Implementing neural network mixed-effects models in Template Model Builder (TMB)

Neural network mixed-effects models (NMMs) have gained traction by combining the strong representation and predictive power of artificial neural networks with the capacity of mixed-effects modeling to capture complex correlation structures. However, existing estimation approaches rely heavily on manual derivations of objective functions and gradients, which inherently forces simplifying approximations and severely constrains the complexity and accuracy of NMMs. In this work, we introduce a general framework for implementing NMMs using Template Model Builder (TMB). By leveraging automatic differentiation and Laplace approximation, TMB requires users to specify only the negative joint log-likelihood and any regularization terms. The framework automatically integrates out random effects and evaluates the marginal objective function alongside its exact gradients, eliminating the need for manual derivations or ad hoc approximations. We demonstrate the efficiency, flexibility, and statistical performance of TMB-based NMMs across two numerical examples, including an application to monotonic NMMs. Reproducible code is provided to facilitate broader adoption.

Extrapolating from Regularised Solutions for Solving Ill-Conditioned Linear Systems in Machine Learning

Rapid prototyping of algorithms is a critical step in modern machine learning. Most algorithms exploit linear algebra, creating a need for lightweight numerical routines which -- while potentially sub-optimal for the task at hand -- can be rapidly implemented. For the numerical solution of ill-conditioned linear systems of equations, the standard solution for prototyping is Tikhonov-regularised inversion using a nugget. However, selection of the size of nugget is often difficult, and the use of data-adaptive procedures precludes automatic differentiation, introducing instabilities into end-to-end training. Further, while data-adaptive procedures perform multiple linear solves to select the size of nugget, only the result of one such solve is returned, which we argue is wasteful. This paper aims to circumvent the above difficulties, presenting autonugget; a Python package for automatic and stable numerical solution of linear systems suitable for rapid prototyping, and fully compatible with automatic differentiation using JAX. autonugget combines multiple linear solves using Richardson extrapolation to determine the solution of the ill-conditioned system, improving in accuracy over approximations based on a single nugget.