)
system: BDA (Replicated) (Claude 3.5 Sonnet backbone) on IL2 (Gupta et al. 2025)