Bayesian Model Discovery with Language Models: Closing the Loop between Hypotheses and Experiments

A primary goal of science is to learn mechanistic world models from limited experimental data, both to explain observations and to predict novel interventions. We introduce the Model Discovery Agent (MDA), which combines LLM proposals for $\mathcal M$-open model discovery, experiment design based on Value of Information, and approximate Bayesian inference over model structures, parameters, and stochastic latent trajectories. We apply MDA to learn symbolic reaction rate laws for ChemBench \citep{kabra2026autoscilab}, partially observed ODE models for GlucoseBench \citep{xie2018simglucose,kovatchev2009insilico}, and partially observed SDE models for a new stochastic single-neuron simulator we create. In the appendix, we also show results on various other domains from BoxingGym \citep{gandhi2025boxinggym}. We show that MDA has improved sample efficiency compared to various baseline methods, and the learned models are good predictors but also provide interpretable abstractions of each domain.

Large language models (LLMs) are increasingly applied across the scientific discovery pipeline, from synthesizing literature to generating hypotheses to informing experimental design. A unifying principle behind these tasks is the need to continuously update beliefs as evidence accumulates, for which Bayesian inference provides a natural framework. However, existing work assumes that LLMs cannot carry out principled Bayesian belief updating in context, instead relying on simplifications and heuristics. To challenge this assumption, we present a principled evaluation of Bayesian reasoning capabilities in LLMs, analyzing both the model's internal consistency as well as its ability to recover an externally determined posterior. Specifically, we build an evaluation framework spanning qualitative epistemological examples to probe probabilistic coherence, quantitative benchmarks of Bayesian inference capabilities, and analyses of the impact of non-Bayesian updates on downstream task performance. Across different scenarios, we find that LLMs generally violate Bayes' rule when updating their beliefs in context. However, when equipped with modern reasoning abilities and code execution capabilities, their performance drastically improves, enabling even the close approximation of analytically intractable posteriors. Our evaluation shows that current LLMs with access to appropriate tools could already be used to make complex belief updates in scientific discovery, enabling rapid acceleration of the efficiency and scale of AI-powered scientific discovery.

Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a $2.4\times$ greater reduction in validation BPB, an $18.2\%$ relative decrease in binding energy, and more than $60\%$ relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.