A cautious user's guide in applying HMMs to physical systems

TL;DR

This paper investigates the applicability and limitations of hidden Markov models (HMMs) for analyzing physical systems evolving continuously, revealing that HMM states often reflect measurement choices more than physical features, and emphasizing cautious use.

Contribution

It provides a critical analysis of HMMs applied to physical systems, highlighting how discrete-state approximations can be misleading and proposing generalizations for better modeling.

Findings

HMM states often reflect measurement protocols more than physical features

Adjusting data acquisition can influence the inferred states

HMM limitations should guide their application in physical modeling

Abstract

Nature, as far as we know, evolves continuously through space and time. Yet the ubiquitous hidden Markov model (HMM)--originally developed for discrete time and space analysis in natural language processing--remains a central tool in interpreting time series data drawn from from physical systems. This raises a fundamental question: What are the implications of applying a discrete-state, discrete-time framework to analyze data generated by a continuously evolving system? Through synthetic data generated using Langevin dynamics in an effective potential, we explore under what circumstances HMMs yield interpretable results. Our analysis reveals that the discrete-state approximation acts primarily as an abstraction with the inferred states visited in time often more closely reflecting the measurement protocol and modeling choices than features of the underlying physical potential. Crucially, we demonstrate that the states visited over the course of a time series recovered by the HMM can be tuned a priori by adjusting the data acquisition scheme even misleadingly recovering reproducible "intermediate" states using different HMM tools for a system evolving in a single well potential. We conclude with a note of measured caution: while HMMs offer a mathematically elegant framework for time series inference, their use in physical modeling should be guided by an awareness of their limitations. In this light, we outline important generalizations of the HMM to continuous space and time and highlight the importance of a well calibrated measurement noise model.