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Jun 12

Causal Longitudinal Prior-Fitted Networks for Counterfactual Outcome Prediction

Longitudinal treatment decisions require predicting potential outcomes under future treatment sequences in the presence of time-varying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically train a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted in-context predictor for longitudinal causal prediction. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CausalLongPFN is frozen: it conditions on support trajectories, a query history, and a proposed future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CausalLongPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a useful frozen alternative when repeated domain-specific training is costly or impractical.

  • 5 authors
·
Jun 3

DyMixOp: Guiding Neural Operator Design for PDEs from a Complex Dynamics Perspective with Local-Global-Mixing

A primary challenge in using neural networks to approximate nonlinear dynamical systems governed by partial differential equations (PDEs) is transforming these systems into a suitable format, especially when dealing with non-linearizable dynamics or the need for infinite-dimensional spaces for linearization. This paper introduces DyMixOp, a novel neural operator framework for PDEs that integrates insights from complex dynamical systems to address this challenge. Grounded in inertial manifold theory, DyMixOp transforms infinite-dimensional nonlinear PDE dynamics into a finite-dimensional latent space, establishing a structured foundation that maintains essential nonlinear interactions and enhances physical interpretability. A key innovation is the Local-Global-Mixing (LGM) transformation, inspired by convection dynamics in turbulence. This transformation effectively captures both fine-scale details and nonlinear interactions, while mitigating spectral bias commonly found in existing neural operators. The framework is further strengthened by a dynamics-informed architecture that connects multiple LGM layers to approximate linear and nonlinear dynamics, reflecting the temporal evolution of dynamical systems. Experimental results across diverse PDE benchmarks demonstrate that DyMixOp achieves state-of-the-art performance, significantly reducing prediction errors, particularly in convection-dominated scenarios reaching up to 86.7\%, while maintaining computational efficiency and scalability.

  • 3 authors
·
Aug 18, 2025

Physics-guided Deep Markov Models for Learning Nonlinear Dynamical Systems with Uncertainty

In this paper, we propose a probabilistic physics-guided framework, termed Physics-guided Deep Markov Model (PgDMM). The framework targets the inference of the characteristics and latent structure of nonlinear dynamical systems from measurement data, where exact inference of latent variables is typically intractable. A recently surfaced option pertains to leveraging variational inference to perform approximate inference. In such a scheme, transition and emission functions of the system are parameterized via feed-forward neural networks (deep generative models). However, due to the generalized and highly versatile formulation of neural network functions, the learned latent space often lacks physical interpretation and structured representation. To address this, we bridge physics-based state space models with Deep Markov Models, thus delivering a hybrid modeling framework for unsupervised learning and identification of nonlinear dynamical systems. The proposed framework takes advantage of the expressive power of deep learning, while retaining the driving physics of the dynamical system by imposing physics-driven restrictions on the side of the latent space. We demonstrate the benefits of such a fusion in terms of achieving improved performance on illustrative simulation examples and experimental case studies of nonlinear systems. Our results indicate that the physics-based models involved in the employed transition and emission functions essentially enforce a more structured and physically interpretable latent space, which is essential for enhancing and generalizing the predictive capabilities of deep learning-based models.

  • 4 authors
·
Oct 16, 2021

simple-idealized-1d-nlse: Pseudo-Spectral Solver for the 1D Nonlinear Schrödinger Equation

We present an open-source Python implementation of an idealized high-order pseudo-spectral solver for the one-dimensional nonlinear Schr\"odinger equation (NLSE). The solver combines Fourier spectral spatial discretization with an adaptive eighth-order Dormand-Prince time integration scheme to achieve machine-precision conservation of mass and near-perfect preservation of momentum and energy for smooth solutions. The implementation accurately reproduces fundamental NLSE phenomena including soliton collisions with analytically predicted phase shifts, Akhmediev breather dynamics, and the development of modulation instability from noisy initial conditions. Four canonical test cases validate the numerical scheme: single soliton propagation, two-soliton elastic collision, breather evolution, and noise-seeded modulation instability. The solver employs a 2/3 dealiasing rule with exponential filtering to prevent aliasing errors from the cubic nonlinearity. Statistical analysis using Shannon, R\'enyi, and Tsallis entropies quantifies the spatio-temporal complexity of solutions, while phase space representations reveal the underlying coherence structure. The implementation prioritizes code transparency and educational accessibility over computational performance, providing a valuable pedagogical tool for exploring nonlinear wave dynamics. Complete source code, documentation, and example configurations are freely available, enabling reproducible computational experiments across diverse physical contexts where the NLSE governs wave evolution, including nonlinear optics, Bose-Einstein condensates, and ocean surface waves.

  • 5 authors
·
Sep 6, 2025

Demystifying the Token Dynamics of Deep Selective State Space Models

Selective state space models (SSM), such as Mamba, have gained prominence for their effectiveness in modeling sequential data. Despite their outstanding empirical performance, a comprehensive theoretical understanding of deep selective SSM remains elusive, hindering their further development and adoption for applications that need high fidelity. In this paper, we investigate the dynamical properties of tokens in a pre-trained Mamba model. In particular, we derive the dynamical system governing the continuous-time limit of the Mamba model and characterize the asymptotic behavior of its solutions. In the one-dimensional case, we prove that only one of the following two scenarios happens: either all tokens converge to zero, or all tokens diverge to infinity. We provide criteria based on model parameters to determine when each scenario occurs. For the convergent scenario, we empirically verify that this scenario negatively impacts the model's performance. For the divergent scenario, we prove that different tokens will diverge to infinity at different rates, thereby contributing unequally to the updates during model training. Based on these investigations, we propose two refinements for the model: excluding the convergent scenario and reordering tokens based on their importance scores, both aimed at improving practical performance. Our experimental results validate these refinements, offering insights into enhancing Mamba's effectiveness in real-world applications.

  • 4 authors
·
Oct 4, 2024

Leslie Population Models in Predator-prey and Competitive populations: theory and applications by machine learning

We introduce a new predator-prey model by replacing the growth and predation constant by a square matrix, and the population density as a population vector. The classical Lotka-Volterra model describes a population that either modulates or converges. Stability analysis of such models have been extensively studied by the works of Merdan (https://doi.org/10.1016/j.chaos.2007.06.062). The new model adds complexity by introducing an age group structure where the population of each age group evolves as prescribed by the Leslie matrix. The added complexity changes the behavior of the model such that the population either displays roughly an exponential growth or decay. We first provide an exact equation that describes a time evolution and use analytic techniques to obtain an approximate growth factor. We also discuss the variants of the Leslie model, i.e., the complex value predator-prey model and the competitive model. We then prove the Last Species Standing theorem that determines the dominant population in the large time limit. The recursive structure of the model denies the application of simple regression. We discuss a machine learning scheme that allows an admissible fit for the population evolution of Paramecium Aurelia and Paramecium Caudatum. Another potential avenue to simplify the computation is to use the machinery of quantum operators. We demonstrate the potential of this approach by computing the Hamiltonian of a simple Leslie system.

  • 5 authors
·
Dec 20, 2024

Respecting causality is all you need for training physics-informed neural networks

While the popularity of physics-informed neural networks (PINNs) is steadily rising, to this date PINNs have not been successful in simulating dynamical systems whose solution exhibits multi-scale, chaotic or turbulent behavior. In this work we attribute this shortcoming to the inability of existing PINNs formulations to respect the spatio-temporal causal structure that is inherent to the evolution of physical systems. We argue that this is a fundamental limitation and a key source of error that can ultimately steer PINN models to converge towards erroneous solutions. We address this pathology by proposing a simple re-formulation of PINNs loss functions that can explicitly account for physical causality during model training. We demonstrate that this simple modification alone is enough to introduce significant accuracy improvements, as well as a practical quantitative mechanism for assessing the convergence of a PINNs model. We provide state-of-the-art numerical results across a series of benchmarks for which existing PINNs formulations fail, including the chaotic Lorenz system, the Kuramoto-Sivashinsky equation in the chaotic regime, and the Navier-Stokes equations in the turbulent regime. To the best of our knowledge, this is the first time that PINNs have been successful in simulating such systems, introducing new opportunities for their applicability to problems of industrial complexity.

  • 3 authors
·
Mar 14, 2022

Learning Semilinear Neural Operators : A Unified Recursive Framework For Prediction And Data Assimilation

Recent advances in the theory of Neural Operators (NOs) have enabled fast and accurate computation of the solutions to complex systems described by partial differential equations (PDEs). Despite their great success, current NO-based solutions face important challenges when dealing with spatio-temporal PDEs over long time scales. Specifically, the current theory of NOs does not present a systematic framework to perform data assimilation and efficiently correct the evolution of PDE solutions over time based on sparsely sampled noisy measurements. In this paper, we propose a learning-based state-space approach to compute the solution operators to infinite-dimensional semilinear PDEs. Exploiting the structure of semilinear PDEs and the theory of nonlinear observers in function spaces, we develop a flexible recursive method that allows for both prediction and data assimilation by combining prediction and correction operations. The proposed framework is capable of producing fast and accurate predictions over long time horizons, dealing with irregularly sampled noisy measurements to correct the solution, and benefits from the decoupling between the spatial and temporal dynamics of this class of PDEs. We show through experiments on the Kuramoto-Sivashinsky, Navier-Stokes and Korteweg-de Vries equations that the proposed model is robust to noise and can leverage arbitrary amounts of measurements to correct its prediction over a long time horizon with little computational overhead.

  • 4 authors
·
Feb 23, 2024

Almost-Linear RNNs Yield Highly Interpretable Symbolic Codes in Dynamical Systems Reconstruction

Dynamical systems (DS) theory is fundamental for many areas of science and engineering. It can provide deep insights into the behavior of systems evolving in time, as typically described by differential or recursive equations. A common approach to facilitate mathematical tractability and interpretability of DS models involves decomposing nonlinear DS into multiple linear DS separated by switching manifolds, i.e. piecewise linear (PWL) systems. PWL models are popular in engineering and a frequent choice in mathematics for analyzing the topological properties of DS. However, hand-crafting such models is tedious and only possible for very low-dimensional scenarios, while inferring them from data usually gives rise to unnecessarily complex representations with very many linear subregions. Here we introduce Almost-Linear Recurrent Neural Networks (AL-RNNs) which automatically and robustly produce most parsimonious PWL representations of DS from time series data, using as few PWL nonlinearities as possible. AL-RNNs can be efficiently trained with any SOTA algorithm for dynamical systems reconstruction (DSR), and naturally give rise to a symbolic encoding of the underlying DS that provably preserves important topological properties. We show that for the Lorenz and R\"ossler systems, AL-RNNs discover, in a purely data-driven way, the known topologically minimal PWL representations of the corresponding chaotic attractors. We further illustrate on two challenging empirical datasets that interpretable symbolic encodings of the dynamics can be achieved, tremendously facilitating mathematical and computational analysis of the underlying systems.

  • 4 authors
·
Oct 18, 2024

A Topological and Operator Algebraic Framework for Asynchronous Lattice Dynamical Systems

I introduce a novel mathematical framework integrating topological dynamics, operator algebras, and ergodic geometry to study lattices of asynchronous metric dynamical systems. Each node in the lattice carries an internal flow represented by a one-parameter family of operators, evolving on its own time scale. I formalize stratified state spaces capturing multiple levels of synchronized behavior, define an asynchronous evolution metric that quantifies phase-offset distances between subsystems, and characterize emergent coherent topologies arising when subsystems synchronize. Within this framework, I develop formal operators for the evolution of each subsystem and give precise conditions under which phase-aligned synchronization occurs across the lattice. The main results include: (1) the existence and uniqueness of coherent (synchronized) states under a contractive coupling condition, (2) stability of these coherent states and criteria for their emergence as a collective phase transition in a continuous operator topology, and (3) the influence of symmetries, with group-invariant coupling leading to flow-invariant synchrony subspaces and structured cluster dynamics. Proofs are given for each theorem, demonstrating full mathematical rigor. In a final section, I discuss hypothetical applications of this framework to symbolic lattice systems (e.g. subshifts), to invariant group actions on dynamical lattices, and to operator fields over stratified manifolds in the spirit of noncommutative geometry. Throughout, I write in the first person to emphasize the exploratory nature of this work. The paper avoids any reference to cosmology or observers, focusing instead on clean, formal mathematics suitable for a broad array of dynamical systems.

  • 1 authors
·
May 14, 2025

Autoregressive Transformer Neural Network for Simulating Open Quantum Systems via a Probabilistic Formulation

The theory of open quantum systems lays the foundations for a substantial part of modern research in quantum science and engineering. Rooted in the dimensionality of their extended Hilbert spaces, the high computational complexity of simulating open quantum systems calls for the development of strategies to approximate their dynamics. In this paper, we present an approach for tackling open quantum system dynamics. Using an exact probabilistic formulation of quantum physics based on positive operator-valued measure (POVM), we compactly represent quantum states with autoregressive transformer neural networks; such networks bring significant algorithmic flexibility due to efficient exact sampling and tractable density. We further introduce the concept of String States to partially restore the symmetry of the autoregressive transformer neural network and improve the description of local correlations. Efficient algorithms have been developed to simulate the dynamics of the Liouvillian superoperator using a forward-backward trapezoid method and find the steady state via a variational formulation. Our approach is benchmarked on prototypical one and two-dimensional systems, finding results which closely track the exact solution and achieve higher accuracy than alternative approaches based on using Markov chain Monte Carlo to sample restricted Boltzmann machines. Our work provides general methods for understanding quantum dynamics in various contexts, as well as techniques for solving high-dimensional probabilistic differential equations in classical setups.

  • 4 authors
·
Sep 11, 2020

ABC: Any-Subset Autoregression via Non-Markovian Diffusion Bridges in Continuous Time and Space

Generating continuous-time, continuous-space stochastic processes (e.g., videos, weather forecasts) conditioned on partial observations (e.g., first and last frames) is a fundamental challenge. Existing approaches, (e.g., diffusion models), suffer from key limitations: (1) noise-to-data evolution fails to capture structural similarity between states close in physical time and has unstable integration in low-step regimes; (2) random noise injected is insensitive to the physical process's time elapsed, resulting in incorrect dynamics; (3) they overlook conditioning on arbitrary subsets of states (e.g., irregularly sampled timesteps, future observations). We propose ABC: Any-Subset Autoregressive Models via Non-Markovian Diffusion Bridges in Continuous Time and Space. Crucially, we model the process with one continual SDE whose time variable and intermediate states track the real time and process states. This has provable advantages: (1) the starting point for generating future states is the already-close previous state, rather than uninformative noise; (2) random noise injection scales with physical time elapsed, encouraging physically plausible dynamics with similar time-adjacent states. We derive SDE dynamics via changes-of-measure on path space, yielding another advantage: (3) path-dependent conditioning on arbitrary subsets of the state history and/or future. To learn these dynamics, we derive a path- and time-dependent extension of denoising score matching. Our experiments show ABC's superiority to competing methods on multiple domains, including video generation and weather forecasting.

  • 6 authors
·
May 4

Linear equivalence of nonlinear recurrent neural networks

Large nonlinear recurrent neural networks with random couplings generate high-dimensional, potentially chaotic activity whose structure is of interest in neuroscience and other fields. A fundamental object encoding the collective structure of this activity is the N times N covariance matrix. Prior analytical work on the covariance matrix has been limited to low-dimensional summary statistics. Recent work proposed an ansatz in which, at large N, the covariance matrix for a typical quenched realization takes the same form as that of a linear network with the same couplings, driven by independent noise, with DMFT order parameters setting the transfer function and the noise spectrum. Here, we derive this ansatz using the two-site cavity method, providing two derivations with complementary perspectives. The first decomposes each unit's activity into a linear response to its local field and a nonlinear residual, and shows that cross-covariances between residuals at distinct sites are strongly suppressed, so the residuals act as independent noise driving a linear network. The second derives a self-consistent matrix equation for the covariance matrix. A naive Gaussian closure for the joint statistics of local fields at distinct sites misses cross terms that, in a linear network, would be generated by an external drive. The cavity method recovers these terms from non-Gaussian contributions, revealing an emergent external drive. Higher-order cross-site moments follow a Wick-like decomposition into products of pairwise covariances at leading order, reducing them to the linear-equivalent form. We verify the predictions in simulations. These results extend linear equivalence from feedforward high-dimensional nonlinear systems, where the activations are independent of the weights, to recurrent networks, where the activations are correlated with the couplings that generate them.

  • 1 authors
·
May 4

Information Theory and Statistical Mechanics Revisited

The statistical mechanics of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. In this paper, we follow the path set out by Jaynes, including elements added subsequently to that original work, to explore the consequences of the purely statistical point of view. We show how standard methods in the equilibrium theory could have been derived simply from a description of the available problem information. In addition, our presentation leads to novel insights into questions associated with symmetry and non-equilibrium statistical mechanics. Two surprising consequences to be explored in further work are that (in)distinguishability factors are automatically predicted from the problem formulation and that a quantity related to the thermodynamic entropy production is found by considering information loss in non-equilibrium processes. Using the problem of ion channel thermodynamics as an example, we illustrate the idea of building up complexity by successively adding information to create progressively more complex descriptions of a physical system. Our result is that such statistical mechanical descriptions can be used to create transparent, computable, experimentally-relevant models that may be informed by more detailed atomistic simulations. We also derive a theory for the kinetic behavior of this system, identifying the nonequilibrium `process' free energy functional. The Gibbs relation for this functional is a fluctuation-dissipation theorem applicable arbitrarily far from equilibrium, that captures the effect of non-local and time-dependent behavior from transient driving forces. Based on this work, it is clear that statistical mechanics is a general tool for constructing the relationships between constraints on system information.

  • 3 authors
·
May 27, 2011

Exact solutions to the nonlinear dynamics of learning in deep linear neural networks

Despite the widespread practical success of deep learning methods, our theoretical understanding of the dynamics of learning in deep neural networks remains quite sparse. We attempt to bridge the gap between the theory and practice of deep learning by systematically analyzing learning dynamics for the restricted case of deep linear neural networks. Despite the linearity of their input-output map, such networks have nonlinear gradient descent dynamics on weights that change with the addition of each new hidden layer. We show that deep linear networks exhibit nonlinear learning phenomena similar to those seen in simulations of nonlinear networks, including long plateaus followed by rapid transitions to lower error solutions, and faster convergence from greedy unsupervised pretraining initial conditions than from random initial conditions. We provide an analytical description of these phenomena by finding new exact solutions to the nonlinear dynamics of deep learning. Our theoretical analysis also reveals the surprising finding that as the depth of a network approaches infinity, learning speed can nevertheless remain finite: for a special class of initial conditions on the weights, very deep networks incur only a finite, depth independent, delay in learning speed relative to shallow networks. We show that, under certain conditions on the training data, unsupervised pretraining can find this special class of initial conditions, while scaled random Gaussian initializations cannot. We further exhibit a new class of random orthogonal initial conditions on weights that, like unsupervised pre-training, enjoys depth independent learning times. We further show that these initial conditions also lead to faithful propagation of gradients even in deep nonlinear networks, as long as they operate in a special regime known as the edge of chaos.

  • 3 authors
·
Dec 20, 2013

Fluctuations and correlations in chemical reaction kinetics and population dynamics

This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or epidemics. After reviewing the assumptions and mean-field type approximations involved in the construction of chemical rate equations for uniform reactant densities, we first discuss spatial clustering in birth-death systems, where non-linearities are introduced through either density-limiting pair reactions, or equivalently via local imposition of finite carrying capacities. The competition of offspring production, death, and non-linear inhibition induces a population extinction threshold, which represents a non-equilibrium phase transition that separates active from absorbing states. This continuous transition is characterized by the universal scaling exponents of critical directed percolation clusters. Next we focus on the emergence of depletion zones in single-species annihilation processes and spatial population segregation with the associated reaction fronts in two-species pair annihilation. These strong (anti-)correlation effects are dynamically generated by the underlying stochastic kinetics. Finally, we address noise-induced and fluctuation-stabilized spatio-temporal patterns in basic predator-prey systems, exemplified by spreading activity fronts in the two-species Lotka-Volterra model as well as spiral structures in the May-Leonard variant of cyclically competing three-species systems akin to rock-paper-scissors games.

  • 1 authors
·
Jul 3, 2018

A Low-complexity Structured Neural Network to Realize States of Dynamical Systems

Data-driven learning is rapidly evolving and places a new perspective on realizing state-space dynamical systems. However, dynamical systems derived from nonlinear ordinary differential equations (ODEs) suffer from limitations in computational efficiency. Thus, this paper stems from data-driven learning to advance states of dynamical systems utilizing a structured neural network (StNN). The proposed learning technique also seeks to identify an optimal, low-complexity operator to solve dynamical systems, the so-called Hankel operator, derived from time-delay measurements. Thus, we utilize the StNN based on the Hankel operator to solve dynamical systems as an alternative to existing data-driven techniques. We show that the proposed StNN reduces the number of parameters and computational complexity compared with the conventional neural networks and also with the classical data-driven techniques, such as Sparse Identification of Nonlinear Dynamics (SINDy) and Hankel Alternative view of Koopman (HAVOK), which is commonly known as delay-Dynamic Mode Decomposition(DMD) or Hankel-DMD. More specifically, we present numerical simulations to solve dynamical systems utilizing the StNN based on the Hankel operator beginning from the fundamental Lotka-Volterra model, where we compare the StNN with the LEarning Across Dynamical Systems (LEADS), and extend our analysis to highly nonlinear and chaotic Lorenz systems, comparing the StNN with conventional neural networks, SINDy, and HAVOK. Hence, we show that the proposed StNN paves the way for realizing state-space dynamical systems with a low-complexity learning algorithm, enabling prediction and understanding of future states.

  • 4 authors
·
Mar 30, 2025

Generalized Teacher Forcing for Learning Chaotic Dynamics

Chaotic dynamical systems (DS) are ubiquitous in nature and society. Often we are interested in reconstructing such systems from observed time series for prediction or mechanistic insight, where by reconstruction we mean learning geometrical and invariant temporal properties of the system in question (like attractors). However, training reconstruction algorithms like recurrent neural networks (RNNs) on such systems by gradient-descent based techniques faces severe challenges. This is mainly due to exploding gradients caused by the exponential divergence of trajectories in chaotic systems. Moreover, for (scientific) interpretability we wish to have as low dimensional reconstructions as possible, preferably in a model which is mathematically tractable. Here we report that a surprisingly simple modification of teacher forcing leads to provably strictly all-time bounded gradients in training on chaotic systems, and, when paired with a simple architectural rearrangement of a tractable RNN design, piecewise-linear RNNs (PLRNNs), allows for faithful reconstruction in spaces of at most the dimensionality of the observed system. We show on several DS that with these amendments we can reconstruct DS better than current SOTA algorithms, in much lower dimensions. Performance differences were particularly compelling on real world data with which most other methods severely struggled. This work thus led to a simple yet powerful DS reconstruction algorithm which is highly interpretable at the same time.

  • 4 authors
·
Jun 7, 2023

VisionLaw: Inferring Interpretable Intrinsic Dynamics from Visual Observations via Bilevel Optimization

The intrinsic dynamics of an object governs its physical behavior in the real world, playing a critical role in enabling physically plausible interactive simulation with 3D assets. Existing methods have attempted to infer the intrinsic dynamics of objects from visual observations, but generally face two major challenges: one line of work relies on manually defined constitutive priors, making it difficult to generalize to complex scenarios; the other models intrinsic dynamics using neural networks, resulting in limited interpretability and poor generalization. To address these challenges, we propose VisionLaw, a bilevel optimization framework that infers interpretable expressions of intrinsic dynamics from visual observations. At the upper level, we introduce an LLMs-driven decoupled constitutive evolution strategy, where LLMs are prompted as a knowledgeable physics expert to generate and revise constitutive laws, with a built-in decoupling mechanism that substantially reduces the search complexity of LLMs. At the lower level, we introduce a vision-guided constitutive evaluation mechanism, which utilizes visual simulation to evaluate the consistency between the generated constitutive law and the underlying intrinsic dynamics, thereby guiding the upper-level evolution. Experiments on both synthetic and real-world datasets demonstrate that VisionLaw can effectively infer interpretable intrinsic dynamics from visual observations. It significantly outperforms existing state-of-the-art methods and exhibits strong generalization for interactive simulation in novel scenarios.

  • 5 authors
·
Aug 19, 2025

Structured Knowledge Accumulation: The Principle of Entropic Least Action in Forward-Only Neural Learning

This paper aims to extend the Structured Knowledge Accumulation (SKA) framework recently proposed by mahi2025ska. We introduce two core concepts: the Tensor Net function and the characteristic time property of neural learning. First, we reinterpret the learning rate as a time step in a continuous system. This transforms neural learning from discrete optimization into continuous-time evolution. We show that learning dynamics remain consistent when the product of learning rate and iteration steps stays constant. This reveals a time-invariant behavior and identifies an intrinsic timescale of the network. Second, we define the Tensor Net function as a measure that captures the relationship between decision probabilities, entropy gradients, and knowledge change. Additionally, we define its zero-crossing as the equilibrium state between decision probabilities and entropy gradients. We show that the convergence of entropy and knowledge flow provides a natural stopping condition, replacing arbitrary thresholds with an information-theoretic criterion. We also establish that SKA dynamics satisfy a variational principle based on the Euler-Lagrange equation. These findings extend SKA into a continuous and self-organizing learning model. The framework links computational learning with physical systems that evolve by natural laws. By understanding learning as a time-based process, we open new directions for building efficient, robust, and biologically-inspired AI systems.

  • 1 authors
·
Apr 4, 2025

Foundation Inference Models for Markov Jump Processes

Markov jump processes are continuous-time stochastic processes which describe dynamical systems evolving in discrete state spaces. These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial. In this work we introduce a methodology for zero-shot inference of Markov jump processes (MJPs), on bounded state spaces, from noisy and sparse observations, which consists of two components. First, a broad probability distribution over families of MJPs, as well as over possible observation times and noise mechanisms, with which we simulate a synthetic dataset of hidden MJPs and their noisy observation process. Second, a neural network model that processes subsets of the simulated observations, and that is trained to output the initial condition and rate matrix of the target MJP in a supervised way. We empirically demonstrate that one and the same (pretrained) model can infer, in a zero-shot fashion, hidden MJPs evolving in state spaces of different dimensionalities. Specifically, we infer MJPs which describe (i) discrete flashing ratchet systems, which are a type of Brownian motors, and the conformational dynamics in (ii) molecular simulations, (iii) experimental ion channel data and (iv) simple protein folding models. What is more, we show that our model performs on par with state-of-the-art models which are finetuned to the target datasets.

  • 5 authors
·
Jun 10, 2024

PROSE: Predicting Operators and Symbolic Expressions using Multimodal Transformers

Approximating nonlinear differential equations using a neural network provides a robust and efficient tool for various scientific computing tasks, including real-time predictions, inverse problems, optimal controls, and surrogate modeling. Previous works have focused on embedding dynamical systems into networks through two approaches: learning a single solution operator (i.e., the mapping from input parametrized functions to solutions) or learning the governing system of equations (i.e., the constitutive model relative to the state variables). Both of these approaches yield different representations for the same underlying data or function. Additionally, observing that families of differential equations often share key characteristics, we seek one network representation across a wide range of equations. Our method, called Predicting Operators and Symbolic Expressions (PROSE), learns maps from multimodal inputs to multimodal outputs, capable of generating both numerical predictions and mathematical equations. By using a transformer structure and a feature fusion approach, our network can simultaneously embed sets of solution operators for various parametric differential equations using a single trained network. Detailed experiments demonstrate that the network benefits from its multimodal nature, resulting in improved prediction accuracy and better generalization. The network is shown to be able to handle noise in the data and errors in the symbolic representation, including noisy numerical values, model misspecification, and erroneous addition or deletion of terms. PROSE provides a new neural network framework for differential equations which allows for more flexibility and generality in learning operators and governing equations from data.

  • 3 authors
·
Sep 28, 2023

Feature Lottery? A Bifurcation Theory of Concept Emergence

Neural networks acquire structured representations at specific moments during training, yet identifying these transitions typically relies on retrospective, label-dependent metrics. We introduce a bifurcation theory of representation dynamics to detect these moments in real time. Analyzing a passive GMM probe attached to the evolving encoder, we show the onset of structure corresponds to a supercritical pitchfork bifurcation driven by the loss Hessian. The system exhibits a theoretically predictable zero-crossing (β_c) that, compared to the network's current state (β), yields a dynamic ratio β(t)/β_c(t): a universal, label-free phase coordinate for representation dynamics, computable entirely from hidden states. We empirically validate four distinct transition regimes predicted by this coordinate across diverse settings: SAEs on language models (Pythia), SSL (CIFAR), and grokking (modular arithmetic). Crucially, under finite dissipation, macroscopic symmetry-breaking can lag the initial zero-crossing by orders of magnitude, which providing a rigorous dynamical account of the delayed escape observed in grokking. Microscopically, the bifurcation creates a shared unstable subspace, forcing collective symmetry breaking. We term this the "feature lottery" in SAE training: a feature's terminal interpretability becomes predictable remarkably early. By only 5% of training, early atom purity robustly predicts final convergence purity, with top-decile early atoms achieving over 12x the baseline purity at convergence. Beyond explaining concept emergence, β/β_c provides a practical early-warning indicator for training health, detecting the onset of usable structure, the crystallization of feature identity, and representational collapse epochs before downstream metrics react.

  • 1 authors
·
May 21

sangkuriang: A pseudo-spectral Python library for Korteweg-de Vries soliton simulation

The Korteweg-de Vries (KdV) equation serves as a foundational model in nonlinear wave physics, describing the balance between dispersive spreading and nonlinear steepening that gives rise to solitons. This article introduces sangkuriang, an open-source Python library for solving this equation using Fourier pseudo-spectral spatial discretization coupled with adaptive high-order time integration. The implementation leverages just-in-time (JIT) compilation for computational efficiency while maintaining accessibility for instructional purposes. Validation encompasses progressively complex scenarios including isolated soliton propagation, symmetric two-wave configurations, overtaking collisions between waves of differing amplitudes, and three-body interactions. Conservation of the classical invariants is monitored throughout, with deviations remaining small across all test cases. Measured soliton velocities conform closely to theoretical predictions based on the amplitude-velocity relationship characteristic of integrable systems. Complementary diagnostics drawn from information theory and recurrence analysis confirm that computed solutions preserve the regular phase-space structure expected for completely integrable dynamics. The solver outputs data in standard scientific formats compatible with common analysis tools and generates visualizations of spatiotemporal wave evolution. By combining numerical accuracy with practical accessibility on modest computational resources, sangkuriang offers a platform suitable for both classroom demonstrations of nonlinear wave phenomena and exploratory research into soliton dynamics.

  • 4 authors
·
Jan 17 2

Multi-marginal Schrödinger Bridges with Iterative Reference Refinement

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

  • 3 authors
·
Aug 12, 2024

Model scale versus domain knowledge in statistical forecasting of chaotic systems

Chaos and unpredictability are traditionally synonymous, yet large-scale machine learning methods recently have demonstrated a surprising ability to forecast chaotic systems well beyond typical predictability horizons. However, recent works disagree on whether specialized methods grounded in dynamical systems theory, such as reservoir computers or neural ordinary differential equations, outperform general-purpose large-scale learning methods such as transformers or recurrent neural networks. These prior studies perform comparisons on few individually-chosen chaotic systems, thereby precluding robust quantification of how statistical modeling choices and dynamical invariants of different chaotic systems jointly determine empirical predictability. Here, we perform the largest to-date comparative study of forecasting methods on the classical problem of forecasting chaos: we benchmark 24 state-of-the-art forecasting methods on a crowdsourced database of 135 low-dimensional systems with 17 forecast metrics. We find that large-scale, domain-agnostic forecasting methods consistently produce predictions that remain accurate up to two dozen Lyapunov times, thereby accessing a new long-horizon forecasting regime well beyond classical methods. We find that, in this regime, accuracy decorrelates with classical invariant measures of predictability like the Lyapunov exponent. However, in data-limited settings outside the long-horizon regime, we find that physics-based hybrid methods retain a comparative advantage due to their strong inductive biases.

  • 1 authors
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Mar 12, 2023

Time evolution of the Boltzmann entropy for a nonequilibrium dilute gas

We investigate the time evolution of the Boltzmann entropy of a dilute gas of N particles, N>>1, as it undergoes a free expansion doubling its volume. The microstate of the system, a point in the 4N dimensional phase space, changes in time via Hamiltonian dynamics. Its entropy, at any time t, is given by the logarithm of the phase space volume of all the microstates giving rise to its macrostate at time t. The macrostates that we consider are defined by coarse graining the one-particle phase space into cells Δ_α. The initial and final macrostates of the system are equilibrium states in volumes V and 2V, with the same energy E and particle number N. Their entropy per particle is given, for sufficiently large systems, by the thermodynamic entropy as a function of the particle and energy density, whose leading term is independent of the size of the Δ_α. The intermediate (non-equilibrium) entropy does however depend on the size of the cells Δ_α. Its change with time is due to (i) dispersal in physical space from free motion and to (ii) the collisions between particles which change their velocities. The former depends strongly on the size of the velocity coarse graining Δv: it produces entropy at a rate proportional to Δv. This dependence is investigated numerically and analytically for a dilute two-dimensional gas of hard discs. It becomes significant when the mean free path between collisions is of the same order or larger than the length scale of the initial spatial inhomogeneity. In the opposite limit, the rate of entropy production is essentially independent of Δv and is given by the Boltzmann equation for the limit Δvrightarrow 0. We show that when both processes are active the time dependence of the entropy has a scaling form involving the ratio of the rates of its production by the two processes.

  • 4 authors
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Mar 12, 2024

Mamba Integrated with Physics Principles Masters Long-term Chaotic System Forecasting

Long-term forecasting of chaotic systems from short-term observations remains a fundamental and underexplored challenge due to the intrinsic sensitivity to initial conditions and the complex geometry of strange attractors. Existing approaches often rely on long-term training data or focus on short-term sequence correlations, struggling to maintain predictive stability and dynamical coherence over extended horizons. We propose PhyxMamba, a novel framework that integrates a Mamba-based state-space model with physics-informed principles to capture the underlying dynamics of chaotic systems. By reconstructing the attractor manifold from brief observations using time-delay embeddings, PhyxMamba extracts global dynamical features essential for accurate forecasting. Our generative training scheme enables Mamba to replicate the physical process, augmented by multi-token prediction and attractor geometry regularization for physical constraints, enhancing prediction accuracy and preserving key statistical invariants. Extensive evaluations on diverse simulated and real-world chaotic systems demonstrate that PhyxMamba delivers superior long-term forecasting and faithfully captures essential dynamical invariants from short-term data. This framework opens new avenues for reliably predicting chaotic systems under observation-scarce conditions, with broad implications across climate science, neuroscience, epidemiology, and beyond. Our code is open-source at https://github.com/tsinghua-fib-lab/PhyxMamba.

  • 5 authors
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May 29, 2025

Chaos as an interpretable benchmark for forecasting and data-driven modelling

The striking fractal geometry of strange attractors underscores the generative nature of chaos: like probability distributions, chaotic systems can be repeatedly measured to produce arbitrarily-detailed information about the underlying attractor. Chaotic systems thus pose a unique challenge to modern statistical learning techniques, while retaining quantifiable mathematical properties that make them controllable and interpretable as benchmarks. Here, we present a growing database currently comprising 131 known chaotic dynamical systems spanning fields such as astrophysics, climatology, and biochemistry. Each system is paired with precomputed multivariate and univariate time series. Our dataset has comparable scale to existing static time series databases; however, our systems can be re-integrated to produce additional datasets of arbitrary length and granularity. Our dataset is annotated with known mathematical properties of each system, and we perform feature analysis to broadly categorize the diverse dynamics present across the collection. Chaotic systems inherently challenge forecasting models, and across extensive benchmarks we correlate forecasting performance with the degree of chaos present. We also exploit the unique generative properties of our dataset in several proof-of-concept experiments: surrogate transfer learning to improve time series classification, importance sampling to accelerate model training, and benchmarking symbolic regression algorithms.

  • 1 authors
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Oct 11, 2021

Better Training of GFlowNets with Local Credit and Incomplete Trajectories

Generative Flow Networks or GFlowNets are related to Monte-Carlo Markov chain methods (as they sample from a distribution specified by an energy function), reinforcement learning (as they learn a policy to sample composed objects through a sequence of steps), generative models (as they learn to represent and sample from a distribution) and amortized variational methods (as they can be used to learn to approximate and sample from an otherwise intractable posterior, given a prior and a likelihood). They are trained to generate an object x through a sequence of steps with probability proportional to some reward function R(x) (or exp(-E(x)) with E(x) denoting the energy function), given at the end of the generative trajectory. Like for other RL settings where the reward is only given at the end, the efficiency of training and credit assignment may suffer when those trajectories are longer. With previous GFlowNet work, no learning was possible from incomplete trajectories (lacking a terminal state and the computation of the associated reward). In this paper, we consider the case where the energy function can be applied not just to terminal states but also to intermediate states. This is for example achieved when the energy function is additive, with terms available along the trajectory. We show how to reparameterize the GFlowNet state flow function to take advantage of the partial reward already accrued at each state. This enables a training objective that can be applied to update parameters even with incomplete trajectories. Even when complete trajectories are available, being able to obtain more localized credit and gradients is found to speed up training convergence, as demonstrated across many simulations.

  • 4 authors
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Feb 3, 2023

Equilibrium Propagation: Bridging the Gap Between Energy-Based Models and Backpropagation

We introduce Equilibrium Propagation, a learning framework for energy-based models. It involves only one kind of neural computation, performed in both the first phase (when the prediction is made) and the second phase of training (after the target or prediction error is revealed). Although this algorithm computes the gradient of an objective function just like Backpropagation, it does not need a special computation or circuit for the second phase, where errors are implicitly propagated. Equilibrium Propagation shares similarities with Contrastive Hebbian Learning and Contrastive Divergence while solving the theoretical issues of both algorithms: our algorithm computes the gradient of a well defined objective function. Because the objective function is defined in terms of local perturbations, the second phase of Equilibrium Propagation corresponds to only nudging the prediction (fixed point, or stationary distribution) towards a configuration that reduces prediction error. In the case of a recurrent multi-layer supervised network, the output units are slightly nudged towards their target in the second phase, and the perturbation introduced at the output layer propagates backward in the hidden layers. We show that the signal 'back-propagated' during this second phase corresponds to the propagation of error derivatives and encodes the gradient of the objective function, when the synaptic update corresponds to a standard form of spike-timing dependent plasticity. This work makes it more plausible that a mechanism similar to Backpropagation could be implemented by brains, since leaky integrator neural computation performs both inference and error back-propagation in our model. The only local difference between the two phases is whether synaptic changes are allowed or not.

  • 2 authors
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Mar 27, 2017

Nonlinear energy-preserving model reduction with lifting transformations that quadratize the energy

Existing model reduction techniques for high-dimensional models of conservative partial differential equations (PDEs) encounter computational bottlenecks when dealing with systems featuring non-polynomial nonlinearities. This work presents a nonlinear model reduction method that employs lifting variable transformations to derive structure-preserving quadratic reduced-order models for conservative PDEs with general nonlinearities. We present an energy-quadratization strategy that defines the auxiliary variable in terms of the nonlinear term in the energy expression to derive an equivalent quadratic lifted system with quadratic system energy. The proposed strategy combined with proper orthogonal decomposition model reduction yields quadratic reduced-order models that conserve the quadratized lifted energy exactly in high dimensions. We demonstrate the proposed model reduction approach on four nonlinear conservative PDEs: the one-dimensional wave equation with exponential nonlinearity, the two-dimensional sine-Gordon equation, the two-dimensional Klein-Gordon equation with parametric dependence, and the two-dimensional Klein-Gordon-Zakharov equations. The numerical results show that the proposed lifting approach is competitive with the state-of-the-art structure-preserving hyper-reduction method in terms of both accuracy and computational efficiency in the online stage while providing significant computational gains in the offline stage.

  • 3 authors
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Oct 17, 2025

On the Dynamics of Acceleration in First order Gradient Methods

Ever since the original algorithm by Nesterov (1983), the true nature of the acceleration phenomenon has remained elusive, with various interpretations of why the method is actually faster. The diagnosis of the algorithm through the lens of Ordinary Differential Equations (ODEs) and the corresponding dynamical system formulation to explain the underlying dynamics has a rich history. In the literature, the ODEs that explain algorithms are typically derived by considering the limiting case of the algorithm maps themselves, that is, an ODE formulation follows the development of an algorithm. This obfuscates the underlying higher order principles and thus provides little evidence of the working of the algorithm. Such has been the case with Nesterov algorithm and the various analogies used to describe the acceleration phenomena, viz, momentum associated with the rolling of a Heavy-Ball down a slope, Hessian damping etc. The main focus of our work is to ideate the genesis of the Nesterov algorithm from the viewpoint of dynamical systems leading to demystifying the mathematical rigour behind the algorithm. Instead of reverse engineering ODEs from discrete algorithms, this work explores tools from the recently developed control paradigm titled Passivity and Immersion approach and the Geometric Singular Perturbation theory which are applied to arrive at the formulation of a dynamical system that explains and models the acceleration phenomena. This perspective helps to gain insights into the various terms present and the sequence of steps used in Nesterovs accelerated algorithm for the smooth strongly convex and the convex case. The framework can also be extended to derive the acceleration achieved using the triple momentum method and provides justifications for the non-convergence to the optimal solution in the Heavy-Ball method.

  • 5 authors
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Sep 22, 2025

Accelerating Neural ODEs Using Model Order Reduction

Embedding nonlinear dynamical systems into artificial neural networks is a powerful new formalism for machine learning. By parameterizing ordinary differential equations (ODEs) as neural network layers, these Neural ODEs are memory-efficient to train, process time-series naturally and incorporate knowledge of physical systems into deep learning models. However, the practical applications of Neural ODEs are limited due to long inference times, because the outputs of the embedded ODE layers are computed numerically with differential equation solvers that can be computationally demanding. Here we show that mathematical model order reduction methods can be used for compressing and accelerating Neural ODEs by accurately simulating the continuous nonlinear dynamics in low-dimensional subspaces. We implement our novel compression method by developing Neural ODEs that integrate the necessary subspace-projection and interpolation operations as layers of the neural network. We validate our approach by comparing it to neuron pruning and SVD-based weight truncation methods from the literature in image and time-series classification tasks. The methods are evaluated by acceleration versus accuracy when adjusting the level of compression. On this spectrum, we achieve a favourable balance over existing methods by using model order reduction when compressing a convolutional Neural ODE. In compressing a recurrent Neural ODE, SVD-based weight truncation yields good performance. Based on our results, our integration of model order reduction with Neural ODEs can facilitate efficient, dynamical system-driven deep learning in resource-constrained applications.

  • 3 authors
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May 28, 2021