From Prompts to Posteriors: Can LLM Agents Perform Bayesian Inference in Context?

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.