Cubature Kalman Filter Based Training of Hybrid Differential Equation Recurrent Neural Network Physiological Dynamic Models
This work addresses the problem of incomplete physiological modeling for researchers in computational biology, though it is incremental as it builds on existing hybrid methods.
The paper tackled the challenge of modeling biological dynamical systems with incomplete knowledge by combining neural networks with physics-based models, using a Bayesian filtering approach to train parameters and estimate states, and demonstrated better accuracy than backpropagation through time in a blood circulation case study.
Modeling biological dynamical systems is challenging due to the interdependence of different system components, some of which are not fully understood. To fill existing gaps in our ability to mechanistically model physiological systems, we propose to combine neural networks with physics-based models. Specifically, we demonstrate how we can approximate missing ordinary differential equations (ODEs) coupled with known ODEs using Bayesian filtering techniques to train the model parameters and simultaneously estimate dynamic state variables. As a study case we leverage a well-understood model for blood circulation in the human retina and replace one of its core ODEs with a neural network approximation, representing the case where we have incomplete knowledge of the physiological state dynamics. Results demonstrate that state dynamics corresponding to the missing ODEs can be approximated well using a neural network trained using a recursive Bayesian filtering approach in a fashion coupled with the known state dynamic differential equations. This demonstrates that dynamics and impact of missing state variables can be captured through joint state estimation and model parameter estimation within a recursive Bayesian state estimation (RBSE) framework. Results also indicate that this RBSE approach to training the NN parameters yields better outcomes (measurement/state estimation accuracy) than training the neural network with backpropagation through time in the same setting.