Data-driven discovery of dynamical models in biology

Abstract

Dynamical systems theory provides a mathematical framework for describing how interacting biological components evolve over time and space, from molecular oscillators to large-scale biological patterns. Such systems often involve nonlinear feedbacks, delays, and multiscale interactions, making mechanistic model construction increasingly challenging as experimental measurements become richer and higher-dimensional. This has motivated the development of data-driven approaches that infer model structure directly from data, offering alternative routes to constructing dynamical models. In this review, we discuss and compare data-driven approaches for model discovery in biological dynamical systems, focusing on three major methodological families: regression-based methods, network-based architectures, and decomposition techniques. We compare how these approaches address three core objectives: forecasting future behavior, identifying interactions between system components, and characterizing qualitative dynamical solutions such as steady states, oscillations, and transitions between them. To enable a direct comparison, representative methods are applied to a common benchmark - the Oregonator model - a minimal nonlinear oscillator that captures shared design principles of chemical and biological systems. By highlighting practical strengths, limitations, and degrees of interpretability, this review aims to guide researchers in selecting appropriate tools for analyzing complex, nonlinear, and high-dimensional biological dynamics.