Pre-trained Large Language Models Learn to Predict Hidden Markov Models In-context

Hidden Markov Models (HMMs) are foundational tools for modeling sequential data with latent Markovian structure, yet fitting them to real-world data remains computationally challenging. In this work, we show that pre-trained large language models (LLMs) can effectively model data generated by HMMs via in-context learning (ICL)-their ability to infer patterns from examples within a prompt. On a diverse set of synthetic HMMs, LLMs achieve predictive accuracy approaching the theoretical optimum. We uncover novel scaling trends influenced by HMM properties, and offer theoretical conjectures for these empirical observations. We also provide practical guidelines for scientists on using ICL as a diagnostic tool for complex data. On real-world animal decision-making tasks, ICL achieves competitive performance with models designed by human experts. To our knowledge, this is the first demonstration that ICL can learn to predict HMM-generated sequences-an advance that deepens our understanding of in-context learning in LLMs and establishes its potential as a powerful tool for uncovering hidden structure in complex scientific data. Our code is available at https://github.com/DaiYijia02/icl-hmm.