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This paper introduces MechHypoBench, the first benchmark designed to evaluate AI agents' capacity to generate mechanistic hypotheses from empirical data across 14 scientific fields. By testing models against datasets with known underlying mechanisms, the study reveals a significant gap between current AI-generated hypotheses and actual causal processes in complex systems. This work is critical for advancing trustworthy AI in scientific discovery, as it directly addresses the need for explainable reasoning rather than mere pattern matching.
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From Scientific Observations to Mechanisms: Benchmarking Hypothesis Generation by AI Scientists

arXiv2 min read

arXiv:2610.05197v1 Announce Type: new Abstract: Data-driven mechanistic hypotheses are essential to scientific discovery because they explain how underlying processes produce observed phenomena. AI agents and AI scientists increasingly support scientific data analysis. However, their ability to turn empirical findings into mechanistic hypotheses remains insufficiently examined. To address this gap, we introduce MechHypoBench, the first benchmark for evaluating whether AI agents and AI scientists can generate such hypotheses from empirical data. It combines paper-derived mechanisms from 14 scientific fields with real-world datasets containing 17.98 million records. The construction retains the observational complexity of empirical data while providing a specified underlying mechanism. Agents analyze the observations and propose open-form hypotheses. We develop an evaluation framework that assesses open-form mechanistic hypotheses through their consequences under withheld conditions. Experiments with general agents and AI scientists reveal a substantial gap between generated hypotheses and the underlying mechanisms.

Abstract:Data-driven mechanistic hypotheses are essential to scientific discovery because they explain how underlying processes produce observed phenomena. AI agents and AI scientists increasingly support scientific data analysis. However, their ability to turn empirical findings into mechanistic hypotheses remains insufficiently examined. To address this gap, we introduce MechHypoBench, the first benchmark for evaluating whether AI agents and AI scientists can generate such hypotheses from empirical data. It combines paper-derived mechanisms from 14 scientific fields with real-world datasets containing 17.98 million records. The construction retains the observational complexity of empirical data while providing a specified underlying mechanism. Agents analyze the observations and propose open-form hypotheses. We develop an evaluation framework that assesses open-form mechanistic hypotheses through their consequences under withheld conditions. Experiments with general agents and AI scientists reveal a substantial gap between generated hypotheses and the underlying mechanisms.

Artificial Intelligence (cs.AI)

arXiv:2610.05197 [cs.AI]

(or arXiv:2610.05197v1 [cs.AI] for this version)

https://doi.org/10.48550/arXiv.2610.05197 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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Full text under the publisher's open licence · 231 words

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