Process-Based Modeling (PBM) and Machine Learning (ML) are often perceived as distinct paradigms in the geosciences. Here we present differentiable geoscientific modeling as a powerful pathway toward dissolving the perceived barrier between them and ushering in a paradigm shift. For decades, PBM offered benefits in interpretability and physical consistency but struggled to efficiently leverage large datasets. ML methods, especially deep networks, presented strong predictive skills yet lacked the ability to answer specific scientific questions. While various methods have been proposed for ML-physics integration, an important underlying theme -- differentiable modeling -- is not sufficiently recognized. Here we outline the concepts, applicability, and significance of differentiable geoscientific modeling (DG). "Differentiable" refers to accurately and efficiently calculating gradients with respect to model variables, critically enabling the learning of high-dimensional unknown relationships. DG refers to a range of methods connecting varying amounts of prior knowledge to neural networks and training them together, capturing a different scope than physics-guided machine learning and emphasizing first principles. Preliminary evidence suggests DG offers better interpretability and causality than ML, improved generalizability and extrapolation capability, and strong potential for knowledge discovery, while approaching the performance of purely data-driven ML. DG models require less training data while scaling favorably in performance and efficiency with increasing amounts of data. With DG, geoscientists may be better able to frame and investigate questions, test hypotheses, and discover unrecognized linkages.

Many physics and engineering applications demand Partial Differential Equations (PDE) property evaluations that are traditionally computed with resource-intensive high-fidelity numerical solvers. Data-driven surrogate models provide an efficient alternative but come with a significant cost of training. Emerging applications would benefit from surrogates with an improved accuracy-cost tradeoff, while studied at scale. Here we present a "physics-enhanced deep-surrogate" ("PEDS") approach towards developing fast surrogate models for complex physical systems, which is described by PDEs. Specifically, a combination of a low-fidelity, explainable physics simulator and a neural network generator is proposed, which is trained end-to-end to globally match the output of an expensive high-fidelity numerical solver. Experiments on three exemplar testcases, diffusion, reaction-diffusion, and electromagnetic scattering models, show that a PEDS surrogate can be up to 3$\times$ more accurate than an ensemble of feedforward neural networks with limited data ($\approx 10^3$ training points), and reduces the training data need by at least a factor of 100 to achieve a target error of 5%. Experiments reveal that PEDS provides a general, data-driven strategy to bridge the gap between a vast array of simplified physical models with corresponding brute-force numerical solvers modeling complex systems, offering accuracy, speed, data efficiency, as well as physical insights into the process.

Implicit layer deep learning techniques, like Neural Differential Equations, have become an important modeling framework due to their ability to adapt to new problems automatically. Training a neural differential equation is effectively a search over a space of plausible dynamical systems. However, controlling the computational cost for these models is difficult since it relies on the number of steps the adaptive solver takes. Most prior works have used higher-order methods to reduce prediction timings while greatly increasing training time or reducing both training and prediction timings by relying on specific training algorithms, which are harder to use as a drop-in replacement due to strict requirements on automatic differentiation. In this manuscript, we use internal cost heuristics of adaptive differential equation solvers at stochastic time points to guide the training toward learning a dynamical system that is easier to integrate. We "close the black-box" and allow the use of our method with any adjoint technique for gradient calculations of the differential equation solution. We perform experimental studies to compare our method to global regularization to show that we attain similar performance numbers without compromising the flexibility of implementation on ordinary differential equations (ODEs) and stochastic differential equations (SDEs). We develop two sampling strategies to trade off between performance and training time. Our method reduces the number of function evaluations to 0.556-0.733x and accelerates predictions by 1.3-2x.

This study presents a systematic machine learning approach for creating efficient hybrid models and discovering sorption uptake models in non-linear advection-diffusion-sorption systems. It demonstrates an effective method to train these complex systems using gradient based optimizers, adjoint sensitivity analysis, and JIT-compiled vector Jacobian products, combined with spatial discretization and adaptive integrators. Sparse and symbolic regression were employed to identify missing functions in the artificial neural network. The robustness of the proposed method was tested on an in-silico data set of noisy breakthrough curve observations of fixed-bed adsorption, resulting in a well-fitted hybrid model. The study successfully reconstructed sorption uptake kinetics using sparse and symbolic regression, and accurately predicted breakthrough curves using identified polynomials, highlighting the potential of the proposed framework for discovering sorption kinetic law structures.

This paper provides a comprehensive tutorial for Bayesian practitioners in pharmacometrics using Pumas workflows. We start by giving a brief motivation of Bayesian inference for pharmacometrics highlighting limitations in existing software that Pumas addresses. We then follow by a description of all the steps of a standard Bayesian workflow for pharmacometrics using code snippets and examples. This includes: model definition, prior selection, sampling from the posterior, prior and posterior simulations and predictions, counter-factual simulations and predictions, convergence diagnostics, visual predictive checks, and finally model comparison with cross-validation. Finally, the background and intuition behind many advanced concepts in Bayesian statistics are explained in simple language. This includes many important ideas and precautions that users need to keep in mind when performing Bayesian analysis. Many of the algorithms, codes, and ideas presented in this paper are highly applicable to clinical research and statistical learning at large but we chose to focus our discussions on pharmacometrics in this paper to have a narrower scope in mind and given the nature of Pumas as a software primarily for pharmacometricians.

Automatic differentiation (AD), a technique for constructing new programs which compute the derivative of an original program, has become ubiquitous throughout scientific computing and deep learning due to the improved performance afforded by gradient-based optimization. However, AD systems have been restricted to the subset of programs that have a continuous dependence on parameters. Programs that have discrete stochastic behaviors governed by distribution parameters, such as flipping a coin with probability $p$ of being heads, pose a challenge to these systems because the connection between the result (heads vs tails) and the parameters ($p$) is fundamentally discrete. In this paper we develop a new reparameterization-based methodology that allows for generating programs whose expectation is the derivative of the expectation of the original program. We showcase how this method gives an unbiased and low-variance estimator which is as automated as traditional AD mechanisms. We demonstrate unbiased forward-mode AD of discrete-time Markov chains, agent-based models such as Conway's Game of Life, and unbiased reverse-mode AD of a particle filter. Our code package is available at https://github.com/gaurav-arya/StochasticAD.jl.

Time series modeling is a very common technique throughout many areas of machine learning. However, many standard recurrent models are known to be susceptible to problems such as the vanishing gradient [Pascanu et al., 2013] or the extreme sensitivity of chaotic systems to their parameterization [Wiggins et al., 2003]. To counter these issues reservoir computing (RC) techniques were introduced as recurrent models which can be trained without requiring gradient-based approaches [Lukoševičius and Jaeger, 2009]. Independently proposed as echo state networks (ESNs) [Jaeger, 2001] and liquid state machines (LSMs) [Maass et al., 2002], these architectures are based on the expansion of the input data using a fixed random internal layer, known as the reservoir, and the subsequent mapping of the reservoir to match an output.

DiffEqFlux.jl is a library for fusing neural networks and differential equations. In this work we describe differential equations from the viewpoint of data science and discuss the complementary nature between machine learning models and differential equations. We demonstrate the ability to incorporate DifferentialEquations.jl-defined differential equation problems into a Flux-defined neural network, and vice versa. The advantages of being able to use the entire DifferentialEquations.jl suite for this purpose is demonstrated by counter examples where simple integration strategies fail, but the sophisticated integration strategies provided by the DifferentialEquations.jl library succeed. This is followed by a demonstration of delay differential equations and stochastic differential equations inside of neural networks. We show high-level functionality for defining neural ordinary differential equations (neural networks embedded into the differential equation) and describe the extra models in the Flux model zoo which includes neural stochastic differential equations. We conclude by discussing the various adjoint methods used for backpropogation of the differential equation solvers. DiffEqFlux.jl is an important contribution to the area, as it allows the full weight of the differential equation solvers developed from decades of research in the scientific computing field to be readily applied to the challenges posed by machine learning and data science.