Learning to Outgrow a Theory: Experimental Discovery Beyond the Initial Hypothesis Space

Scientific discovery depends on the ability to form hypotheses, test them through experiments, and revise them when evidence disagrees. Existing LLM agents support this process by improving their reasoning or actions, but their scientific beliefs are often scattered across free-form reasoning and difficult to update coherently. This makes it difficult to identify what failed, what should change, and whether revisions remain consistent with prior evidence. We introduce EvoSCM, which represents scientific beliefs as a population of structural causal model (SCM) hypotheses that can be tested and revised across experiments. EvoSCM formulates scientific discovery as a closed loop in which causal hypotheses guide experimentation and experimental outcomes drive causal model evolution. Competing SCM hypotheses make falsifiable predictions and guide discriminative experiments that separate alternative explanations. When observations contradict these predictions, EvoSCM distills discrepancies into correction rules identifying which aspects of the hypotheses fail to explain the evidence. These rules guide revisions to causal dependencies, latent factors, mechanisms, and parameters. Revised hypotheses are validated against accumulated evidence and carried forward to guide subsequent experiments, allowing scientific beliefs to evolve cumulatively. We evaluate EvoSCM across physics, chemistry and materials, and biology. It consistently outperforms baseline agents and existing evolution methods, yielding more accurate explanations and predictions with more effective use of experimental budgets. The evolved SCMs also transfer across base models, suggesting reusable scientific knowledge beyond any single model's reasoning process.

Scientific discovery is a closed-loop process in which hypotheses guide data acquisition and observations refine the hypothesis space. Yet most approaches reduce discovery to supervised learning over fixed datasets, where limited observations can support multiple plausible mechanisms that fit locally but fail to generalize. Thus, the key challenge is selecting informative observations to resolve uncertainty, shifting the focus from static inference to adaptive data acquisition. To address this, we propose LLM-AutoSciLab, a closed-loop framework that couples hypothesis generation with hypothesis-conditioned experiment selection and mechanism refinement. Rather than fitting models to passively collected data, LLM-AutoSciLab iteratively proposes plausible hypotheses, selects informative experiments to distinguish or refine them, and updates its state using the resulting evidence. To evaluate dynamic, closed-loop scientific discovery with active data acquisition, we introduce ActiveSciBench, comprising two datasets: ActiveSciBench-Chem with 57 enzyme-kinetics tasks and ActiveSciBench-GRN with 45 gene-regulatory-network tasks. These datasets model discovery as a budget-constrained process requiring adaptive experiment design, variable selection, and recovery of true mechanisms. Across NewtonBench, ActiveSciBench-Chem, and ActiveSciBench-GRN, LLM-AutoSciLab outperforms prior methods, achieving 67.6% and 35.1% symbolic accuracy on NewtonBench and ActiveSciBench-Chem, respectively, and 31.1% exact graph recovery on ActiveSciBench-GRN. Moreover, hypothesis-guided experimentation is 2-5x more sample-efficient than the strongest competing baselines. Code and data are available at: https://github.com/scientific-discovery/LLM-AutoSciLab

Autonomous scientific discovery systems increasingly use large language models (LLMs) to propose new hypotheses, but many such systems condition primarily on experimental memory: archives of high-scoring candidates or heuristic summaries of recent trials. We argue that discovery agents should instead maintain explicit, uncertainty-aware beliefs about hypothesis quality. We introduce BayesEvolve, a belief-guided discovery framework that converts experimental evidence into a predictive belief state and uses this belief to guide future experimentation. As a controlled testbed for belief-guided discovery, we evaluate BayesEvolve on shifted BBOB-style black-box optimization tasks, leaving program and laboratory discovery domains to future work. BayesEvolve improves sample efficiency over memory- and archive-guided LLM baselines under a fixed evaluation budget. We further show that the belief state is predictive on held-out candidate pools, that controlled decision-rule ablations favor belief-guided selection with an annealed uncertainty bonus, and that BayesEvolve exhibits productive late-stage concentration rather than unfocused exploration.