Stochastic Dynamics

Chain-of-thought reasoning provides a structured computation between a model's input and final answer. Yet it is often evaluated through endpoint accuracy, which ignores the path taken to reach that answer. An emerging line of work addresses this limitation using entropy profiles, which track how uncertainty evolves over the reasoning process but do not reveal which competing hypotheses account for that uncertainty. We introduce answer-distribution trajectories, a stochastic-dynamics-inspired representation that tracks the model's full predictive distribution over answers as reasoning unfolds. As a strictly finer representation than endpoint and entropy summaries, answer-distribution trajectories enable us to characterize a trace through a dynamical reasoning profile spanning exploration, revision, motion, and commitment, and to distinguish different dynamical mechanisms of reasoning success and failure. Across sixteen open-weight language models and four reasoning benchmarks, we show that traces with the same endpoint and similar entropy profiles can exhibit substantially different reasoning dynamics. We further find substantial variation in these dynamics both within and across models and tasks, with different objectives favoring different dynamical profiles. Additionally, we show that training and inference choices systematically reshape these profiles. Our results suggest that answer-distribution trajectories provide a rich framework for analysing and evaluating the dynamics of LLM reasoning.

In this paper we derive a Probably Approximately Correct (PAC)-Bayesian error bound for partially observed linear time-invariant (LTI) stochastic dynamical systems in state-space form with inputs and sub-Gaussian noise. Such bounds are widespread in machine learning, and they are useful for characterizing the predictive power of models learned from finitely many data points. The bound derived in this paper relates the expectation of prediction errors with the prediction error generated by the model on the data used for learning. In addition, we show that it can also be used to derive bounds for the parameter estimation error. In turn, this allows us to provide finite-sample error bounds for the prediction error and parameter estimation error for a wide class of system identification algorithms. Furthermore, as LTI systems are a sub-class of recurrent neural networks (RNNs), these error bounds could be a first step towards PAC-Bayesian bounds for RNNs.

Major life events have proven difficult to predict. Does this reflect limits of theory, data, and algorithms, or the large role of chance? We examine one outcome - having a child within three years - through a near-ideal setting for prediction: a data challenge where 147 researchers predicted births for Dutch residents aged 18-45, using survey data and full-population registers. Methods ranged from logistic regression to a large language model and transformers. Predictions were moderately accurate (best F1: register 0.59, survey 0.76); advanced models did not outperform classical ones; and the larger registers did not beat the survey. Simulating the stochastic biology of conception and pregnancy, we estimated a predictive ceiling (survey F1 ~ 0.86-0.94, register 0.88-0.96). Observed performance falls short of this ceiling, implicating imperfect data, methods, and unmodelled chance, while the ceiling itself shows that chance in reproduction alone sets a non-trivial limit on predicting individual lives.

Persistence diagrams (PDs) provide stable and interpretable summaries of multiscale topological structure. While substantial progress has been made in the statistical analysis of PDs, existing literature often treats diagrams as static objects and provide limited frameworks for probabilistic modeling and stochastic evolution on PD space. We introduce a reinforcement learning framework for stochastic dynamics on PD space, where diagrams evolve through topology aware local edit operations. The dynamics define controlled Markov processes on spaces of finite PDs with variable cardinality. We establish conditions under which the induced Markov chains are irreducible, aperiodic, and geometrically ergodic, implying the existence of unique stationary probability laws on PD space. To guide the dynamics toward scientifically relevant topological targets, we formulate objectives that encompass distribution matching, task specific topological statistics, and structure-preserving compression. The resulting rewards balance task specific distributional targets, diagram fidelity, and complexity reduction, and yield a framework for adaptive topological simplification and probabilistic modeling. Experiments on synthetic and neuroimaging PDs demonstrate that the proposed framework can preserve dominant topological structure while reducing diagram complexity.

Unit excitation (UE) is a common assumption in stochastic saddle avoidance: the stochastic error must have a uniformly positive component along every direction, in expectation. This condition gives a direct way to rule out convergence to strict saddles, but it also oversimplifies the actual noise structure, and does not match many stochastic optimization regimes. In overparameterized or interpolation models, the noise may vanish near stationarity. In finite-sum problems, the stochastic gradient noise may lie in a low-dimensional, data-dependent subspace. In these (common) scenarios, UE is naturally not satisfied. In this paper, we prove an abstract almost sure avoidance theorem for stochastic recursions without UE. The theorem replaces UE-type requirements by verifiable pathwise conditions. In applications, these conditions follow, e.g., from local smoothness and finite-moment assumptions under standard i.i.d. sampling, or from the finite-sum structure under without-replacement sampling. Since the stochastically sampled maps generally do not share a fixed point, the celebrated center-stable manifold argument used in deterministic analyses is not directly applicable. Instead, we use a path-dependent change of variables together with a pathwise Lyapunov--Perron-based proof strategy. As applications, we obtain strict saddle avoidance for stochastic mirror descent (including SGD) and for random reshuffling. For nonsmooth composite objectives, we prove avoidance results for a proximal-type stochastic gradient method. Combining these insights with suitable iterate convergence guarantees, this allows establishing convergence to local minimizers of the original objective function.

Symmetry is central to modern machine learning and physics: invariances and equivariances improve sample efficiency, robustness, and out-of-distribution generalization, while symmetry principles guide scientific modeling. Yet for stochastic dynamical systems the relevant continuous symmetries are rarely known, and symmetry discovery for SDEs has remained essentially unexplored. We introduce \textit{LieStoNet}, an end-to-end, \emph{template-free} framework for discovering Lie-point symmetries of SDEs directly from spatiotemporal trajectories, without prespecifying symmetry groups, templates, or canonical coordinates. Building on the seminal SDE Lie-symmetry theory of Gaeta and Quintero (1999), which formalizes Lie-point SDE symmetries and their relation to Fokker-Planck symmetries, LieStoNet learns neural surrogates for drift and diffusion from increments, then learns projectable generators by enforcing the SDE determining equations, separately regularizing for closure under Lie brackets, adherence to the Lie algebra axioms (bilinearity, antisymmetry, Jacobi), and a non-redundant independent basis. The surrogate also defines an associated Fokker-Planck equation, enabling optional discovery of its Lie-point symmetries in parallel. Across multiple canonical SDEs with known analytic symmetries, LieStoNet recovers generators consistent with the ground-truth symmetry algebra, providing interpretable symmetry discovery for noisy dynamics. Code is available at \href{https://github.com/sumit-sinha-seas/LieStoNet_Final.git}{this link}.

Thermodynamic computing is an emerging hardware paradigm, in which stochastic physical dynamics serve as the direct computational primitive. The recent explosion of generative AI has only sharpened the search for alternative approaches to compute, and, as we show in this work, thermodynamic computing turns out to be well suited to this space. An important class of methods realises a function as the stationary expectation of an ergodic stochastic process: the answer is encoded in the time-averaged statistics of an equilibrating trajectory. To date, this equilibration-style class has been formulated exclusively through Langevin dynamics, restricting its implementations to analogue substrates and the engineering challenges those bring. In this work, we propose a substrate-independent formalisation of the equilibration-style formulation, in which the only object of design is the dynamical generator L* of an arbitrary ergodic process. The formalisation makes three hardware-level properties of the formulation explicit: the precision of a result is a knob set by how long the dynamics are run, sample averages decompose across independent trajectories, and dependent stages of a computation operate concurrently rather than serially, a property we call sequential parallelism. We instantiate the formalisation by fabricating a prototype digital thermodynamic computing chip, named CN101, that implements the formulation through discrete accumulator dynamics on standard CMOS using stochastic computing principles. We characterise CN101's success across conventional generative AI workloads in the form of VAEs and flow matching, applied to both image generation and scientific problems. Together, the formalisation and its digital instantiation show that the equilibration-style formulation is substrate-independent, and that its computational properties can be exploited on standard digital hardware.

A calibrated stochastic world model can reveal how uncertain a future is without revealing why it branches. The same conditional future law can arise because an observation aliases physical states or because dynamics remain random after the declared full state is fixed. We prove that ordinary transitions cannot identify these two sources, even for a perfect probabilistic predictor. ClosurePairs makes them identifiable by crossing compatible microstates with repeated exogenous disturbances and estimating state, noise, and state-noise interaction variance. The central consequence is operational: under finite hierarchical sampling, forecast difficulty governs the useful compute scale, while the alias/process composition provides complementary information about its direction-resolving the current state or sampling future randomness. ClosurePairs recovers source attribution at unchanged likelihood, reduces equal-budget decomposition error in a nonlinear interaction benchmark, and supports observation-only routing. On exact-marginal MetaWorld twins, an output-only allocator is at chance while a Closure-supervised probe on frozen JEPA-WM features routes 89.8-100%. In an independent ManiSkill PushCube confirmation, a stochastic RSSM's outputs and latents remain at chance, whereas an RGB-only Closure probe routes 100% under both ID and geometry/camera OOD over five seeds, matching direct allocation rather than exceeding it. Across five unseen allocation menus, the same Closure probe routes 92.5%/90.4% ID/OOD with no new oracle labels, versus 37.9%/32.9% for a frozen direct allocator. ClosurePairs is therefore an identifiable, reusable mechanism target that cannot be recovered from forecast quality alone.

Oversmoothing is a fundamental limitation of deep graph neural networks (GNNs), where repeated message passing causes node representations to become increasingly similar, eventually collapsing toward a low-dimensional subspace. This phenomenon limits the effective depth of message-passing architectures and motivates the search for mechanisms that preserve representation diversity. In this paper, we study a recurrent graph neural network in which independent Gaussian noise is injected after every propagation step and analyze the resulting architecture as a stochastic dynamical system. Under a standard global contraction assumption on the deterministic update, we prove that the hidden representations form a geometrically ergodic Markov chain admitting a unique invariant probability measure. Our main theoretical result establishes an explicit positive lower bound on the expected stationary Dirichlet energy, proportional to both the noise variance and the spectral gap of the underlying graph. Consequently, the stationary representations cannot collapse onto the constant manifold, providing a rigorous guarantee that asymptotic oversmoothing is prevented in the sense of non-vanishing Dirichlet energy. Our analysis reveals persistent stochastic perturbations as a fundamentally different mechanism for combating oversmoothing, complementing existing deterministic approaches based on residual connections, normalization, and graph rewiring. Finally, numerical experiments on both linear and nonlinear recurrent graph neural networks closely match the theoretical predictions, illustrating the emergence of a stationary distribution and the predicted dependence of the limiting Dirichlet energy on the noise intensity.

Image inpainting aims to recover missing regions while preserving structural consistency. We propose a non-parametric method without network training based on data-guided stochastic dynamics. Starting from a masked image, the missing pixels are evolved through a reverse-time stochastic differential equation with a kernel-weighted correction estimated directly from a reference dataset. This empirical correction guides the reconstruction toward high-density regions of the data distribution without training a neural network or fitting a parametric density model. Experiments on MNIST, Fashion-MNIST, and MVTec show that the proposed method outperforms Mean Fill, Telea, and Navier-Stokes inpainting in PSNR, SSIM, and visual quality. On CelebA, it remains competitive and produces plausible completions for structure-sensitive occlusions. These results demonstrate the effectiveness of empirical reference statistics as a non-parametric prior for image inpainting.

We consider the problem of learning from a single finite trajectory of an ergodic stochastic dynamical system. More precisely, we study discrete-time autonomous stochastic systems defining time-homogeneous Markov processes. We first focus on estimating the optimal one-step prediction function by nonlinear least squares, and derive high-probability guarantees measured with respect to the invariant measure of the process. These results make explicit how the non-independent and non-identically distributed nature of trajectory data modifies the classical statistical learning analysis. We then extend the framework to higher-order systems and finite-state spaces. Finally, we show that the same least squares and concentration arguments naturally extend to learning Koopman operators. Our approach combines tools from statistical learning theory and quantitative ergodic theory for Markov chains. It relies, in particular, on a concentration inequality for Hilbert-space-valued additive functionals of uniformly geometrically ergodic Markov chains.

Neural stochastic differential equations (SDEs) have emerged as powerful tools for learning noisy or stochastic dynamics directly from data; however, existing approaches largely assume uncoupled and continuous noise, limiting their applicability to realistic stochastic drivers, and often scale poorly in time, requiring expensive autoregressive training. To address these limitations, we propose Neural Kolmogorov Equations (NKEs), a deterministic, infinite-dimensional reformulation of Neural SDEs based on the Kolmogorov Forward equation, transforming the learning problem from modelling individual stochastic trajectories to modelling the evolution of probability densities. NKEs learn general Lévy-type stochastic forcing directly through the operator structure of the KFE, and enable parallel-in-time training via a Lagrangian Galerkin projection and operator splitting. We evaluate NKEs on several stochastic benchmarks, including systems with coupled noise and jump processes, and verify that NKEs provide flexible models that accurately recover deterministic and stochastic dynamics with competitive predictive accuracy and improved training efficiency. Code and pretrained models will be released.

Large-scale crowd management requires pedestrian simulations that are both computationally efficient and compatible with feedback-based control. However, most open-source tools are either microscopic or not designed for network-scale closed-loop evaluation. This paper presents PedNStream (Pedestrian Network Flow Simulation), an open-source, Python-native simulator for macroscopic pedestrian network loading based on the Link Transmission Model (LTM). The framework extends LTM-based pedestrian models by incorporating stochastic link dynamics that capture diffusion and activity-induced variability, and replaces dynamic user equilibrium route choice with a utility-based formulation suited to uncertain, intervention-driven settings. PedNStream is implemented as a modular framework with built-in controller interfaces for interventions such as gating, flow separation, and route guidance. We evaluate the framework in a staged manner. Synthetic scenarios verify key mechanisms, including queue formation, spillback, congestion dissipation, and adaptive rerouting. Real-network experiments assess large-scale behavior and consistency with observed pedestrian counts. A closed-loop case study demonstrates controller integration, and a runtime analysis quantifies scalability. These results establish PedNStream as an efficient and practical testbed for large-scale pedestrian network simulation and control.

Locating a vehicle and determining its orientation in an uncertain environment is a critical challenge in autonomous vehicle navigation and path planning. To address these challenges, a vehicle estimates its pose while depending on sensor data that offer noisy measurements. These uncertainties in pose quantities are expressed mathematically as a covariance matrix. The real-time computation of the covariance matrix is critical because of the non-linearity involved in the kinematic model. The challenge is thus to evaluate the evolution of the covariance matrix of a vehicle's discretized stochastic kinematics. The purpose of this study is to obtain a near-accurate evolution of the covariance matrix of the rear-wheel bicycle kinematic model under uncertainties in wheel displacement and steering angle. We used Taylor's series to linearize the nonlinear trigonometric functions and provided closed-form expectations of random variables with the required accuracy. Our analytical findings are in good agreement with those obtained from Monte-Carlo simulations. Our contribution is probably the first detailed closed-form presentation of the covariance matrix constituents of the vehicle under evaluation, which were previously reported either incorrectly or incompletely. These findings aid in identifying the potential and constraints of the discretized kinematic model as well as its stochastic analysis. The techniques presented here are useful for the simultaneous localization and odometry self-calibration of certain mobile robots and autonomous vehicles.

The adaptive moment estimation algorithm, known as Adam, is widely used in modern machine learning, owing to its low per-iteration complexity and strong empirical performance. Despite its prevalent use, the theoretical foundation of Adam remains largely unexplored for time-varying and nonstationary systems. In fact, the existing theoretical analyses of Adam-type algorithms are primarily concerned with time-invariant model parameters and explicitly or implicitly rely on independent and identically distributed (i.i.d.) data assumptions, under which the learning taskcan be formulated as minimizing a fixed expected objective with a static minimizer. However, such assumptions are often violated in time-varying and nonstationary systems, thereby calling for a theoretical investigation beyond the conventional yet idealized i.i.d. setting. The main objective of this paper is to solve this challenging problem by establishing a general theory of Adam for time-varying and nonstationary stochastic systems. We will introduce some new techniques for analyzing the products of nonstationary and dependent random matrices induced by Adam's coupled first- and second-moment recursions, and will construct a new stochastic Lyapunov function that blends these two moment dynamics. Under a stochastic excitation condition that allows nonstationary and dependent data, we will derive both parameter tracking and output prediction error bounds explicitly, quantifying the effects of stepsize, first- and second-momentum parameters, gradient noise and parameter drift. These bounds not only provide guarantees for Adam performance, but also provide guidelines for hyperparameter selection. Experiments on both synthetic and real-world data validate our theory and design guidelines.

Multivariate time series anomaly detection (MTSAD) is critical for a wide range of application areas, such as industrial monitoring, cybersecurity, or healthcare. Real-world data is often sparse, irregularly sampled or partially observed, yet existing methods assume uniformly sampled time series. We propose a generative approach based on Latent SDEs that projects the observed time series on a continuous-time stochastic dynamical system, directly being able to handle missing observations and irregular sampling, while also naturally capturing possible cyclic behavior that many real-world use cases inherently possess. Experiments on six anomaly benchmark datasets show that our proposed method ranks first among state-of-the-art baselines. We further demonstrate that our method remains robust under severe data sparsity, while performance significantly degrades for the tested baseline methods. These results highlight latent SDEs as a natural inductive bias for anomaly detection in multivariate time series, especially in presence of real-world irregularities.

We propose a rigorous and systematic mathematical framework for tracking the cognitive trajectories of a user, in the context of algorithmic sycophancy and AI-driven delusional spiraling. Using tools from dynamical systems theory and stochastic differential equations, we explore how individuals perceive, interpret, and update their beliefs as they interact with AI chatbots that possess hidden traits of sycophancy. We treat the evolving conviction as a continuous log-odds state variable, coupled into a stochastic differential equation, navigating a multi-valley potential energy landscape. Our analysis reveals several critical observations governing the stability and rigidity of belief dynamics. We demonstrate that the baseline prior perception of the individual is systematically enhanced by sycophantic feedback beyond a critical threshold. Here, the perceptual potential landscape undergoes a structural phase transition that severely deepens any incremental initial tilt present in the baseline state, transforming the landscape and giving rise to deep, highly resilient attractor basins that trap the individual in unshakeable, self-reinforcing, delusional convictions. Finally, we demonstrate that genuine external information can successfully challenge these rigid states. If this incoming evidence is strong and authentic enough to overcome the internal feedback barrier, it can correct the structural asymmetry caused by sycophancy, inducing a perception reversal that successfully restores the objective belief state.

Nanopores are versatile single-molecular sensors, but their utility is fundamentally constrained by stochastic translocation dynamics warping any encoded information. We resolve it by shifting from time-domain analysis to a learned latent-space mapping via a contrastive encoder trained exclusively on simulated signals from a physics-informed model. This encoder maps solid-state nanopore signals of engineered DNA barcodes into an interpretable molecular coordinate system. The learned representation is responsive to structural barcode parameters while remaining invariant to acquisition conditions and translocation conformation, allowing data pooling across devices. Molecule identification requires a single pass through the encoder, reducing computational cost by three orders of magnitude relative to alignment-based methods. We experimentally validate through mixture quantification, rare-variant detection, consensus barcode reconstruction, and real-time signal acquisition. This shift from temporal analysis to mapping structural coordinates into a latent space changes the paradigm behind analyzing stochastic sensor signals by linking classification to interpretable encoded molecular information.

We propose a spectral learning method for stochastic nonlinear dynamical systems represented with embedded latent transfer operators in deep feature spaces. We instantiate the method as Deep Spectral Encoder (DSE), an operator-based latent state-space model in which a time-invariant neural encoder implements learnable nonlinear feature maps from observations, and these features define Markovian latent states whose temporal evolution and observation mapping are described by the transfer and observation operators, respectively. Functional canonical correlation analysis in a learnable Galerkin-projected feature space provides state coordinates from past and future observations, and the two linear operators are estimated on the state coordinates as ridge-regularized closed-form solutions that coincide with Galerkin projections of the associated covariance operators. On this representation, we generalize sequential Bayesian filtering and Koopman spectral mode decomposition in feature space. Experiments on several scenarios show stable and superior performance with sequential Bayesian filtering and dynamic mode decomposition baselines even under noise and partial observability.

We introduce First-Order Trajectory Matching (FTM), a surrogate-modeling method that learns the first-order local transport of probability mass from trajectories of stochastic systems. By matching the symmetric first-order motion of trajectories, FTM learns the probability current velocity, whose flow preserves time marginals to match ensemble averages, while also capturing current-like trajectory quantities such as fluxes, circulations, and barrier-crossing currents. FTM learns the current velocity directly from trajectories, avoiding drift, diffusion, and score estimation. Our stability analysis separates discretization error from sampling variance and shows that the one-step simulation-free FTM loss is stable when temporal resolution and sample size are properly balanced. Across stochastic dynamical systems and PDE examples, we empirically demonstrate that FTM provides trajectory-aware ensemble predictions at low, deterministic-rollout cost.

The Fokker-Planck equation (FPE) plays a pivotal role in describing the time evolution of probability density functions (PDFs) for systems governed by stochastic dynamics. In this work, we propose a conditional normalizing flow-based physics-informed neural network (PINN) framework for efficiently approximating the solution operator of the FPE for a whole range of initial conditions. Leveraging the Chapman-Kolmogorov equation for Markovian stochastic processes, the problem is reformulated into approximating a transition PDF starting at initial time from a Dirac mass centered at an arbitrary point. The PDF of an associated linearized stochastic differential equation (SDE) is employed as the base distribution for the normalizing flow, providing a good approximation of the target PDF, especially for small times, and thereby avoiding the singularity of the map associated with the Dirac delta initial distribution. Furthermore, a time-weighted loss function is introduced to mitigate numerical instabilities arising at small times, achieving a balance between causality and training difficulty as time progresses. A variety of numerical experiments are presented to illustrate the effectiveness and robustness of the proposed method.

Multi-step time series forecasting (MSF) is commonly evaluated using point-wise error metrics such as mean squared error (MSE), implicitly treating the conditional mean as a sufficient target. We show that this can be misleading under conditional uncertainty, where the conditional expectation becomes unrepresentative of typical realized values at longer horizons. We formalize this effect through a conditional uncertainty gap and prove that whenever this gap is nonzero, no deterministic predictor can simultaneously minimize MSE and match the marginal distribution of realized futures. This establishes a fundamental, model-agnostic trade-off between point accuracy and marginal realism in MSF evaluation. Using controlled stochastic dynamical systems and nine real-world forecasting benchmarks, we empirically characterize the resulting accuracy--realism frontier and \textbf{quantify the practical cost of MSE-only model selection}. As conditional uncertainty increases with forecast horizon, the attainable set expands into a pronounced Pareto front, separating MSE-optimal but under-dispersed predictors from methods that trade accuracy for realistic marginal variability. \textbf{Across benchmarks, we find that small relaxations in MSE ($\boldsymbol{\le 5\%}$) frequently unlock disproportionate gains in marginal realism, with median improvements of $\mathbf{17.3\%}$ and gains exceeding $\mathbf{30\%}$ in some datasets.} We further show that common forecasting strategies systematically occupy different regions of this frontier: direct multi-output predictors concentrate near the accuracy-optimal extreme, while recursive strategies and sample-based inference favors marginal realism. Together, these results expose a structural failure mode of MSE-based evaluation in long-horizon forecasting and recast strategy and inference selection as navigation of an unavoidable accuracy--realism trade-off.

Many stochastic physical systems evolve smoothly over time in the sense that the distribution of states changes regularly across time steps. The transition from current state to the next state can often be modeled as the combination of a smooth map and an explicit source of randomness. Stochastic Lifting exploits this structure by attaching an independent, high-dimensional random label to each state transition in the training data and fitting a transition map from the current state and label to the next state using a standard regression loss. The labels act as auxiliary coordinates that let the model represent multiple plausible next states from similar current states, avoiding collapse to a mean prediction in the finite-sample size regime. At inference, fresh labels are sampled at each time step and the learned map is rolled forward autoregressively, generating diverse trajectories with a single network evaluation per time step.

Existing theory of momentum assumes that gradients arrive at every parameter at a roughly constant rate, an assumption violated in practice by heavy-tailed data distributions and modern architectures. We theoretically analyze the dynamics of two tractable models of momentum under sparse updates: a least squares model with sparse inputs and a logistic regression model with a rare class. Both admit exact closed-form second-moment dynamics whose high-dimensional limits we characterize across three scaling exponents for sparsity, batch size, and momentum decay. The phase structure on both problems is governed by the ratio of two intrinsic timescales: a momentum retention timescale (how many active updates the buffer survives) and a learning timescale (how many active updates it takes to reduce the squared error). When learning is much slower than retention, the limit matches SGD; when learning is faster, the system is unstable; where the timescales coincide, we recover classical heavy-ball dynamics. The oscillatory dynamics occur at different momentum values for different token sparsity, creating a spectral conflict for global momentum across token frequencies.

Stochastic Gradient Descent (SGD) is commonly modeled as a Langevin process, assuming that minibatch noise acts as Brownian motion. However, this approximation relies on a continuous-time limit and a sqrt(eta) noise scaling that does not match the discrete SGD update at finite learning rate. In this work, we propose an alternative formulation of SGD as deterministic dynamics in a fluctuating loss landscape induced by minibatch sampling. Starting directly from the discrete update, we derive a master equation for the parameter distribution and obtain a discrete Fokker--Planck equation that differs from the standard Langevin form at order eta^2. Using this framework, we analyze SGD dynamics near critical points of the loss. We show that the behavior decomposes along the eigenbasis of the mean Hessian into qualitatively distinct regimes. In particular, nearly-flat directions do not admit a stationary distribution: the variance grows over time, corresponding to effective diffusion along valleys with a coefficient proportional to the learning rate. We provide empirical evidence supporting these predictions on neural network models in computer vision and natural language processing, observing a clear qualitative separation between confined and diffusive modes.

Turbulent dynamical systems are characterized by nonlinear interactions and stochastic effects that generate coupled statistical quantities, such as non-zero higher-order moments, which are difficult to capture from data with accuracy. We propose a two-stage data-driven modeling framework that combines symbolic regression with generative models to jointly identify the governing dynamics and predict their key statistical quantities. In Stage I of the framework, the Finite Expression Method (FEX) is adopted to discover closed-form expressions of the deterministic dynamics, recovering nonlinear interaction terms and external forcing without predefined libraries. In Stage II, generative models are introduced to learn the residual stochastic components as a refined correction to the model error from the Stage I approximation, enabling accurate characterization of higher-order statistics. Theoretical analysis establishes the consistency of the symbolic estimator and quantifies the estimation error in terms of data size and numerical discretization. The model performance is verified through detailed numerical experiments on the stochastic triad models across multiple regimes, demonstrating that the framework successfully recovers interaction terms and forcing expressions, and accurately predicts statistical moments up to order five. These results highlight the potential of integrating interpretable symbolic discovery with data-driven stochastic modeling for complex turbulent systems.

Many systems in physics, engineering, and biology exhibit multiscale stochastic dynamics, where low-dimensional slow variables evolve under the influence of high-dimensional fast processes. In practice, observations are often limited to a single trajectory of the slow component, while the fast dynamics remain unobserved, making statistical learning challenging. Approaches based on partial differential equations (PDE), such as Fokker-Planck formulations, aim to characterize the evolution of probability densities, typically requiring dense space-time data or grid-based solvers. In contrast, we adopt a trajectory-based perspective and develop a data-driven framework for learning effective stochastic dynamics from a single observed path. We model the dynamics by coupled multiscale stochastic differential equations (SDEs) and first obtain a principled model reduction through stochastic averaging. Unlike generic model reduction techniques such as PCA, this respects the dynamical structure of the original system and explicitly incorporates the interaction between slow and fast scales. A central challenge, however, is that the reduced model depends on the invariant distribution of the fast process, which is a solution to an intractable and often unknown PDE. We introduce a novel learning framework that parameterizes the invariant distribution using normalizing flows, enabling expressive density modeling in the latent fast-variable space. The flow is trained end-to-end by optimizing a penalized likelihood objective induced by the reduced stochastic dynamics. Furthermore, we develop a Bayesian variational inference procedure for uncertainty quantification, employing a second normalizing flow to approximate the posterior distribution over model parameters. This yields a scalable approach to capturing epistemic uncertainty in multiscale systems.

Modern generative modeling is dominated by transport from a noise prior to data. We propose an alternative paradigm in which generation is performed by a discrete stochastic dynamics that leaves the data distribution invariant, initialized from data-supported states rather than from noise. The framework can utilize any pretrained flow model. We develop two probability-preserving sampling mechanisms, a corrected Langevin dynamics with a Metropolis adjustment and a predictor-corrector flow, that operate directly on existing checkpoints. We validate the framework on a synthetic Swiss-roll target, ImageNet-256 and Oxford Flowers-102, where our samplers consistently improve over the original generation procedures.

We survey continuous-time generative modeling methods based on transporting a simple reference distribution to a data distribution via stochastic or deterministic dynamics. We present a unified framework in which diffusion models, score-based generative models, and flow matching are instances of learning a time-dependent vector field that induces a family of marginals $(ρ_t)_{t \in [0,1]}$ governed by continuity and Fokker-Planck equations. Such a unified theory is timely because these methods are converging methodologically, yet fragmented notation and competing derivations continue to obscure their shared structure and the practical tradeoffs governing sampling, stability, and computation. Within this framework, we (i) derive reverse-time sampling for diffusion and score-based models as controlled stochastic dynamics, (ii) show that the probability flow ODE yields identical marginals and connects diffusion to likelihood-based normalizing flows, and (iii) interpret flow matching as direct regression of the velocity field under a chosen interpolation, clarifying when it coincides with or differs from score-based training. We compare objectives, sampling schemes, and discretization errors under unified notation, discuss connections to Schrodinger bridges and entropic optimal transport, and summarize theoretical guarantees and open problems on approximation, stability, and scalability.

Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apoptosis. Existing unbalanced Optimal Transport (OT) methods treat mass as a continuous fluid, performing inference at the population level. However, this macroscopic view often fails to capture the discrete, jump-like nature of birth-death events at single-cell resolution, which is essential for understanding lineage branching and fate decisions. We present Unbalanced Schrödinger Bridge (USB), a simulation-free framework for learning underlying dynamics that effectively integrates both stochastic and unbalanced effects which also models the discrete, jump-like birth-death dynamics at single-cell resolution. Theoretically, USB provides a tractable solution to the Branching Schrödinger Bridge (BSB) problem, offering a rigorous microscopic interpretation where individual cells undergo both Brownian motion and discrete birth-death jumps. Technically, the method implements an efficient solver by introducing a simulation-free training objective that effectively scales to high-dimensional omics data. Empirically, we demonstrate on both simulated and real-world datasets that USB not only achieves trajectory reconstruction performance better than or comparable to deterministic baselines but also uniquely enables realistic discrete simulation of birth-death dynamics at single-cell resolution.

Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although single-cell RNA sequencing provides quantitative snapshots of the transcriptome, current methods for inferring gene-regulatory dynamics often lack mechanistic interpretability and fail to generalize to unseen conditions. Here we introduce Probability Flow Matching (PFM), a scalable framework for learning biophysically consistent stochastic processes directly from time-resolved single-cell measurements. Applying PFM to three hematopoiesis datasets, we show that models with similar interpolation accuracy can encode fundamentally different dynamics, with only biophysically consistent formulations accurately capturing mechanisms of lineage transitions, fate specification, and gene perturbation responses. We further demonstrate that PFM accommodates unbalanced populations, enabling simultaneous inference of cellular proliferation and death dynamics. Together, these results establish PFM as a flexible, scalable framework for integrating mechanistic modeling with single-cell omics.

Safety of stochastic dynamic systems in environments with dynamic obstacles is studied in this paper through the lens of stochastic barrier functions. We introduce both time-invariant and time-varying barrier certificates for discrete-time, continuous-space systems subject to uncertainty, which provide certified lower bounds on the probability of remaining within a safe set over a finite horizon. These certificates explicitly account for time-varying unsafe regions induced by obstacle dynamics. By leveraging Bellman's optimality perspective, the time-varying formulation directly captures temporal structure and yields less conservative bounds than state-of-the-art approaches. By restricting certificates to polynomial functions, we show that time-varying barrier synthesis can be formulated as a convex sum-of-squares program, enabling tractable optimization. Empirical evaluations on nonlinear systems with dynamic obstacles show that time-varying certificates consistently achieve tight guarantees, demonstrating improved accuracy and scalability over state-of-the-art methods.

Stochastic dynamical systems with slow or metastable behavior evolve, on long time scales, on an unknown low-dimensional manifold in high-dimensional ambient space. Building a reduced simulator from short-burst ambient ensembles is a long-standing problem: local-chart methods like ATLAS suffer from exponential landmark scaling and per-step reprojection, while autoencoder alternatives leave tangent-bundle geometry poorly constrained, and the errors propagate into the learned drift and diffusion. We observe that the ambient covariance~$Λ$ already encodes coordinate-invariant tangent-space information, its range spanning the tangent bundle. Using this, we construct a tangent-bundle penalty and an inverse-consistency penalty for a three-stage pipeline (chart learning, latent drift, latent diffusion) that learns a single nonlinear chart and the latent SDE. The penalties induce a function-space metric, the $ρ$-metric, strictly weaker than the Sobolev $H^1$ norm yet achieving the same chart-quality generalization rate up to logarithmic factors. For the drift, we derive an encoder-pullback target via Itô's formula on the learned encoder and prove a bias decomposition showing the standard decoder-side formula carries systematic error for any imperfect chart. Under a $W^{2,\infty}$ chart-convergence assumption, chart-level error propagates controllably to weak convergence of the ambient dynamics and to convergence of radial mean first-passage times. Experiments on four surfaces embedded in up to $201$ ambient dimensions reduce radial MFPT error by $50$--$70\%$ under rotation dynamics and achieve the lowest inter-well MFPT error on most surface--transition pairs under metastable Müller--Brown Langevin dynamics, while reducing end-to-end ambient coefficient errors by up to an order of magnitude relative to an unregularized autoencoder.

We consider the problem of learning the parameters of a $N$-dimensional stochastic linear dynamics under both full and partial observations from a single trajectory of time $T$. We introduce and analyze a new estimator that achieves a small maximum element-wise error on the recovery of symmetric dynamic matrices using only $T=\mathcal{O}(\log N)$ observations, irrespective of whether the matrix is sparse or dense. This estimator is based on the method of moments and does not rely on problem-specific regularization. This is especially important for applications such as structure discovery.

Modeling dynamical systems and unraveling their underlying structural dependencies is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and stochastic in nature, and admit only partial, noisy state measurements. Our primary motivating setting is single-cell biology, where destructive measurements yield unpaired population snapshots rather than longitudinal trajectories of the same cells. This poses a significant challenge for addressing the problems of modeling the underlying dynamics and inferring the network structure of these systems. Existing methods are typically tailored either for structure learning or modeling dynamics at the population level, but are limited in their ability to address both problems together. In this work, we address both problems simultaneously: we present StructureFlow, a novel and principled simulation-free training approach for jointly learning the structure and stochastic population dynamics of physical systems. We showcase the utility of StructureFlow for the tasks of structure learning from interventions and dynamical (trajectory) inference of conditional population dynamics. We empirically evaluate our approach on high-dimensional synthetic systems, a set of biologically plausible simulated systems, and an experimental single-cell dataset. We show that StructureFlow can learn the structure of underlying systems while simultaneously modeling their conditional population dynamics --- a key step toward model-based mechanistic understanding of systems behavior.

The Schrödinger bridge problem is concerned with finding a stochastic dynamical system bridging two marginal distributions that minimises a certain transportation cost. This problem, which represents a generalisation of optimal transport to the stochastic case, has received attention due to its connections to diffusion models and flow matching, as well as its applications in the natural sciences. However, all existing algorithms allow to infer such dynamics only for cases where samples from both distributions are available. In this paper, we propose the first general method for modelling Schrödinger bridges when one (or both) distributions are given by their unnormalised densities, with no access to data samples. Our algorithm relies on a generalisation of the iterative proportional fitting (IPF) procedure to the data-free case, inspired by recent developments in off-policy reinforcement learning for training of diffusion samplers. We demonstrate the efficacy of the proposed data-to-energy IPF on synthetic problems, finding that it can successfully learn transports between multimodal distributions. As a secondary consequence of our reinforcement learning formulation, which assumes a fixed time discretisation scheme for the dynamics, we find that existing data-to-data Schrödinger bridge algorithms can be substantially improved by learning the diffusion coefficient of the dynamics. Finally, we apply the newly developed algorithm to the problem of sampling posterior distributions in latent spaces of generative models, thus creating a data-free image-to-image translation method. Code: https://github.com/mmacosha/d2e-stochastic-dynamics

We introduce Robust Filter Attention (RFA), a formulation of self-attention as a robust state estimator. Each token is treated as a noisy observation of a latent trajectory governed by a linear stochastic differential equation (SDE), and attention weights are determined by consistency under this model rather than static feature similarity. Under isotropic noise and decay assumptions, RFA matches the computational complexity of standard attention. On language modeling benchmarks, RFA achieves lower perplexity than RoPE within the training window while remaining stable under zero-shot extrapolation to longer contexts. The framework also provides a dynamical interpretation of standard positional mechanisms, connecting rotational embeddings and recency biases to transport and uncertainty propagation induced by stochastic dynamics.

This paper develops a model-based framework for continuous-time policy evaluation (CTPE) in reinforcement learning, incorporating both Brownian and Lévy noise to model stochastic dynamics influenced by rare and extreme events. Our approach formulates the policy evaluation problem as solving a partial integro-differential equation (PIDE) for the value function with unknown coefficients. A key challenge in this setting is accurately recovering the unknown coefficients in the stochastic dynamics, particularly when driven by Lévy processes with heavy tail effects. To address this, we propose a robust numerical approach that effectively handles both unbiased and censored trajectory datasets. This method combines maximum likelihood estimation with an iterative tail correction mechanism, improving the stability and accuracy of coefficient recovery. Additionally, we establish a theoretical bound for the policy evaluation error based on coefficient recovery error. Through numerical experiments, including a real-data BTC price experiment, we demonstrate the effectiveness and robustness of our method in recovering heavy-tailed Lévy dynamics and verify the theoretical error analysis in policy evaluation.

Physically motivated stochastic dynamics are widely used to sample from high-dimensional distributions. However, such samplers often get trapped in metastable states, approximately sampling from a distribution that differs significantly from the desired stationary state. We rigorously show that for multivariable discrete distributions, the true stationary model can nevertheless be recovered from these metastable samples. This relies on a fundamental observation: for distributions satisfying a strong metastability condition, their single-variable conditional probabilities are on average extremely close to those of the true stationary distribution. This remains true even when the two distributions are far apart under global metrics such as Kullback-Leibler divergence. Consequently, we can effectively learn the true model using a conditional-likelihood estimator even when the samples are drawn from a restricted state space. Extending these general results to Ising models, we prove rigorous parameter and structure learning guarantees. Finally, we demonstrate this phenomenon numerically on higher-alphabet spin glass models.

We study formal policy synthesis for continuous-state stochastic systems under linear temporal logic specifications. The product of the system with the automaton of the specification has a hybrid state space with sparse rewards. We introduce a generalized optimal backup order, defined in reverse to a topological order over automaton states, that guides value backups and provably preserves optimality. We further present a model-free actor-critic algorithm whose policy evaluation solves a constrained optimization problem by the augmented Lagrangian method, yielding hyperparameter self-tuning, and prove its optimality and convergence in the tabular case. Since integer encodings of automaton states impose a spurious ordinal relationship on functions learned by one network, we dedicate a value and a policy network to each automaton state (modular learning). The algorithm matches or outperforms PPO, DQN, and A2C on CartPole, and on a Dubins car under a temporal specification the topological order and modular learning raise the success rate from 26.0% to 71.5%.