Physics-Informed Neural Networks for Biological 2\mathrm{D}{+}t Reaction-Diffusion Systems

Many biological processes are governed by complex dynamical mechanisms that remain incompletely understood despite increasing volumes of experimental data. Biologically-informed neural networks (BINNs) seek to address this challenge by embedding mechanistic differential equations into neural network training, enabling interpretable constitutive operators to be recovered directly from sparse and noisy observations. However, reliable operator recovery depends sensitively on network architecture, optimisation strategy, and data informativeness. Here, we present a systematic empirical study of how these factors influence mechanistic inference using BINNs applied to canonical one-dimensional advection-diffusion-reaction partial differential equation models. Across a suite of benchmark problems, we investigate how network expressivity, learning rate, loss weighting, and batch size influence optimisation behaviour and operator recovery. We show that successful mechanistic inference depends on balancing competing objectives rather than maximising any single aspect of the model or optimisation. Moderately expressive architectures outperform overly complex networks, intermediate learning rates improve optimisation stability, balanced data and PDE losses are essential for accurate operator recovery, and intermediate batch sizes provide the best compromise between computational efficiency and reproducibility. We further identify practical diagnostics for recognising common failure modes, including over-fitting, unstable optimisation, and poor mechanistic recovery when the ground truth is unavailable. Together, these findings provide evidence-based guidelines for deploying BINNs as credible tools for biological model discovery.

We propose a linearized Physics-Informed Neural Network (lPINN), a reduced-order neural basis method for forward and inverse differential equations. In an offline stage, lPINN learns operator-compatible continuous neural basis functions from an ensemble of numerical solutions. The basis functions are differentiable through automatic differentiation and are pretrained using solution data together with either derivative information or physics residuals. For each new problem instance, the basis functions are frozen and the solution is obtained by minimizing the governing-equation residual together with applicable initial, boundary, regularization, and observational terms. Unlike surrogate and operator-learning methods, the training data define the trial space offline, while the instance-specific solution is computed online by enforcing the governing physics. Relative to vanilla PINNs, lPINN pretrains the nonlinear hidden-layer representation offline and performs online inference only in the final linear layer. We evaluate lPINN on forward and inverse problems for the advection-diffusion equation, Burgers' equation, and the nonlinear pendulum equation. Compared with vanilla PINNs, lPINN achieves lower solution and parameter errors while reducing online inference times by approximately one to more than three orders of magnitude, with the largest gains generally observed for limited residual or measurement data. Cross-resolution experiments show that the learned continuous representation can be evaluated on finer meshes without retraining and with nearly unchanged accuracy.

We revisit the analogy between feed-forward deep neural networks (DNNs) and discrete dynamical systems derived from neural integral equations and their corresponding partial differential equation (PDE) forms. A comparative analysis between the numerical/exact solutions of the Burgers' and Eikonal equations, and the same obtained via PINNs is presented. We show that PINN learning provides a different computational pathway compared to standard numerical discretization in approximating essentially the same underlying dynamics of the system. Within this framework, DNNs can be interpreted as discrete dynamical systems whose layer-wise evolution approaches attractors, and multiple parameter configurations may yield comparable solutions, reflecting the degeneracy of the inverse mapping. In contrast to the structured operators associated with finite-difference (FD) procedures, PINNs learn dense parameter representations that are not directly associated with classical discretization stencils. This distributed representation generally involves a larger number of parameters, leading to reduced interpretability and increased computational cost. However, the additional flexibility of such representations may offer advantages in high-dimensional settings where classical grid-based methods become impractical.