Neural Ordinary Differential Equations

Tracking neurite morphology over time helps characterize structural changes during neuronal development and deterioration, but long-term time-lapse imaging is resource-intensive and difficult to scale. Forecasting future morphology could reduce this burden. Existing neurite digital-twin models such as gated spatiotemporal attention (gSTA) produce a single deterministic forecast without representing variability among plausible futures. We introduce Morphology-Gated Residual Diffusion (MGRD), a compact stochastic surrogate that jointly forecasts twenty future neurite-morphology frames from ten observed frames while conditioning on morphology features derived from the latest observation. On controlled phase-field trajectories, MGRD reduces trajectory-wise mean MAE by 9.7% relative to a matched control while updating 4.46 times fewer parameters. On human iPSC-derived neuron microscopy, MGRD improves all four reported metrics over gSTA, including a 39.6% reduction in trajectory-wise mean MAE and a 45.3% increase in skeleton F1. Without mouse-domain retraining or fine-tuning, MGRD also improves MAE and skeleton F1 on mouse cortical-neurosphere microscopy across 10-40-min sampling intervals and forecast horizons beyond 13 hours. Repeated sampling provides a case-level variance score for ranking forecast difficulty. Retaining approximately 60% of the lowest-variance cases reduces mean MAE by 17.6% on iPSC microscopy and 16.8% on simulation data. MGRD uses 1.01% of gSTA's parameters, requires less than one tenth of its training-update time, and generates a 50-step DDIM trajectory 7.9% faster when morphology features are cached. These results establish MGRD as a compact stochastic surrogate for neurite-morphology forecasting and case prioritization across simulation and microscopy datasets.

A learned simulator can reproduce its training conditions accurately yet fail in two distinct ways once those conditions change. Over long rollouts, small errors accumulate until the trajectory drifts away from physically plausible behavior; under an intervention on a physical parameter, the model may continue to follow the law seen during training rather than the intervened one. We show that these two failures require different structural remedies. Evolving a learned energy with a symplectic integrator preserves the geometry of the conservative dynamics and keeps rollouts bounded and physically meaningful for up to $100\times$ the training horizon, while equal-capacity predictors, an energy-regularized predictor, and a tuned neural ODE diverge. By contrast, encoding the physical coupling through an explicit linear factorization enables the model to follow a never-seen sign of that coupling, whereas an unrestricted parameterization remains locked to the training law. Crucially, the two mechanisms are separable: removing the structure responsible for long-horizon stability leaves counterfactual transfer intact, while removing the factorized coupling destroys counterfactual transfer without eliminating stability. This double dissociation, established with matched controls that remove or replace one structural component at a time, persists beyond the headline three-body system and remains visible when the physical state must be inferred from pixels rather than provided directly. The result is a concrete design principle for physical world models: long-horizon stability and changed-law generalization arise from distinct structural commitments, and each can be imposed deliberately without requiring the other.

We present a physics-informed machine learning framework based on Neural Ordinary Differential Equations that solves the holographic inverse problem: reconstructing the bulk spacetime and gauge field of a charged AdS black hole directly from boundary fermionic spectral functions. Encoding the UV asymptotics, horizon regularity, and zero temperature extremality as hard constraints in the neural network architecture, our framework reliably reconstructs the extremal Reissner-Nordström AdS geometry across three quantum critical regimes set by the $U(1)$ probe charge---non-Fermi liquid, marginal Fermi liquid (strange metal), and Fermi-liquid-like states---and can jointly infer the probe charge itself to sub-percent accuracy. Relaxing the near-AdS boundary constraint uncovers a geometrical degeneracy: bulk profiles that differ throughout the radial direction but share the same near-horizon $AdS_2 \times \mathbb{R}^2$ data reproduce identical spectral functions near the Fermi surface. This isospectral non-uniqueness is precisely the bulk degeneracy expected on general holographic grounds at zero temperature, and its spontaneous emergence across independent training runs shows that the network isolates the IR CFT universality rather than overfitting a single UV completion.

We propose to learn the unknown dynamics in the proximity of a small body directly from tracking data, representing them as a feed-forward neural network embedded in the system Hamiltonian. The equations of motion form a Neural Hamiltonian Ordinary Differential Equation, whose variational equations provide exact training gradients: estimation uses position and velocity arcs at realistic noise levels, without acceleration or potential labels, and a continual learning approach warm-starts the network as new data are acquired. The known part of the Hamiltonian carries whatever is available, from the central term and spin state to the constant-density model of the imaged shape. We assess the method against a normalized spherical harmonics expansion estimated from identical arcs through the same machinery, on scenarios built on the shapes of Itokawa, 67P, Bennu and Eros. The network remains usable inside the Brillouin sphere: it plans ballistic descents at Itokawa to \SI{4.6}{m} median touchdown error from tracking alone, against 5.1--\SI{48.9}{m} for harmonics of degree 4--12, and to \SI{0.9}{m} with the imaged shape as prior, a configuration that also recovers localised density anomalies invisible to any harmonics degree. The two representations are complementary, and we discuss their combined use across the phases of a small-body mission.

This paper addresses infinite-dimensional Bayesian inference for inverse problem of partial differential equations with model parameters in infinite-dimensional Hilbert space. To effectively incorporate prior information, we propose a novel continuous normalizing flows based infinite-dimensional model. Specifically, by introducing a well-defined neural ordinary differential equation in infinite-dimensional space, a simple reference measure can be transformed into a more complex measure which encodes the prior information. A corresponding theoretical framework is established to ensure the well-posedness of our proposed Bayesian prior in infinite-dimensional space. We also provide training methods of the prior for two distinct data settings, along with two sampling algorithms for the resulting Bayesian posterior. The proposed framework is applied to three representative inverse problems: the simple smooth inverse problem, inverse scattering problem, and the inverse heat conduction problem. Numerical experiments support the theoretical analysis and demonstrate the efficiency of the proposed algorithms.

Longitudinal cohort studies produce repeated data that enable the assessment of time-varying association patterns between exposures and health outcomes. Classical linear mixed-effects models (LMMs) can accommodate a large variety of association patterns while accounting for the irregularly spaced, partially observed measurement. But they require the analyst to pre-specify the functional form linking the exposure history to the outcome. We propose the Neural ODE-LMM, which embeds a Neural Ordinary Differential Equation (Neural ODE) within the linear mixed-effects framework: a learned vector field encodes covariate trajectories into a continuous-time latent state that drives both the fixed- and random-effect design, while preserving the standard LMM observation model. This retains classical likelihood-based inference while learning complex, potentially cumulative, covariate effects flexibly. All parameters are estimated by maximising a penalised marginal likelihood. To quantify covariate effects, we introduce contrasts of counterfactual predictions that compare the expected outcome under alternative covariate trajectories with variance estimated via the delta method. In simulations, the model recovers both instantaneous and cumulative-burden effects without prior specification of the functional form. Applied to the Trois-Cités (3C) cohort, a population-based study of 7{,}324 participants, the method reveals trajectory-dependent associations of BMI and fasting glucose with cognitive decline.

Large language models (LLMs) have shown promise for spatio-temporal forecasting, but existing approaches often rely on regularly sampled token sequences and struggle with irregular observations because of temporal asynchrony, representation-space misalignment, and limited context windows. We propose LLMODE, a token-efficient framework for irregular spatio-temporal forecasting with a frozen LLM backbone. LLMODE first uses a graph-aware ODE encoder to reconstruct irregular graph observations as a continuous-time latent trajectory. A Fixed-Budget Perceiver Resampler then compresses this variable-length trajectory into a fixed number of dynamic memory tokens. In parallel, compact statistical descriptors are encoded and resampled into context memory tokens. A dual-source gated cross-attention module injects both memories into the frozen LLM, enabling controlled utilization of external spatio-temporal evidence. Experiments on three real-world urban datasets and two physical-dynamics benchmarks show competitive overall performance, with clearer advantages under sparse or dynamically complex irregular sampling. Additional evaluations on unseen urban regions further demonstrate strong zero-shot generalization without adaptation.

Accurate modeling and forecasting of power transformer thermal behavior are critical for reliability, asset lifetime, and optimized power system operation. Numerical approaches such as finite element methods (FEM) and computational fluid dynamics (CFD) offer high fidelity but are computationally expensive, require complex mesh generation, and are often impractical for real-time or large-scale applications, particularly when transformer geometries are unknown. Lumped-parameter thermal models are more practical but depend on transformer-specific thermal constants and may fail to capture dynamic responses under varying operating and environmental conditions. Purely data-driven machine learning methods, including artificial neural networks, convolutional neural networks, and long short-term memory (LSTM) networks, have shown success in forecasting transformer temperatures but typically require large volumes of high-quality training data and may produce physically inconsistent or uninterpretable results. This paper develops a physics-aware Neural Ordinary Differential Equation (Neural ODE) framework for forecasting transformer thermal behavior from real-world time-series data. Neural ODEs model system dynamics in continuous time, providing smooth trajectory prediction and a natural representation of continuously evolving thermal dynamics. A key contribution is the integration of simplified heat-transfer equations directly into the Neural ODE formulation. The model is evaluated across datasets from fifteen transformers in different regions of Norway with varying designs and cooling mechanisms. The results demonstrate that the developed Neural ODE framework provides a standardized, physics-aware, and robust forecasting approach for heterogeneous transformer units.

We study the approximation of dynamical systems by semi-autonomous neural ordinary differential equations (SA-NODEs) over long time horizons. For a single network trained on the whole horizon, the available error bound deteriorates double exponentially in the horizon length. We develop two training strategies that avoid this barrier, each built on a reset of the state. The model predictive strategy partitions the horizon adaptively and restarts every window from observed data: when training meets a prescribed tolerance on every window, the composite model meets it uniformly in time, with a parameter budget linear in the horizon for targets with a bounded, uniformly regular reachable tube. The Floquet strategy addresses autonomous targets with a stable limit cycle and uses no data at deployment: a certified contraction of the learned return map confines the error to linear growth in the number of elapsed periods. For the time-periodic architecture we deploy, the scalar certificate degenerates; we prove instead a uniform-in-time orbital guarantee whose hypotheses are measured on the trained model, and an obstruction showing that, for an exactly periodic learned field, small one-period error and a contracting stroboscopic map cannot hold at once. Numerical experiments on four benchmarks confirm the predicted error laws and measure the hypotheses of every guarantee.

Cross-subject electroencephalogram (EEG)-based emotion recognition remains challenging due to substantial inter-individual variability and discrete formulation that overlooks affective continuity. Existing methods operate in Euclidean space and focus on marginal distribution alignment, failing to preserve the semantic structure of emotions across subjects. This article proposes MGMCL, reconceptualizing emotion recognition as learning continuous representations on symmetric positive definite (SPD) Riemannian manifolds. The frame?work introduces multi-granularity manifold contrastive learning at instance, emotion, and trajectory levels while preserving semantic ordering. Neural ordinary differential equations on manifolds model continuous emotion dynamics. Cross-subject generalization employs Gromov-Wasserstein manifold alignment. Weakly-supervised learning enables continuous valence-arousal-dominance prediction from discrete labels. Extensive experiments on three public datasets demonstrate state-of-the-art performance: 91.23% accuracy on SEED, 73.82% on SEED-IV, and 76.38% on DEAP, achieving consistent improvements of 1.89%, 1.66%, and 1.28% over previous best methods, respectively.

Computational models of blood clotting improve understanding of thrombus formation, but their clinical application remains limited because many model inputs are difficult to measure and patient-specific data are often sparse. We present a computational framework based on latent neural differential equations that infers unknown model parameters from sparse measurements and forecasts thrombosis progression. We demonstrate the framework using data generated from a multiphysics blood-clotting model in which clot growth is governed by the coagulation cascade and diffusion. Four known biochemical inputs (fibrinogen and factors IX, VIII, and V), together with sparse early clot-size observations, are used to infer the tissue-factor parameter and predict subsequent clot growth. We compare seven probabilistic methods: stochastic neural ordinary differential equations (SNODE), stochastic neural functional differential equations (SNFDE), a latent neural-process baseline, a monotone probabilistic deep ensemble, empirical trajectory retrieval, PCA-ridge Gaussian posterior, and Gompertz-curve retrieval. SNODE achieved the best performance in inferring the unknown input and forecasting future clot-growth trajectories. SNFDE performed similarly and consistently outperformed the other non-differential models. Prediction accuracy improved as more observations became available, whereas longer forecasting horizons increased uncertainty and decreased accuracy. Latent neural differential equations thus effectively combine parameter inference and clot-growth forecasting from sparse measurements, providing a promising foundation for personalized thrombosis modeling.

Neural networks applied to sequential decision-making tasks typically rely on latent representations of environment states. While environment dynamics dictate how semantic states evolve, the corresponding latent transitions are usually left implicit, creating a potential misalignment between the two. We propose to model latent dynamics explicitly by drawing an analogy between Markov decision process (MDP) trajectories and ordinary differential equation (ODE) flows: in both cases, the current state fully determines its successors. Building on this view, we introduce a neural ODE-based regularization method that enforces latent embeddings to follow consistent ODE flows, thereby aligning representation learning with environment dynamics. Although broadly applicable to deep learning agents, we demonstrate its effectiveness in reinforcement learning by integrating it into Actor-Critic algorithms. Our approach yields major performance gains across various standard Atari benchmarks for A2C and gridworld environments for PPO.

In this paper, we address the certification of datadriven feedforward control for periodic tracking of unknown nonlinear systems under partial state measurements. To this end, we adopt an invertible neural network (INN) as a surrogate for the unknown system. This choice allows us to bypass solving a nonconvex inversion problem, eliminating the associated inversion errors and reducing tracking error certification to a surrogate modeling problem. We then apply conformal prediction to provide finite-sample probabilistic guarantees on the surrogate modeling error which, through the derived tracking error bound, yield marginal certificates on feedforward tracking error. Finally, we demonstrate the approach on a DC-motor-driven mechanical load with nonlinear friction.

Vision Transformers (ViTs) achieve strong image-recognition performance, but their parameter count grows linearly with depth when each block is independently parameterized. Single-block recurrent ViTs (bViT) remove this growth by repeatedly applying one shared block. Rather than proposing a new architecture, we fix a bViT and provide a controlled empirical characterization of three training and inference regimes under a common CIFAR-100 protocol, asking: (i)~when does recurrence beat independently parameterized depth---at matched FLOPs or at matched parameter memory? (ii)~when a residual recurrent block is trained through an ODE solver, does solver order act as numerical refinement or as an architectural bias? and (iii)~what does robustness beyond the training horizon cost in nominal accuracy? We find that standard ViTs remain preferable when FLOPs are the primary constraint, whereas recurrent ViTs offer a better accuracy--parameter trade-off under memory constraints. Consistent with the standard view of residual networks as Euler discretizations of ODEs, the continuous-time analogue of a residual recurrent block is the state-subtracted vector field $\dot{z}=F_θ(z)-z$; although known in principle, this distinction is easy to violate when the block is wrapped as a black-box vector field, and we qualify the cost at few accuracy points. Because the vector field is learned jointly with the solver, higher-order solvers act as a solver-induced architectural bias rather than a numerical-accuracy improvement, and their gains are not uniform. Finally, stage-wise deep supervision traces an accuracy--robustness frontier: it does not improve nominal accuracy, but degrades gracefully far beyond the training horizon, where naive recurrence collapses to near-random performance.

Understanding and controlling complex dynamical systems often requires executing thousands of numerical simulations across vast parametric landscapes, which is time-consuming. Machine learning surrogates significantly accelerate simulation by predicting state trajectories across different initializations and parameter values. However, surrogate models are specialized to one simulation model. Modifying the underlying differential equations - e.g., adding a physiological state or altering an epidemiological contact network - renders trained models obsolete and forces computationally expensive retraining from scratch. We introduce HyperODE, a surrogate capable of operating across an entire class of approximately mass-conserving compartmental models without retraining. By mapping the structure of ordinary differential equations (ODEs) into directed hypergraphs, HyperODE decouples the functional form of system interactions from the neural network architecture. HyperODE takes a compartmental model in the form of an ODE with an arbitrary parameter distribution defined through quantiles and transforms it into a hypergraph. It outputs the distribution of the trajectories for all the states in the original ODE in the form of quantiles. We then use this surrogate to build an encoder that takes a noisy trajectory and outputs a distribution over the parameters of the original ODE, thus calibrating the model in a single pass. On families and system sizes never seen in training, HyperODE produces calibrated quantile bands in a single forward pass, with weighted-interval score and coverage on par with specialized surrogates for each structure. For inverse inference, HyperODE produces calibration from noisy state trajectories in a few milliseconds with a single shared encoder, competitive with existing methods. HyperODE extends zero-shot to ODEs that break mass conservation and to external forcing.

In this paper, we study the extension of Neural Jump ODEs to infinite-dimensional function spaces. In particular, the underlying process $X$ now takes values in $L^2(Ξ, \mathbb{R}^{d_X})$ instead of $\mathbb{R}^{d_X}$ and the Operator NJ-ODE approximates the optimal predictor of this process by producing a representative of the conditional expectation. The NJ-ODE model is a framework for online learning the optimal prediction of continuous-time stochastic processes, given discrete, possibly irregular and incomplete past observations. In a series of works, this model has been extended to deal with generic path-dependent processes, with observation noise and dependent observations, with long-term predictions, and with input-output systems. However, throughout all of these works, the underlying processes were restricted to be finite-dimensional. In particular, function-valued problems, like yield curve or volatility surface predictions, could only be handled through discretization, which inherently leads to a loss of information. In this work, we build on ideas from Neural Operator methods that allow us to extend the NJ-ODE framework to an infinite-dimensional output process. To prove convergence of the NJ-ODE to the optimal prediction process, we develop a new approximation strategy that also generalizes previous works in the finite-dimensional setting by considerably weakening the assumptions.

We show how large-deviation statistics allows one to obtain reliable estimates of the multiplicity of stable fixed-points in a model of neural ordinary differential equations previously employed in computational tasks. The result is obtained by developing a suitable perturbative method in the amplitude of the disorder. It turns out that for not-too-large coupling strengths there are no qualitative differences between the symmetric case, when the dynamics is a purely gradient evolution, and the asymmetric case, when limit cycles and chaos can, in principle, arise. The selection of this specific model is dictated by pedagogical reasons, but we are confident that the approach can be extended to other many-degree-of-freedom dynamical models characterized by different classes of random coupling matrices.

Modeling continuous object deformation is important for many computer vision and robotics tasks, such as manipulation and simulation. Existing approaches rely on learning-based methods or physics simulators to model shape deformations. However, these approaches either use discrete time steps or are too computationally intensive for real-time applications. We present ODeform, a novel extension of Neural Ordinary Differential Equations to continuous 4D dynamics of deformable objects in 3D space. Our method transforms 3D point clouds and physical conditions (like material properties) into a unified latent space. By solving the resulting ordinary differential equations over time, we model deformations as continuous flows within this learned embedding, eliminating the need for discrete time steps while maintaining computational efficiency. We evaluate our approach on unseen physical parameter configurations, showing improved motion prediction accuracy over baseline methods. Our experiments further demonstrate a successful transfer to real 3D captured objects with novel shapes, along with effective interpolation and extrapolation of the learned dynamics. Our code and data will be made publicly available.

Unsteady aerodynamic phenomena, such as gusts, turbulence, and fluid-structure interactions affect an aircraft during flight. For design, optimisation and certification, it is indispensable to quantify such unsteady aerodynamic effects. Industry-standard computational fluid dynamics methods, such as solving the unsteady Reynolds-averaged Navier-Stokes equations or the linearized frequency domain method, are either computationally expensive or restricted by assumptions like linearity. Once trained, machine learning methods are capable of computing non-linear relationships very fast, making them suitable as surrogate models. By autoregressively applying graph neural networks (GNNs), operating on a discretised spatial domain, spatio-temporal predictions can be made. However, autoregressive GNNs suffer from error accumulation leading to unstable rollouts over time. Here we show that combining GNNs with augmented Neural Ordinary Differential Equations yields temporally stable predictions of the surface forces on a pitching airfoil. We found that our approach, called GNODE, based on Graph Neural Ordinary Differential Equations, provides temporally more stable, spatially smoother, and overall more accurate results than an autoregressive GNN baseline. Tests are conducted on a dataset consisting of a simulations of a pitching airfoil, including transonic shocks, transient behaviour and dynamic non-linearities. Augmenting GNODEs with additional latent dimensions improves the expressivity and accuracy by capturing underlying history effects. The developed method demonstrates an approach that is suitable to model non-linear spatio-temporal systems with exogenous inputs.

Ordinary differential equations (ODEs) are widely used to model dynamical systems in physics, biology, neuroscience, and physiology, but in many applications some equations of the dynamics are unknown and only a subset of the state variables are measured. We propose a hybrid neural--physics framework in which the known components of the ODE are kept explicit and the missing components are represented by a neural network. The proposed method consists of two stages where we alternate between state and parameter estimation and iterate until a predetermined criterion is met. Specifically, in the first step, we treat the model parameters as being known and we infer the latent states from the available measurements using a Rauch--Tung--Striebel (RTS) smoother. In the second stage, we treat the smoothed trajectories as being known and use them to estimate the neural networks' parameters through backpropagation. We evaluate the method on benchmark systems spanning linear, nonlinear, and stiff dynamics under partial state observation. Across these settings, the proposed method learns missing ODE components from incomplete measurements while exploiting and retaining interpretable mechanistic structure and improving latent-state reconstruction and long-horizon prediction.

Many real-world systems evolve continuously, yet most machine learning models interpret time series as discrete sequences. Continuous-time approaches instead treat time series as samples from an underlying input path, a formulation that naturally accommodates irregularly sampled or oversampled data. Among these, Neural Controlled Differential Equations (NCDEs) are a maximally expressive class of models that parametrise a vector field using a neural network and evolve their hidden state by solving a dynamical system driven by the input path. NCDEs typically use a non-linear vector field, so their expressive power and continuous-time flexibility come at the cost of a forward pass that is both computationally expensive and inherently sequential, limiting their scalability and practical applicability. This thesis advances the training and scalability of NCDEs through three complementary contributions. First, building on neural rough differential equations, Log-NCDEs apply the Log-ODE method to efficiently approximate an NCDE's solution during training, improving both computational speed and empirical performance. Second, Linear NCDEs replace the non-linear vector field with a linear one, enabling closed-form solutions and parallel-in-time computation without sacrificing theoretical expressivity. Third, Structured Linear NCDEs use structured linear vector fields to further enhance efficiency while maintaining theoretical expressiveness and empirical performance. Collectively, these methods reduce the time per training step for an NCDE by up to three orders of magnitude while achieving state-of-the-art performance across diverse time series benchmarks.

Accurately predicting the temporal evolution of clinical biomarkers is crucial for the early diagnosis and management of neurodegenerative diseases such as Alzheimer's disease. However, this relies on longitudinal data to capture biomarker changes over time, which is often sparse and irregular due to the high cost, labor-intensive nature, and patient burden. To address these challenges, we propose ENC-ODE, an Event-level Neurodegenerative modeling in Continuous time with neural Ordinary Differential Equations. ENC-ODE predicts future biomarker evolution by modeling clinical events through diagnosis-conditioned continuous dynamics. A target-conditioned attention mechanism weights and aggregates event-level predictions for the target time and modality without history compression. Extensive experiments on Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate that ENC-ODE outperforms representative sequence models while offering a scalable and neuroscientifically grounded solution for clinical support. The code is available at https://github.com/JardinDelSol/enc-ode.

In precipitation forecasting, not only accuracy but also temporal resolution is critical. However, increasing temporal resolution is constrained by observational limitations and the computational cost of dense discrete modeling. To overcome this limitation, we reformulate precipitation forecasting as a continuous-time dynamical system and propose RainODE, a framework that models precipitation evolution in latent space using a Neural ODE. This formulation enables derivative-consistent temporal dynamics and captures the dominant large-scale advective motion of precipitation systems. Nevertheless, a purely deterministic ODE struggles to represent non-advective intensity changes such as localized growth, decay, and sub-grid variability, often leading to over-smoothed predictions. To address this issue, we introduce a stochastic source modeling module based on a Brownian Bridge formulation, which refines residual intensity variations and restores fine-grained structures while preserving advective consistency. By combining deterministic continuous dynamics with stochastic refinement, RainODE enables arbitrary-time inference while maintaining sharp predictions. Experiments on SEVIR and the newly introduced Radar-based Precipitation Integrated Dataset (RAPID) demonstrate consistent improvements across multiple temporal intervals and precipitation regimes. The code is available at https://github.com/SeongYE/RainODE.

Hamiltonian Neural Networks (HNNs) integrate physical priors into neural models by learning a system's Hamiltonian, improving generalization and sample efficiency. Identifying the system Hamiltonian from noisy observations of state variables is a challenging task. For simulations to faithfully reflect the long-term behavior of Hamiltonian systems, especially energy conservation, it is essential to use symplectic integrators, which preserve the system's geometric structure. This fidelity comes at a cost: implicit symplectic integrators are more computationally intensive and make backpropagation through the ODE solver non-trivial. However, by leveraging the fact that symplectic discretizations of the adjoint system yield the same sensitivities associated by backpropagation, we obtain an efficient method of training the Neural Network parameters. In our work, we explore this alternate method of HNN training under noisy observation of trajectories with our HNN model based on an implicit symplectic integrator. Computationally, a predictor-corrector based ODE solver and fixed point iteration help to mitigate the computational cost of the implicit timestepping, resulting in more efficient generation of gradient updates. We showcase the numerical advantage, in experiments, in system identification and energy preservation on a range of non-separable, chaotic systems and the efficient computation and memory complexity of our method. We also observe that the post-processing of the learned Hamiltonian using backward error analysis yields a modified Hamiltonian that is a more accurate approximation of the true Hamiltonian without the need to use more accurate discretizations of the flow map.

Graph Neural Differential Equations (GNDEs) model continuous-time graph dynamics by parameterizing Neural ODE velocity fields with Graph Neural Networks. Their local, size-independent filters suggest a zero-shot size-transfer principle: train on a small graph and deploy on larger, similar graphs without retraining. We develop a quantitative theory for this principle on sparse random graphs sampled from graphons. We consider Graphon Neural Differential Equations (Graphon-NDEs) and adjoint Graphon-NDEs as the infinite-node limits of the forward and adjoint GNDE systems, and establish well-posedness. For an $n$-node random graph with sparsity parameter $α_n$, we prove trajectory-wise convergence of GNDE solutions to Graphon-NDE solutions at rate $O((α_n n)^{-1/2})$, up to logarithmic factors, with high probability. We also establish uniform-in-time convergence bounds for adjoint systems governing hidden-state and parameter gradients. We further study discretize-then-optimize (DTO) and optimize-then-discretize (OTD) training. Under explicit Euler discretization with $M$ steps, we show that DTO and OTD are asymptotically consistent, with hidden-state and local parameter-gradient discrepancies of orders $O(1/M)$ and $O(1/M^2)$, respectively, up to sparsity and logarithmic factors. Experiments on HSBM and tent graphons support the theoretical rates, while zero-shot transfer experiments across four graphon classes demonstrate accurate deployment of learned GNDEs on larger independently sampled graphs.

Mammalian cell-culture processes underpin the manufacture of many biopharmaceuticals, yet keeping a run on track is hard: critical process parameters drift over days, and an off-specification trend is often confirmed too late to intervene. Early-stage, multi-day forecasts could enable timely adjustment of feeding, sampling, and control, but bioprocess forecasting is challenging because measurements are sparse and irregularly sampled, operating conditions are heterogeneous across cell lines and media, and runs with near-identical early behaviour can diverge into different futures. We propose an adaptive framework combining a Gated Bottleneck Latent Ordinary Differential Equation (GB-Latent ODE) with Multi-Path Just-In-Time Fine Tuning (MP-JIT-FT). The GB-Latent ODE augments the stan dard Latent ODE with learnable variable-wise gating and a mask-aware bottleneck that compress high-dimensional sparse inputs, improving learning under limited data. Given a partially observed run, MP-JIT-FT retrieves similar historical trajectories, clusters the local neighbourhood into candidate regimes, and fine-tunes a separate model per regime to produce multiple plausible paths, each with a reconstruction-based confidence score, not a single averaged forecast. We further fuse Raman spectroscopy data: a machine-learning soft sensor turns dense Raman spectra into pseudo-observations that enrich the sparse offline measurements for more robust training. On 38 fed-batch 5L bioreactor runs spanning 14 conditions, MP-JIT-FT with Raman fusion achieves the best average rank and outperforms a global Latent ODE baseline on 8 of 9 target variables. Using local-divergence metrics, we show the multi-path gains are largest when locally similar prefixes diverge, whereas Raman fusion helps most when early dynamics are representative of later behaviour.

In this work, Neural ODEs equipped with a curated collection of equilibrium points have been successfully employed for classification tasks. The planted attractors serve as indicators for the target classes, while the velocity field leveraging the universal approximation capabilities of the architecture shapes the dynamical landscape. This process defines the basins of attraction of the trained model, effectively directing each input (provided as an initial condition) toward its corresponding destination target.

Standard continuous-depth models, such as Neural Ordinary Differential Equations (NODEs), offer significant advantages in modeling physical systems by learning continuous vector fields rather than discrete temporal steps. However, when applied to complex dynamical systems, standard NODEs frequently struggle with highly nonlinear dynamics. This paper investigates the Frequency-domain Neural ODE (FNODE), an architecture that projects continuous temporal dynamics into the frequency domain using the Fast Fourier Transform (FFT). By operating in the frequency domain, the model provides better generalization to the dynamical system. The architecture is empirically evaluated against discrete models, specifically Gated Recurrent Units (GRUs) and Long Short-Term Memory (LSTMs), and other continuous-depth variants, including Augmented Neural ODE (ANODE), across four distinct dynamical systems: the Lotka-Volterra model, the forced Duffing oscillator, the Van der Pol oscillator, and the Lorenz system. To rigorously assess generalization and robustness, curriculum and ensemble learning are used to evaluate the model's convergence by estimating confidence intervals across different ensemble models. The empirical results demonstrate that the FNODE architecture achieves better generalization while exhibiting remarkable convergence stability.

Long-horizon spacecraft trajectory forecasting suffers from error accumulation due to the absence of corrective observations in the forecast regime, making reliable uncertainty estimation crucial for safety-critical decision-making such as space domain awareness and conjunction assessment. While high-fidelity physics-based orbit propagators provide accurate deterministic forecasts, they typically lack calibrated uncertainty estimates over long horizons. We introduce a Predictor--Corrector framework in which a physics-based continuous-time $\textit{deterministic}$ forecaster is augmented with a learned continuous-time $\textit{probabilistic}$ Corrector that models forecast errors. The proposed Corrector can be wrapped around an existing deterministic propagator to improve forecast accuracy while producing sharp and calibrated full-covariance uncertainty estimates. The Corrector is based on Latent Neural Controlled Differential Equations (Latent NCDEs) and models the probabilistic temporal evolution of forecast errors in continuous time, naturally supporting irregular sampling and missing features. We further introduce a loss function that promotes calibration and sharpness in long-horizon uncertainty propagation. We evaluate the proposed framework on long-horizon spacecraft trajectory forecasting using real-world data from NASA's Crustal Dynamics Data Information System (CDDIS), wrapping the Corrector around NASA's General Mission Analysis Tool (GMAT). Across forecast horizons of 2--4 days without observations and six rolling test windows, the proposed approach consistently improves accuracy and uncertainty calibration compared to deterministic baselines and Latent ODE-based correctors, demonstrating the effectiveness of the continuous-time probabilistic Corrector for trajectory forecasting.

Neural Controlled Differential Equations (NCDE) provide a powerful continuous-time framework for forecasting time series, but standard graph-based extensions typically learn spatial structure purely from data, even in settings where a directed graph structure is known a priori. We introduce Informed Neural controlled Differential EQuationS (INDEQS), a graph-based NCDE forecasting method that incorporates prior knowledge of a directed graph at distinct architectural positions. INDEQS separates inner mixing of hidden states across graph nodes from outer mixing between vector field and control, and offers both a lightweight graph-constrained variant and a more expressive variant, learning additional graph connections from data via adaptive graph convolutions. To systematically study when graph informedness is beneficial in forecasting, we devise a continuous advection simulation on directed graphs, yielding synthetic spatio-temporal datasets with known ground-truth flow structure. We then evaluate INDEQS on two real-world tasks: river discharge forecasting on a hydrological network and traffic flow prediction on PeMS08. Across these synthetic and real-world benchmarks, outer informedness consistently improves mean absolute error over an uninformed NCDE with comparable parameter count, particularly on larger graphs, while inner informedness offers a more parameter-efficient alternative when strict adherence to a known adjacency is desired. A comparison of discrete convolutional and continuous-time decoders further shows that continuous decoders yield better accuracy and greater temporal flexibility on real-world tasks. An implementation of INDEQS and the advection simulation is available at https://github.com/Mitchi1/indeqs.

Neural dynamical systems are expressive temporal predictors that capture continuous-time dynamics through fine-grained state updates. However, this sequential structure maps poorly onto digital hardware optimized for dense matrix operations, a mismatch that analog neuromorphic computing, with its native continuous-time dynamics, can resolve. We introduce FerroNDS, a neuromorphic system built from two analog primitives: an integrator for temporal accumulation and an oscillator for frequency-selective filtering. We map this system onto compute-in-memory hardware based on multi-bit ferrodiodes. A 128-neuron instance of FerroNDS computes short-time Fourier transform and forecasts a 500-ms horizon for periodic, quasi-periodic, and chaotic signals. The system achieves sub-watt real-time operation with per-neuron per-inference energy of 1.64 $μ$J (200 Hz) and 0.29 $μ$J (10 kHz), 25-40$\times$ area reduction over SRAM-based digital systems, and per-layer latency of 3.18 ms (200 Hz) and 63.87 $μ$s (10 kHz). To our knowledge, this is the first end-to-end integration of a ferrodiode into a neuromorphic computational framework, establishing ferroelectric compute-in-memory as a practical substrate for analog neural dynamical systems.

Biophysical neuron models link measurements of neural activity to underlying cellular mechanisms. Yet, a central challenge is that the kinetics of many ion channels are poorly characterized, and practical simplifications -- omitting channels or reducing morphological detail -- introduce systematic gaps between model and biology. Bridging these gaps requires approaches that can flexibly discover unmodeled dynamics while preserving mechanistic interpretability. Here, we introduce a hybrid modeling framework that embeds neural ordinary differential equations into conductance-based biophysical models to capture unknown currents or mis-specified channel kinetics. By parameterizing the neural ODE in terms of voltage-dependent steady-state and time-constant functions, we recover interpretable gating dynamics directly from voltage recordings without assuming a functional form. We show that the hybrid model fits the gating kinetics of 2400 ion channel models and recovers unknown gating dynamics from single current-clamp recordings, generalizing to out-of-distribution stimulus regimes under realistic inputs and parameter misspecification. We also use our method to reduce a multicompartment model of a cortical neuron into a single-compartment hybrid model with a learned axial current, yielding up to an order of magnitude lower computational cost. Together, our results establish a plug-and-play framework for selectively replacing unknown components of conductance-based models with neural ODEs while preserving their mechanistic structure.

Neural ordinary differential equations (neural ODE) gained attention in safety critical settings such as continuous-time controllers for cyber-physical systems and classifiers integrated into automated decision pipelines, raising the question whether their behavior can be formally verified. Existing tools dedicated to neural ODE provide only a single reachability call without iterative input-set refinement, limiting the precision of their verdicts to whatever one reachability call can deliver. We present TNODEV, the first formal verifier for neural ODE that integrates a falsification checker, a fast interval-based reachability backend based on continuous-time mixed monotonicity, a verification and refinement loop with three input-set splitting heuristics, and a parallel scheduler in a single end-to-end pipeline. TNODEV supports safe-set inclusion verification on pure neural ODE, neural ODE in closed loop with a neural network controller and general neural ODE (GNODE), with the safe set specified either as an interval or as the half-space intersection induced by a target classification label. We evaluate TNODEV on a range of benchmarks across safe-set inclusion and classification-robustness properties, including a direct reachability comparison against NNV 2.0 and CORA and a verification comparison against NNV 2.0 on MNIST general neural ODE classifiers.

Scientific Machine Learning (SciML) methods such as Neural Ordinary Differential Equations (NODEs), Physics-Informed Neural Networks (PINNs), and Universal Differential Equations (UDEs) are most effective when structural priors reflect reliable governing dynamics. We ask what happens when this assumption is violated. Using macroeconomic forecasting as a stress-test domain, we evaluate five model families, ARIMA, LSTM, NODE, PINN, and UDE, across 23 countries using sparse annual data, multiple temporal splits, and five random seeds. Our results show that none of the evaluated models achieve consistently strong forecasting performance, highlighting the difficulty of low-frequency macroeconomic prediction. However, a clear relative hierarchy emerges: less-constrained models, particularly ARIMA and NODE, consistently outperform more-constrained heuristic-prior models such as PINN and UDE. Rather than treating this as a rejection of SciML, we interpret it as a diagnostic result: structural priors can act as misregularizers when they do not match the data-generating process. We identify failure modes including prior misalignment, regime shifts, structural breaks, and optimization instability, and argue that SciML practitioners should test whether structure helps before assuming that more structure is beneficial.

Robotic systems deployed in uncertain and dynamically changing environments often face variations in contact conditions, aerodynamic effects, and external disturbances that challenge reliable control. To remain effective under model-based control, these systems require dynamics models that can adapt to such changes, especially when direct access to complete environmental information is limited. To enable adaptability and facilitate integration with model predictive control, we propose a context-aware dynamics model based on neural ordinary differential equations, which infers environmental factors from state-action histories using a two-phase training procedure. We validate the approach across diverse robotic platforms, including a quadrotor in simulation, as well as a Sphero BOLT robot and a Fanuc manipulator in real-world experiments. The results demonstrate that our method effectively adapts to temporally and spatially varying environmental changes across different tasks. Videos are available at https://youtu.be/PY0sNyF2rqE , and the source code is available at https://github.com/syyu410-yu/context-aware-neural-ode-control.git .

Time series prototype learning is fundamentally challenged by observational ambiguity. Discrete architectures fail to resolve this, as they lack the capacity to decouple stochastic noise from continuous dynamics. Furthermore, rigid closed-set assumptions fail to capture unseen diversity. To address these limitations, we propose a hierarchical ordinary differential equation clustering network, which utilizes neural ordinary differential equation to model latent state evolution as a continuous integral curve. This formulation enforces temporal continuity to effectively disentangle smooth feature trends from stochastic noise, while our adaptive hierarchical mechanism autonomously determines the appropriate number of prototypes without rigid prior constraints. Validated on the early link failure detection task with irregularly sampled time series, the proposed method effectively extracts underlying physical prototypes, thereby enabling robust failure detection. Our code is available at https://github.com/NJ-LNN/Hierarchical-ODE.

In this work, we present COGENT, a continuous graph emulator with Neural Ordinary Differential Equations for long-term physical forecasting on irregular geospatial meshes. COGENT encodes a finite history of system states and associated forcing fields and external forcings with a graph-based history encoder, producing node-wise context vectors that capture both local spatial interactions and temporal evolution. These context vectors initialize and condition a latent Neural Ordinary Differential Equation whose dynamics are driven by interpolated future forcings and explicit relative rollout time. By modeling the forecast trajectory as a continuous latent dynamical system, COGENT can generate predictions at arbitrary future times rather than being restricted to a fixed temporal discretization. A residual decoder maps the resulting latent trajectories back to future physical states, enabling direct multi-step forecasting without repeatedly feeding predicted states back into the model. This formulation combines graph-based spatial representation, history-conditioned latent dynamics, and continuous-time rollout in a unified framework for mesh-based physical simulation emulation. In order to stabilize training with long-horizon supervision, we also propose effective rollout-horizon sampling and a progressive rollout-horizon scheduling strategy. We evaluate COGENT on transient ice-sheet simulations generated by the Ice-sheet and Sea-level System Model, demonstrating improved long-range stability over autoregressive graph baselines. These results suggest that continuous graph Neural ODEs provide a promising methodology for scalable physical forecasting on irregular geospatial meshes, particularly in applications that require stable long-horizon predictions and the ability to query system states at arbitrary times.

This work proves that an $n$-dimensional hybrid system can be embedded into an $m$-dimensional Euclidean space equipped with a continuous vector field on its embedded image whenever $m>2n$. This result suggests that an intrinsically discontinuous hybrid system generically admits a continuous extrinsic representation that is well-posed for differentiable optimization. Building on this existence theorem, we show that a latent Neural ODE with consistency loss in both the latent and state space can accurately recover the flow of hybrid systems. Extensive experiments suggest the proposed method outperforms the existing method in learning hybrid systems with varying geometries from only time series data.

Scientists have historically relied on mathematical models based on differential equations to relate system inputs -- forces, fluxes, or heat sources -- to outputs, such as displacement, velocity, concentration, and temperature. These models rely on deep domain knowledge to determine the form of the governing differential equation, which is then calibrated with data by solving an inverse problem. In recent years, the field of Scientific Machine Learning has introduced a variety of alternative modeling strategies for physical systems. A method called Sparse Identification of Nonlinear Dynamics learns the governing equation as a sparse linear combination of terms in a user-defined library. Neural Ordinary Differential Equations construct the governing equation by taking in the state and its derivatives at the input layer of a neural network. Entirely foregoing the modeling framework of differential equations, neural operators directly learn a non-linear mapping between the system inputs and outputs. From inverse problems to neural operators, all of these modeling strategies can be conceptualized as data-driven machinery to predict a system's response over a range of inputs. It is then natural to wonder how exactly these various strategies relate to each other, and whether they can be neatly taxonomized. Drawing from the philosophical literature on scientific models, we argue that many model types have a common structure, differing only in the assumed model class of the input-output relation they define. Connecting to philosophical ideas on mechanism, and arguing that data from physical systems arises from solutions to parsimonious differential equations, we propose that only certain models are capable of mechanism discovery, and thus generalization. Our analysis is intended to unite apparently disparate modeling strategies and provide insight into their appropriate use cases.

Vessel trajectory prediction from Automatic Identification System (AIS) data is essential for maritime situational awareness, yet it remains challenging due to irregular sampling, missing reports, and complex dynamics. Beyond accurate point forecasts, maritime applications also demand well-calibrated uncertainty estimates for reliable decision-making. Bayesian Neural Ordinary Differential Equations (ODEs) offer a principled framework for continuous-time trajectory modeling with uncertainty quantification by placing a prior over the neural vector field parameters. However, the commonly used isotropic Gaussian weight prior fails to encode informative structural properties of vessel dynamics, such as smoothness and locality. Existing function-space Bayesian neural network methods address this limitation for static mappings, but do not transfer directly to Neural ODEs, where the primary quantity of interest is the trajectory rather than the vector field itself. In principle, one could place a Gaussian process (GP) prior directly over ODE solutions, but this requires propagating distributions through a nonlinear ODE solver, which is analytically intractable. To address this challenge, we adopt a practical approach that imposes a GP-kernel-based prior directly on the vector field evaluated at a finite set of measurement points. Specifically, we augment the standard weight-space variational objective with a kernel-based regularizer that penalizes deviations of the vector field from the structure implied by a GP prior. To handle long and irregular AIS trajectories, we further combine this function-space regularization with probabilistic multiple shooting, which decouples inference across temporal segments while maintaining global consistency.

Advances in computational modeling, neuroimaging, and artificial intelligence are revolutionizing the modeling of neurological disorders for improved diagnostics, prognosis, and treatment planning. Mechanistic models provide valuable scientific insight into the disorders, but in practice they are often simplified with assumptions or computationally expensive and slow to solve. However, while purely data driven approaches provide speed and scalability, they require large, high quality data to train and generally suffer from interpretability and generalization issues. This perspective paper presents a structured overview of hybrid modeling strategies, which combine deep learning models with physics based solvers, and are categorized into parallel, series, and parallel-series architectures. Three main approaches that have been emphasized are residual modeling for missing or incomplete physics, Neural Ordinary Differential Equations (NODEs) for continuous time dynamics approximation, and solver in the loop that accelerates traditional solvers with neural approximations. These hybrid models integrate the governing differential equation based formulations and deep learning to characterize the evolution of neurological disorders, and promise advanced personalized neurological modeling. In addition, the study explores and proposes different hybrid configurations to improve diagnosis accuracy, predict disease progression, and inform treatment strategies across a range of neurological disorders. These capabilities outperform standalone mechanistic or purely data driven approaches, making hybrid modeling a powerful tool, especially in applications involving modeling the progression and treatment responses in neurological conditions such as brain tumors, Alzheimer's disease, and stroke.

Learning from demonstratins (LfD) is usually performed over Euclidean spaces, while the robot state, e.g. orientation, naturally evolves over curved spaces. Therefore, to ensure natural, complex motion generation, we investigate learning from demonstrations over Riemannian manifolds that are capable of encoding both position and orientation data. Here, geodesic paths provide for natural motion between two arbitrary points within the manifold. We propose to numerically estimate geodesics via neural ordinary differential equations, mitigating large computational overhead of existing approaches. Finally, these geodesics can be decoded back into the original task space before deploying on the robot. In this extended abstract, we discuss the architecture of our framework, provide some initial insights from our simulation experiments, including comparison to other geodesic computation mechanisms, and discuss the challenges and prospects for future work.

Neural rough differential equations (NRDEs) stay accurate under irregular sampling while taking far fewer integration steps than standard neural differential equations, summarising a finely sampled driver by its log-signature and advancing the hidden state over coarse intervals using the log-ODE method. This efficiency rests on the shuffle algebra, the algebraic counterpart of Stratonovich calculus. This reliance means NRDEs cannot expose the quadratic-variation terms Itô dynamics require, nor the ordered covariant derivatives that govern Itô flows on connection-equipped manifolds. Ameliorating this, we introduce Branched Neural Rough Differential Equations (B-NRDEs), a Hopf-algebraic framework that recasts the NRDE log-ODE step as geometric numerical integration on the state-space manifold, matching the driving algebra to the governing calculus: Grossman--Larson rooted trees for Euclidean Itô dynamics, Munthe-Kaas--Wright planar rooted trees for ordered covariant derivatives on manifolds, and the shuffle algebra in the classical Stratonovich case. This yields intrinsic coarse-step dynamics that exactly preserve manifold constraints. Finally, we introduce a branched signature-kernel objective to enable Itô-consistent law matching by making quadratic-variation terms visible during training. On rough Bergomi volatility, sim-to-real $\mathrm{SO}(3)$ dynamics forecasting, and SPD covariance dynamics, B-NRDEs offer a unified, effective approach to stochastic and manifold-valued dynamics beyond the Euclidean--Stratonovich setting.

Accurate prediction of polymerization dynamics is essential for process design, control, and optimization. Yet, purely mechanistic models require labor-intensive parameterization of partially characterized kinetics, while purely data-driven models demand large, diverse datasets that are costly to obtain, particularly in early-design stages. We propose a hybrid Neural Ordinary Differential Equation (NODE) framework for data-efficient modeling of free-radical polymerization. Using batch polymerization of methyl methacrylate (MMA) as a case study, the mechanistic mass balances are retained explicitly, and only the partially-characterized effective radical concentration governing monomer consumption is learned from data through a neural network surrogate, while established reactions such as initiator decomposition, propagation, and termination remain physically modeled. The hybrid NODE is evaluated against a discrete-time feedforward neural network and a purely data-driven NODE under sparse data conditions, with models trained on as few as ten measurements under both regular and irregular sampling. The hybrid NODE consistently achieves lower prediction errors and more physically consistent extrapolations than both purely data-driven baselines. In a generalization scenario with noisy data and unseen operating conditions, the hybrid NODE achieves an RMSE of 0.013, compared to 0.31 for the data-driven NODE and 0.68 for the discrete-time model, demonstrating that learning only a closure term rather than the full dynamics is sufficient for reliable prediction under limited data availability.

Counterfactual explanations (CEs) are essential for actionable recourse, yet their reliability is often compromised in low-density regions, where classifiers exhibit high variance. Unlike existing methods that rely on expensive ensemble intersections to define stability, we propose \textit{DensityFlow}, a generative framework that constructs robust CEs by adhering to the high-confidence data manifold. Specifically, we model the counterfactual generation as continuous-time dynamics parameterized by Neural ODE, guided by a differentiable density score to actively avoid uncertain, low-density areas. This density score is learned via Noise Contrastive Estimation, effectively leveraging a $(K{+}1)$-way discriminator to estimate density ratios. For black-box settings, we introduce a local proxy distillation mechanism that aligns a lightweight surrogate with the target model strictly within the trajectory of CE generation, enabling efficient gradient-based optimization with minimal queries. Experiments demonstrate that \textit{DensityFlow} achieves superior validity under model multiplicity while significantly reducing query costs compared to ensemble-based baselines. Our implementation is available at https://github.com/G-AILab/DensityFlow.

Continuous-time models are a natural choice for irregular and asynchronous data. A central design choice is how to embed discrete observations into continuous time. Interpolation- and imputation-based embeddings reconstruct a continuous observation path, making the model sensitive to the choice of reconstruction. We show that this reconstruction step is unnecessary; under mild conditions, compact-set universality on the model input space transfers to the data space whenever the embedding from data to input is continuous and injective. Guided by this result, and building on the rectilinear control path for Neural Controlled Differential Equations (NCDEs), we introduce a continuous and injective embedding for Log-NCDEs, a universal class of continuous-time models. Our approach records observations as increments and composes them over arbitrary query intervals to directly form log-signatures. This provides interval-level summaries without first interpolating the observed variables, while supporting online computation. Experiments on synthetic controlled dynamics and real-world time-series datasets show that the representation is accurate, efficient, and robust to irregular, asynchronous, and sparse observations.

Recent work on the sequence universality of State Space Models (SSMs) has introduced efficient, maximally expressive continuous-time approaches for time-series modelling. While these works focus on discriminative settings, we extend this perspective to generative time-series modelling by proving that maximally expressive Structured Linear Controlled Differential Equations (SLiCEs) are universal time-series generators, in the sense that they can approximate the induced path laws of continuous causal pushforwards on compact latent sets in $W_\infty$. Building on these theoretical results, we propose Generative SLiCEs (G-SLiCEs), a maximally expressive continuous-time model for flow matching on path-space. Empirically, we show that expressivity improves performance in probabilistic forecasting and downstream tasks, while retaining the advantages of continuous-time models such as generalising to arbitrary observation grids. This is particularly beneficial for irregular grids, where fixed-grid models often struggle.

We propose Lie group embedded dynamical neural networks (LieEDNN) and the corresponding learning algorithms based on gradient descent and metric projection on smooth manifold, where we treat Lie group as an intrinsic representation for continuous symmetry of manifold geometry. Thereby we achieve learnable and stable dynamics on the underlying manifold for general Lie group, and we are able to utilize the powerful representation capability of Lie group such as SO(3) and SE(3) to solve real world engineering problems in areas such as robotics, graphics, and control. Two core challenges are: (i) General Lie groups are incompatible with addition arithmetic, which is necessary for neural network interactions. (ii) The dynamics evolve in the nonlinear representation space of special algebra rather than the normal Euclidean space, which violates the paradigm of common neural ODEs. To address these two challenges, we firstly introduce adjoint Lie group action on the Lie algebra, which induces a linear mapping and transfer to the block-wise structure of weight matrices, such that addition could operate on the Lie algebra as a vector space. Then we parameterize the Lie algebra and the adjoint action as linear transformation so that the architecture is aligned with neural network perceptrons. Explicitly, this embedding appears as block-wise manifold constraints on weights, and we develop algorithms to learn the equilibrium with stability guarantees of the temporal neural network dynamics. Experiments are implemented on a specific Lie group SE(3), with the application scenario of telescopic manipulators.

Temporal surrogate models are effective for predicting chaotic dynamical systems where computational cost can be prohibitive. Several deep neural network architectures can be used for such purposes. In this work, a few commonly used architectures are compared using a common training protocol. The objective is to fairly assess the impact of model architectures for long-horizon prediction stability. Experiments are carried out for three problems, the double pendulum, the Kuramoto-Sivashinsky equations, and the Kolmogorov flow. The experiments are carried out with matching model capacity. Analysis is also carried out for a scenario where each model is individually optimized. It is observed that in both scenarios, the models exhibit categorical differences in long-horizon rollouts. For a concrete quantification, stepwise error injections and perturbation amplifications are analyzed using metrics such as local jacobian, relative one-step bias, and finite-time Lyapunov growth. Additionally, an attractor analysis is also conducted to assess how well the learned models replicate the underlying system geometry. An ablation study to isolate the impact of each component of a continuous-update architecture is also carried out. It is concluded that models that having integrator-like updates show lower bias and perturbation amplification yielding stable long-horizon rollout and more accurate predictions.

Ordinary differential equation models of biochemical reactions are often formulated as stoichiometric systems in which the dynamics arise from a collection of interacting processes. A central challenge is that the functional form of each process is rarely known a priori and may be difficult to infer from data. We propose biochemically informed neural ordinary differential equations (BINODEs), a neural-ODE framework that retains the stoichiometric structure of mechanistic models while representing individual processes by neural networks. In BINODEs, the outputs of neural network processes (NNPs) are mapped to state derivatives through a linear layer analogous to a stoichiometric matrix. This architecture allows biological side information, such as process-specific inputs, sign constraints, and monotonicity assumptions, to be built directly into the model. We characterize the approximation properties of NNPs for several standard biochemical rate laws and show that the proposed framework recovers both trajectories and process-level structure in Monod, Lotka--Volterra, pharmacokinetic, and ultradian endocrine models. These results suggest that BINODEs offer a useful compromise between mechanistic interpretability and data-driven flexibility for modeling partially known biochemical or biological dynamical systems.

When learning dynamical systems from data, embedding physical structure can constrain the solution space and improve generalization, but many physics-informed models assume access to the full system state. This limits their use in partially observed settings, where some state variables are completely unobserved and must be inferred without direct supervision. Here, we present neural Hamiltonian ordinary differential equations (NHODE), a framework that combines Hamiltonian neural networks (HNNs) with neural ordinary differential equations (neural ODEs) to learn partially observed dynamical systems from data. The Hamiltonian structure enforces energy conservation by construction, while the neural ODE framework enables a flexible training procedure that allows the loss to be defined only on observed variables. We also incorporate additional physical constraints through symmetry-aware coordinate transformations and separable energy formulations. The framework is evaluated on systems of increasing complexity, from linear and nonlinear mass-spring systems to the chaotic three-body problem. Across all examples, increasing the amount of embedded physical structure improves the accuracy and long-horizon stability of the predictions. Even in the most challenging regimes, the NHODE framework captures both observed and latent dynamics, whereas purely data-driven baselines become unstable.

Complex dynamical systems governed by holomorphic maps such as $z^2 + c$ exhibit fractal boundaries with extreme sensitivity to initial conditions. Accurately modelling these structures from data requires methods that respect the underlying complex-analytic geometry, yet Multi-Layer Perceptrons (MLPs) within Neural Ordinary Differential Equations (Neural ODEs) lack complex-analytic priors, violate the Cauchy--Riemann conditions, and function as opaque approximators incapable of yielding governing equations. We introduce Holomorphic KAN-ODE, a framework that replaces the MLP with a Kolmogorov-Arnold Network (KAN) whose learnable B-spline activations reside on network edges, and incorporates Cauchy--Riemann equations as a differentiable regularization to preserve holomorphic structure. We evaluate on six families of complex dynamical systems spanning polynomial and transcendental classes. With only 280 parameters ($16\times$ fewer than the MLP baseline), the network achieves velocity-field $R^2 > 0.95$ on all six systems, correctly identifies all six governing symbolic families through automatic spline-to-formula fitting, and reconstructs Julia set fractal boundaries with up to 98.0% agreement. Crucially, the model exhibits only 4% MSE degradation under 10% observation noise versus $15.2\times$ for MLPs, and achieves 90.4% improvement in transfer learning from quadratic to cubic dynamics. While the MLP attains lower pointwise reconstruction error due to its larger capacity, the KAN uniquely provides interpretable symbolic equations, enforced holomorphic structure, and superior noise resilience, capabilities that are entirely absent in black-box architectures. These results establish KANs as a parameter-efficient, interpretable alternative to MLPs for physics-informed discovery of holomorphic dynamics.

Neural processes amortize Gaussian process inference, replacing the exact $O(n^3)$ posterior with a learned $O(n)$ map from context sets to predictive distributions. For a class of latent neural processes, we bound the Kullback--Leibler (KL) divergence between the GP and LNP predictives, decomposing it into three interpretable sources, namely label contamination as the neural process uses label values to estimate a quantity that is label-independent in the exact GP, an information bottleneck because the finite-dimensional representation cannot resolve the full context geometry, and amortization error from a single encoder network shared across all contexts. The bottleneck truncation term decays in the representation dimension $d$ as $O(e^{-cd^{2/d_x}})$ for squared-exponential kernels on $\mathbb{R}^{d_x}$ where $c > 0$ is a kernel-dependent constant and as $O(d^{-2ν/d_x})$ for Matérn-$ν$ kernels, directly linking architecture sizing to kernel smoothness and input dimension. The label contamination term is $O(1)$ in general, with only the observation-noise component decaying as $O(1/n)$, identifying a persistent cost of routing uncertainty estimation through a label-dependent representation. These results characterize the costs of amortization within the analyzed class and yield architectural recommendations to predict variance from context locations alone in the GP-amortization regime, and replace mean aggregation with second-order pooling to close the dominant amortization gap.

Single-cell RNA sequencing provides insights into gene expression at single-cell resolution, yet inferring temporal processes from these static snapshot measurements remains a fundamental challenge. Current approaches utilizing neural differential equations and flows are sensitive to overfitting and lack careful considerations of biological variability. In this work, we propose a generative framework that models population trends using a latent heteroscedastic Gaussian process (GP) approximated by Hilbert space methods. To address the absence of genuine cell trajectories, we leverage an optimal transport (OT) objective that aligns generated and observed population distributions. Our method explicitly captures biological heterogeneity by incorporating cell-specific latent time and cell type conditioning to disentangle temporal asynchrony and trajectories to different cell types. We demonstrate state-of-the-art performance on complex interpolation and extrapolation benchmarks and introduce a novel gradient-based strategy for inferring perturbation trajectories.

Functional MRI data exhibit high-dimensional spatiotemporal structure, making both prediction and decoding challenging. In this work, we investigate neural integral-operator-based models for encoding and decoding tasks in fMRI, with particular emphasis on the role of nonlocal spatiotemporal context. We implement a latent neural integral operator framework that performs fixed point iterations in an auxiliary space from which classification and stimuli prediction is performed via a decoder. We evaluate our model on two open-source fMRI datasets. Our experiments examine both decoding of stimuli from fMRI recordings and encoding of fMRI dynamics from stimulus representations. A main focus is the effect of spatiotemporal context: we systematically compare short and long temporal windows, as well as the use of visual cortex vs whole brain recordings, and analyze their influence on performance and latent-space geometry. Across tasks and datasets, larger temporal windows generally improve results and produce more structured learned representations. In decoding experiments, the learned latent space often provides clearer class separation than the raw data. In encoding experiments, although absolute performance remains moderate due to the difficulty of the task, longer temporal windows still yield consistent gains. These findings suggest that neural integral operators provide a promising framework for modeling fMRI dynamics and that broader spatiotemporal context can be beneficial for both prediction and representation learning. More broadly, the results indicate that exploiting distributed nonlocal structure in brain dynamics requires model architectures specifically designed to capture such dependencies.

Efficient neural network models that generate brain-like dynamic activity can be a valuable resource for generating synthetic data, analyzing differences in brain transients under conditions such as testing perturbation activity or inferring the underlying generative dynamics. However, large language models (LLMs) or standard recurrent neural networks (RNNs) ignore the anatomical organization and therefore do not produce components that align with brain regions. On the other hand, graph-based networks often have very simple message passing rules that are not sufficiently expressive for brain-like dynamics. To address this, we introduce BrainDyn, a sheaf neural ordinary differential equation (neural ODE) model for continuous-time dynamics on structured brain graphs. BrainDyn encodes the recent activity history of each brain region using a long short-term memory (LSTM) model over a sliding temporal window to produce hidden states, or stalks, that are projected through learnable restriction maps into edge-specific shared spaces. Discrepancies between neighboring nodes in these shared spaces are characterized by a sheaf Laplacian that can facilitate message passing between neuronal units. The output of these messages is then fed to a neural ODE that governs the continuous-time evolution of neuronal activity. We evaluated BrainDyn on resting-state fMRI (PNC dataset), scalp EEG with focal epilepsy (TUSZ dataset), and simulated activity from the NEST spiking network simulator. BrainDyn achieves strong forecasting ability across modalities, and the resulting representations support downstream tasks including in silico perturbation prediction.

Transformers have become the dominant architecture in modern machine learning, yet the theoretical understanding of their training dynamics remains limited. This paper develops a rigorous mathematical framework for analyzing gradient-based training of transformers in the mean-field regime, where both the depth (number of layers) and width (number of attention heads) tend to infinity. While ResNet training can be understood as controlling a neural ODE, transformer training corresponds to controlling a neural PDE, due to the coupling of multiple token distributions through the attention mechanism. Our mean-field model features two types of measure representations: token distributions evolving through layers and attention parameters at each layer. We establish well-posedness of the forward pass through infinitely deep transformers, characterizing token evolution via flow maps that satisfy ODEs in function spaces. Using adjoint sensitivity analysis, we derive an explicit formula for the conditional Wasserstein gradient of the training risk, involving adjoint variables governed by backward ODEs. We prove the existence and uniqueness of gradient flow curves in the conditional Wasserstein metric space, establishing a rigorous foundation for gradient-based transformer training. A key technical contribution is providing necessary and sufficient conditions for injectivity of the Neural Tangent Kernel (NTK) for attention mechanisms: we show that NTK injectivity is equivalent to linear independence of log-sum-exp functions modulo affine functions, a condition satisfied by diverse token distributions, including discrete distributions, uniform distributions, and Gaussian mixtures. Under this NTK injectivity assumption, we prove that gradient flow converges to global minima when the initial loss is sufficiently small, eliminating spurious local minima from the optimization landscape.

A diffusion model trained on Hamiltonian trajectories can achieve rollout MSE near $10^{-3}$, but the standard deviation of its energy over time is between 7500 and 36000 times larger than the ground-truth energy standard deviation, indicating a failure to preserve conservation laws. This gap motivates our central question of whether neural networks can learn or select globally conserved quantities from physical trajectories. We investigate this across three Hamiltonian systems: projectile motion, pendulum, and spring-mass. We use a structured $T(v)+V(q)$ energy model, a black-box Conservation Discovery Network (CDN), a polynomial CDN, and a conditional diffusion baseline. The structured network reaches $R^2 \geq 0.9999$ against analytical energy on clean data, while the black-box CDN reaches $R^2 \geq 0.996$ when trained with temporal consistency plus a small alignment loss to analytical energy at $t=0$ ($λ_{\mathrm{align}}=0.2$). With $λ_{\mathrm{align}}=0$, CDN Pearson $R^2$ collapses on pendulum and spring-mass ($< 10^{-3}$), showing that temporal consistency alone is not enough to reliably identify the true energy. Under $1\%$ additive Gaussian noise, the CDN outperforms the structured model on the projectile and spring-mass systems, suggesting that the CDN may be more robust to noisy inputs in this setting. However, the polynomial CDN is sensitive to training configuration: it achieves $R^2=0.78$ under a short training schedule on the pendulum system, but reaches $R^2=0.9998$ with more training time and data, regardless of whether noise is added.

Neural ordinary differential equations (Neural ODEs) often fit training trajectories while generalizing poorly to unseen initial conditions and long horizons. We propose MPINeuralODE, which combines a soft physics-informed residual with a Multiple-Initial-Condition (MIC) multiple-shooting curriculum whose ingredients are structurally complementary: the physics term anchors the vector-field magnitude on the support that MIC enlarges. We evaluate along three axes: out-of-sample error, long-horizon stability, and Hamiltonian drift, which together expose whether the learned dynamics recover the underlying vector field. On Lotka-Volterra, MPINeuralODE achieves the lowest out-of-sample and long-horizon MSE among data-driven methods, with a 24% reduction over the baseline Neural ODE, while essentially matching the PINN ablation on Hamiltonian drift.

We introduce steerable neural ordinary differential equations on homogeneous spaces $M=G/H$. These models constitute a novel geometric extension of manifold neural ordinary differential equations (NODEs) that transport associated feature vectors transforming under the local symmetry group $H$. We interpret features as sections of associated vector bundles over $M$, and describe their evolution as parallel transport. This results in a coupled system of ODEs consisting of a flow equation on $M$ and a steering equation acting on features. We show that steerable NODEs are $G$-equivariant whenever the vector field generating the flow and the connection governing parallel transport are both $G$-invariant. Furthermore, we demonstrate how steerable NODEs incorporate existing NODE models and continuous normalizing flows on Lie groups. Our framework provides the geometric foundation for learning continuous-time equivariant dynamics of general vector-valued features on homogeneous spaces.