DrugTargetWorld: A Synthetic Biobank for Training and Benchmarking AI Scientists

arXiv:2610.09558v1 Announce Type: new Abstract: Drug target discovery requires distinguishing molecules that causally drive disease from those that are merely associated with it. Training and evaluating AI agents to perform this workflow end-to-end is difficult because real world biobanks lack known causal ground truth and participant-level data is access controlled. We introduce DrugTargetWorld, a framework that procedurally generates simulated biobanks, or "worlds," with known but concealed causal structure. Each world contains genotypes, proteins, health records, outcomes, and synthetic magnetic resonance imaging (MRI) for 54,000 participants. Agents must construct a disease phenotype, identify causal driver proteins, infer the beneficial direction of modulation, and optionally conduct virtual 'wet lab' experiments. We evaluated nine agents in 540 episodes across 20 cardiovascular worlds and three experimental budgets. Opus 5 and GPT-5.6 Sol achieved the highest mean composite scores, 39.98 and 35.38 of 100, respectively, and both recovered 64% of causal drivers on average. However, no agent reliably distinguished misleading non-causal proteins, and performance remained limited by the integrative judgments required to connect phenotype construction, causal evidence, and intervention decisions. By making each world's causal structure known to the evaluator but hidden from the agent, DrugTargetWorld turns end-to-end drug target discovery into a scalable training and evaluation problem with verifiable reward.

Abstract:Drug target discovery requires distinguishing molecules that causally drive disease from those that are merely associated with it. Training and evaluating AI agents to perform this workflow end-to-end is difficult because real world biobanks lack known causal ground truth and participant-level data is access controlled. We introduce DrugTargetWorld, a framework that procedurally generates simulated biobanks, or "worlds," with known but concealed causal structure. Each world contains genotypes, proteins, health records, outcomes, and synthetic magnetic resonance imaging (MRI) for 54,000 participants. Agents must construct a disease phenotype, identify causal driver proteins, infer the beneficial direction of modulation, and optionally conduct virtual 'wet lab' experiments. We evaluated nine agents in 540 episodes across 20 cardiovascular worlds and three experimental budgets. Opus 5 and GPT-5.6 Sol achieved the highest mean composite scores, 39.98 and 35.38 of 100, respectively, and both recovered 64% of causal drivers on average. However, no agent reliably distinguished misleading non-causal proteins, and performance remained limited by the integrative judgments required to connect phenotype construction, causal evidence, and intervention decisions. By making each world's causal structure known to the evaluator but hidden from the agent, DrugTargetWorld turns end-to-end drug target discovery into a scalable training and evaluation problem with verifiable reward.

34 pages main text, 92 pages supplementary material; 6 main figures. Project: this https URL. Code: this https URL. Data: this https URL

Artificial Intelligence (cs.AI)

arXiv:2610.09558 [cs.AI]

(or arXiv:2610.09558v1 [cs.AI] for this version)

https://doi.org/10.48550/arXiv.2610.09558 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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DrugTargetWorld: A Synthetic Biobank for Training and Benchmarking AI Scientists

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