Propensity Straight-Through Gradients for Discrete Stochastic Systems

Continuous-time Markov chains (CTMCs) provide the backbone for modeling discrete stochastic dynamics across applied, physical, and biological sciences. Their integration with modern gradient-based machine learning, however, is limited by the hard categorical event selection intrinsic to Gillespie-type simulation algorithms. We exploit the affine state update to obtain the exact one-step conditional-mean sensitivity by differentiating normalized reaction propensities. We pair this backward rule with exact forward trajectories to define the propensity straight-through (PST) estimator. At the trajectory level, we show that one-step sensitivities composed across events can depart from the exact multistep sensitivity. We derive the resulting per-step discrepancy in closed form and prove that it vanishes identically for affine downstream dependence. PST matches the accuracy of Gumbel-Softmax straight-through across all benchmarks: reversible dimerization (0.06% error), a genetic oscillator (1.7% error), a 50-task repressilator suite (0.17% median error), and patch-clamp ion-channel recordings ($R^2$ = 0.988). Under matched settings, PST converges 3.0-fold faster on the oscillator and 2.1-fold faster on the ion channel. At deep-learning scale, PST trains a 203,796-parameter stochastic reaction network with hard sampling, reaching 98.22% MNIST digit classification accuracy. By differentiating an exact conditional mean rather than a relaxed sample, PST offers a temperature- and Gumbel-free path to scalable gradient-based learning through exact stochastic trajectories.

Data-driven Effective Modeling of Stochastic Chemical Reaction Networks

The Stochastic Simulation Algorithm (SSA), widely considered an exact algorithm for stochastic chemical reaction networks, suffers from high computational cost. In this work, we propose a data-driven effective model that operates on a user-defined coarse time step independent of the underlying microscopic reaction-event scale. This is accomplished by directly approximating the finite-time transition kernel of the continuous-time Markov chain induced by SSA, using a generative machine learning model trained on short bursts of SSA simulation data. The trained model constructs a stochastic propagator that recursively generates statistically consistent trajectories at the constant coarse time step, with significantly reduced computational cost. In this paper, we employ conditional normalizing flow as the stochastic propagator. A comprehensive set of numerical examples is presented to demonstrate the accuracy and efficiency of the proposed method.

Stochastic generator of trajectories from record data: application to the fluctuations of a glacier's frontal position from a sample of moraines

The record values theory study elements of a time series that exceed all previous observations, which are of particular interest in fields such as sports or climate science. In this paper, we propose a statistical method based on the construction of a Brownian stochastic simulator to reconstruct entire time series solely from such record values, even in a non-stationary case. We then implement a procedure, which can be compared to a Neural-Based Inference (NBI) procedure, to choose the optimal generator hyper parameters. To illustrate our method and motivate its development, we apply it to a glaciological problem. Understanding the past dynamics of glacier fronts is a major challenge to mitigate related mountain hazards, assess water resources, and evaluate contributions to sea-level rise. Field-visible indicators such as moraines provide spatio-temporal evidence of these front position evolution (refered as trajectories) and can be interpreted as the records of a non-stationary process. As a benchmark case, the two hyper parameters of our NBI approach are tuned from the well documented French alpine Glacier des Bossons. Our purely data-based approach offers new perspectives for challenging and further developing physical models of glacier dynamics and inferring the response of glaciers to climate change on centennial to millenial time scales. Beyond the glacier case, it has potential for the various problems for which record series is the sole available data.