appendixa
NoLimits.jl: Flexible and Composable Nonlinear Mixed-Effects Modeling in Julia
Huth, Manuel, Arruda, Jonas, Schmid, Nina, Gusinow, Roy, Wieland, Vincent, Peiter, Clemens, Hasenauer, Jan
Nonlinear mixed-effects models are widely used to analyze longitudinal data, but existing open-source software often supports only a limited subset of the model structures, inference methods, machine-learning components, automatic differentiation techniques, and random-effects distributions required in modern applications. We introduce NoLimits.jl, an open-source Julia package for flexible and composable nonlinear mixed-effects modeling. Its macro-based modeling language enables observation and latent-state models to be constructed from diverse building blocks, including ordinary differential equations, Markov models, and neural networks. NoLimits.jl supports flexible, covariate-dependent observation and random-effects distributions and provides a unified interface to frequentist inference through Laplace approximation, stochastic expectation maximization, and Bayesian Markov chain Monte Carlo methods. We demonstrate the package on three case studies showcasing its workflows, integration of differentiable machine-learning components, and data-driven estimation of random-effects distributions using normalizing flows. Together, these capabilities substantially expand the range of nonlinear mixed-effects models that can be specified, estimated, and compared within a single open-source framework.
FourierNetsenablethedesignofhighlynon-local opticalencodersforcomputationalimaging
More challenging computational imaging applications, such as3D snapshot microscopywhichcompresses 3Dvolumes intosingle2Dimages, require ahighly non-local optical encoder. We show that existing deep network decoders have a locality bias which prevents the optimization of such highly non-local optical encoders. We address this with a decoder based on a shallow neural network architecture using global kernel Fourier convolutional neural networks (FourierNets).