Model Discovery Agent: LLM-assisted Bayesian experiment design for data-efficient discovery of mechanistic world models

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arXiv:2608.09696v2 Announce Type: replace Abstract: Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a \emph{mechanistic}, causal model, not a curve fit; and learning such a model requires \emph{experiments}, because passive data leaves its mechanisms unidentified. Experiments are expensive, so the central problem is \emph{data efficiency}. We present the Model Discovery Agent (MDA), which couples a large language model (LLM), used as a \emph{proposer} of candidate structures, with standard Bayesian machinery --- sequential Monte Carlo (SMC) for parameter and structure posteriors, simulation-based inference (SBI) for intractable likelihoods, and value-of-information (VoI) for experiment design --- to discover latent mechanistic world models from few interventions. MDA operates in the M-open setting: when the truth lies outside the current hypothesis class, a predictive check flags the inadequacy and the proposer expands the hypothesis space with a new model whose parameters are then identified by designed experiments. We show that \emph{discovery and design reinforce}: the design step identifies the mechanism the discovery step proposes, and the identified mechanism improves predictions, enabling further discoveries from the remaining unexplained residuals. On three different benchmarks --- covering physics (\DPbench, \citep{wiemann2026discoverphysics}), chemistry (\CHEMbench, \citep{kabra2026autoscilab}) and biology (\HHbench, a new partially observed single-neuron electrophysiology benchmark we create) …

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