Topological Entropy Correlates with the Predictive Power of Multiplexed Ensemble Reservoir Computing

Modeling nonlinear, multiscale, and transiently chaotic biological processes remains a major challenge in computational biology. Traditional deep learning models, while powerful, require large datasets and lack mechanistic interpretability, limiting their effectiveness for time-resolved biological systems. Reservoir computing (RC) offers a promising alternative by leveraging the rich transient dynamics of fixed nonlinear systems, yet standard RC architectures struggle with high-dimensional biological data and complex temporal regimes. Here, we introduce Dynamical System Machine Learning (DynML), a multiplexed reservoir framework designed to model gene-expression dynamics in systems such as liver regeneration and Drosophila embryogenesis. DynML encodes biological signals using heterogeneous Lorenz reservoirs and employs a single global readout to capture stage-dependent dynamics with high predictive accuracy. We further show that reservoir topological entropy quantitatively predicts model performance, linking dynamical richness to biological forecasting accuracy. Beyond biological time-series modeling, we demonstrate the generality of DynML on the MNIST handwritten digit classification task using a Rössler-based chaotic reservoir, showing that fixed dynamical cores with linear readouts can also support high-dimensional static classification. Overall, DynML provides a scalable, interpretable, and computationally efficient framework that unifies biological time-series modeling and conventional machine-learning tasks within a single dynamical systems paradigm.