Neural simulation-based inference enables parameter estimation for complex models, but typically requires the user to specify a simulator encoding a fixed model structure. We present a framework for joint model selection and parameter estimation that combines large language models for program synthesis with neural simulation-based inference. Given a natural language description of the system and data under investigation, an LLM proposes candidate simulator programs which are iteratively refined via feedback-driven mutation and evaluated using neural density estimation. The approach enables simulation-based inference over a pool of models, not just parameters within a fixed model. On benchmarks spanning deterministic dynamics, stochastic epidemic models, and dark matter substructure inference from gravitational-lensing images, the method identifies plausible model families from open-ended prompts, with accuracy that reflects the information content of the data and identifiability of candidate models.
Empirical Bayes (EB) performs simultaneous inference across many related latent variables. Classical EB assumes that the likelihood p(x | z) is tractable. In many scientific applications, however, the likelihood is available only through a simulator. This paper develops EB for su…
Simulation-based inference (SBI) with machine learning is an increasingly important tool for solving inverse problems in science and engineering, including parameter inference and the inversion of detector effects. We provide an overview of the Bayesian and frequentist statistica…
We investigate a forecasting framework based on a simple discrete-time dynamic model with coefficients varying in time. The parameters of the model are recovered within a deep learning framework, which makes it possible to retain a transparent parametric structure while simultane…
Gene regulatory networks (GRNs) link transcription factor (TF) proteins to their target genes, yet reconstructing these networks from genome-wide data remains challenging under practical and methodological constraints. Many methods couple modeling assumptions to a specific infere…
Prior work has shown that transformers can perform exact Bayesian filtering within a fixed hypothesis class. Can they also perform Bayesian model selection -- identifying the correct hypothesis class from data? We introduce model-selection Bayesian wind tunnels: controlled enviro…
Sample-based generative models are increasingly used for probabilistic forecasting in high-stakes decision settings, yet their training objectives are blind to the decision maker's cost structure. These models are commonly trained with strictly proper scoring rules, such as the e…