Coupled spatiotemporal forecasting is important for predicting the future evolution of multiple interacting dynamical systems, such as in climate models. However, existing methods are severely constrained by the persistent bottleneck of compounding errors. In coupled systems, errors from each subsystem simulator propagate and amplify one another, a phenomenon we term Reciprocal Error Amplification leading to a rapid collapse of long-range predictions. To address this challenge, we propose a universal framework called PnP-Corrector (Plug-and-Play Corrector). The core idea of our framework is to decouple the physical simulation from the error correction process: it freezes pre-trained physics simulation engines and exclusively trains a lightweight correction agent to proactively counteract the systematic biases emerging from the coupled system. Furthermore, we design an efficient predictive model architecture, DSLCast, to serve as the backbone of this framework. Extensive experiments demonstrate that our method significantly enhances the long-term stability and accuracy of coupled forecasting systems. For instance, in the challenging task of a 300-day global ocean-atmosphere coupled forecast, our PnP-Corrector framework reduces the prediction error of the baseline model by 28% and surpasses state-of-the-art models on several key metrics. Codes link: \url{https://anonymous.4open.science/r/Anonymous_PnP-E365}.
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General Machine Learning · Sequential, Network, and Time Series Modeling
We present Mesh Field Theory (MeshFT) and its neural realization, MeshFT-Net: a structure-preserving framework for mesh-based continuum physics that cleanly separates the physics’ topological structure from its metric structure. Imposing minimal physical principles (locality, permutation equivariance, orientation covariance, and energy balance/dissipation inequality), we prove a reduction theorem for mesh-based physics. Under these conditions, the physical dynamics admit a local factorization into a port–Hamiltonian form: the conservative interconnection is fixed uniquely by mesh topology, whereas metric effects enter only through constitutive relations and dissipation. This reduction clarifies what must be fixed and what should be learned, directly informing MeshFT-Net’s design. Across evaluations on analytic and realistic datasets, physics-consistency tests, and out-of-distribution validation, MeshFT-Net achieves near-zero energy drift and strong physical fidelity (correct dispersion and momentum conservation) along with robust extrapolation and high data efficiency. By eliminating non-physical degrees of freedom and learning only metric-dependent structure, MeshFT provides a principled inductive bias for stable, faithful, and data-efficient learning-based physical simulation.
Applications · Chemistry, Physics, and Earth Sciences
Chaos arises in many complex dynamical systems, from weather to power grids, but is difficult to accurately model using data-driven emulators, including neural operator architectures. For chaotic systems, the inherent sensitivity to initial conditions makes exact long-term forecasts theoretically infeasible, meaning that traditional squared-error losses often fail when trained on noisy data. Recent work has focused on training emulators to match the statistical properties of chaotic attractors by introducing regularization based on handcrafted local features and summary statistics, as well as learned statistics extracted from a diverse dataset of trajectories. In this work, we propose a family of adversarial optimal transport objectives that jointly learn high-quality summary statistics and a physically consistent emulator, all from a single trajectory. We theoretically analyze and experimentally validate a Sinkhorn divergence formulation (2-Wasserstein) and a WGAN-style dual formulation (1-Wasserstein). Our experiments across a variety of chaotic systems, including systems with high-dimensional chaotic attractors, show that emulators trained with our approach exhibit significantly improved long-term statistical fidelity.
Deep Learning · Generative Models and Autoencoders
We propose a methodology that combines generative latent diffusion models with physics-informed machine learning to generate solutions of parametric partial differential equations (PDEs) conditioned on partial observations, which includes, in particular, forward and inverse PDE problems. We learn the joint distribution of PDE parameters and solutions via a diffusion process in a latent space of scaled spectral representations, where Gaussian noise corresponds to functions with controlled regularity. This spectral formulation enables significant dimensionality reduction compared to grid-based diffusion models and ensures that the induced process in function space remains within a class of functions for which the PDE operators are well defined. Building on diffusion posterior sampling, we enforce physics-informed constraints and measurement conditions during inference, applying Adam-based updates at each diffusion step. We evaluate the proposed approach on Poisson, Helmholtz, and incompressible Navier--Stokes equations, demonstrating improved accuracy and computational efficiency compared with existing diffusion-based PDE solvers, which are state of the art for sparse observations. Code is available at https://anonymous.4open.science/r/PISD-32A0/.
Probabilistic Methods · Everything Else
Dominant approaches for modelling Partial Differential Equations (PDEs) rely on deterministic predictions, yet many physical systems of interest are inherently chaotic and uncertain. While training probabilistic models from scratch is possible, it is computationally expensive and fails to leverage the significant resources already invested in high-performing deterministic backbones. In this work, we adopt a training-efficient strategy to transform pre-trained deterministic models into probabilistic ones via retrofitting with a proper scoring rule: the Continuous Ranked Probability Score (CRPS). Crucially, this approach is architecture-agnostic: it applies the same adaptation mechanism across distinct model backbones with minimal code modifications. The method proves highly effective across different scales of pre-training: for models trained on single dynamical systems, we achieve $20–54\%$ reductions in rollout CRPS and up to $30\%$ improvements in variance-normalised RMSE (VRMSE) relative to compute-matched deterministic fine-tuning. We further validate our approach on a PDE foundation model, trained on multiple systems and retrofitted on the dataset of interest, to show that our probabilistic adaptation yields an improvement of up to $40\%$ in CRPS and up to $15\%$ in VRMSE compared to deterministic fine-tuning. Validated across diverse architectures and dynamics, our results show that probabilistic PDE modelling need not require retraining from scratch, but can be unlocked from existing deterministic backbones with modest additional training cost.
Applications · Chemistry, Physics, and Earth Sciences
We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and refining structural details over scales. To achieve this, PAR consists of three key components: (i) multi-scale downsampling operations that represent protein structures across multiple scales during training; (ii) an autoregressive transformer that encodes multi-scale information and produces conditional embeddings to guide structure generation; (iii) a flow-based backbone decoder that generates backbone atoms conditioned on these embeddings. Moreover, autoregressive models suffer from exposure bias, caused by the training and the generation procedure mismatch, and substantially degrades structure generation quality. We effectively alleviate this issue by adopting noisy context learning and scheduled sampling, enabling robust backbone generation. Notably, PAR exhibits strong zero-shot generalization, supporting flexible human-prompted conditional generation and motif scaffolding without requiring fine-tuning. On the unconditional generation benchmark, PAR effectively learns protein distributions and produces backbones of high design quality, and exhibits favorable scaling behavior. Together, these properties establish PAR as a promising framework for protein structure generation.
Applications · Chemistry, Physics, and Earth Sciences
We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and refining structural details over scales. To achieve this, PAR consists of three key components: (i) multi-scale downsampling operations that represent protein structures across multiple scales during training; (ii) an autoregressive transformer that encodes multi-scale information and produces conditional embeddings to guide structure generation; (iii) a flow-based backbone decoder that generates backbone atoms conditioned on these embeddings. Moreover, autoregressive models suffer from exposure bias, caused by the training and the generation procedure mismatch, and substantially degrades structure generation quality. We effectively alleviate this issue by adopting noisy context learning and scheduled sampling, enabling robust backbone generation. Notably, PAR exhibits strong zero-shot generalization, supporting flexible human-prompted conditional generation and motif scaffolding without requiring fine-tuning. On the unconditional generation benchmark, PAR effectively learns protein distributions and produces backbones of high design quality, and exhibits favorable scaling behavior. Together, these properties establish PAR as a promising framework for protein structure generation.
General Machine Learning · Causality
The problem of domain generalization concerns learning predictive models that are robust to distribution shifts when deployed in new, previously unseen environments. Existing methods typically require labeled data from multiple training environments, limiting their applicability when labeled data are scarce. In this work, we study domain generalization in an anti-causal setting, where the outcome causes the observed covariates. Under this structure, environment perturbations that affect the covariates do not propagate to the outcome, which motivates regularizing the model's sensitivity to these perturbations. Crucially, estimating these perturbation directions does not require labels, enabling us to leverage unlabeled data from multiple environments. We propose two methods that penalize the model's sensitivity to variations in the mean and covariance of the covariates across environments, respectively, and prove that these methods have worst-case optimality guarantees under certain classes of environments. Finally, we demonstrate the empirical performance of our approach on a controlled physical system and a physiological signal dataset.
Deep Learning · Foundation Models
AI applications have shifted from single, mono-lithic foundation models (FM) to compound agentic systems. Yet today’s stacks remain fragmented: even as protocols (e.g., MCP, A2A) ease tool/agent connectivity, each framework embeds an implicit runtime for state, memory, budgets, and guardrails, making behavior non-portable and governance brittle. It mirrors computing before operating systems, when every program re-implemented basic services. This position paper argues that the field now needs a Foundation Model Operating System (FMOS): a system layer that virtualizes FM interactions analogous to how virtual machines abstract physical hardware, giving applications the illusion of dedicated, trustworthy FM instances with effectively unbounded capabilities. Internally, the FMOS orchestrates knowledge across memory tiers, model selection and resource allocation, and verification and policy enforcement. Like the human brain switching between fast intuition and slow deliberation, the FMOS learns when to intervene and when to let inference proceed directly and continuously adapting its policies based on operational experience.
Applications · Computer Vision
Privacy protection has become a critical requirement in the era of ubiquitous visual data sharing, imposing higher demands on efficient and robust privacy detection algorithms. However, current robust detection models are severely hindered by the lack of comprehensive datasets. Existing privacy-oriented datasets often suffer from limited scale, coarse-grained annotations, and narrow domain coverage, failing to capture the intricate details of sensitive information in real-world environments. To bridge this gap, we present a large-scale, fine-grained Visual Privacy Dataset (VPD-100K), designed to facilitate generalized privacy detection. We establish a holistic taxonomy comprising four primary domains: Human Presence, On-Screen Personally Identifiable Information (PII), Physical Identifiers, and Location Indicators, containing 100,000 images annotated with 33 fine-grained classes and over 190,000 object instances. Statistical analysis reveals that our dataset features long-tailed distributions, small object scales, and high visual complexity. These characteristics make the dataset particularly valuable for demanding, unconstrained applications such as live streaming, where actors frequently face unintentional, real-time information leakage. Furthermore, we design an effective frequency-enhance lightweight module consisting of frequency-domain attention fusion and adaptive spectral gating mechanism that breaks the limitations of spatial pixel intensity to better capture the subtle details of sensitive information. Extensive experiments conducted on both diverse image and streaming videos benchmarks consistently demonstrate the effectiveness of our VPD-100K dataset and the well-curated frequency mechanism.
Applications · Chemistry, Physics, and Earth Sciences
Sampling from unnormalized probability densities is a central challenge in computational science. Boltzmann generators are generative models that enable independent sampling from the Boltzmann distribution of physical systems at a given temperature. However, their practical success depends on data-efficient training, as both simulation data and target energy evaluations are costly. To this end, we propose off-policy log-dispersion regularization (LDR), a novel regularization framework that builds on a generalization of the log-variance objective. We apply LDR in the off-policy setting in combination with standard data-based training objectives, without requiring additional on-policy samples. LDR acts as a shape regularizer of the energy landscape by leveraging additional information in the form of target energy labels. The proposed regularization framework is broadly applicable, supporting unbiased or biased simulation datasets as well as purely variational training without access to target samples. Across all benchmarks, LDR improves both final performance and data efficiency, with sample efficiency gains of up to one order of magnitude.
Deep Learning · Large Language Models
Geo-temporal understanding, the ability to infer location, time, and contextual properties from visual input alone, is a core aspect of human intelligence and underpins applications such as disaster management, traffic planning, embodied navigation, world modeling, and geography education. Although recent vision–language models (VLMs) have made progress in image geo-localization using salient cues like landmarks or road signs, their ability to reason about temporal signals and physically grounded spatial cues remains underexplored. To address this gap, we introduce ***TimeSpot***, a benchmark for evaluating real-world geo-temporal reasoning in VLMs. ***TimeSpot*** consists of 1,455 ground-level images from 80 countries and requires structured prediction of temporal attributes (season, month, time of day, daylight phase) and geographic attributes (continent, country, climate zone, environment type, latitude-longitude) directly from visual evidence. The benchmark further includes spatial–temporal reasoning tasks that probe physical plausibility and cue integration under real-world uncertainty. Evaluations of state-of-the-art open- and closed-source VLMs show consistently low performance, particularly for temporal inference, and while supervised fine-tuning yields measurable gains, it remains insufficient, highlighting the need for new approaches to achieve robust, physically grounded geo-temporal understanding. By jointly evaluating spatial and temporal inference with diagnostic rigor, ***TimeSpot*** provides a principled framework for assessing physically grounded, real-world geo-temporal reasoning. We will release ***TimeSpot*** upon acceptance.
Generating physically consistent 3D tabletop scenes is a fundamental yet underexplored problem for interactive and generalist robotic learning. The challenge stems from dense object hierarchies and irregular affordances. Existing methods, ranging from decoupled symbolic solvers to end-to-end regression models, often suffer from error propagation or overfitting to noisy supervision containing widespread physical violations. To address these limitations, we introduce PhyScene3D, a framework that reformulates generation as a Human-Mimetic Constructive Process. The proposed Cognitive Topological Reasoning Chain (CTRC) factorizes scene synthesis into a sequential, anchor-conditioned process under the novel 3D Axis-Aligned Bounding Box (3D AABB)-based placement scheme, thereby imposing a strong structural inductive bias. To address imperfect supervision and physical infeasibility, we introduce Physics-Aware Denoising Alignment (PADA), which integrates a differentiable Signed Distance Field (SDF) with Test-Time Optimization (TTO) to project generated scenes onto a physics-feasible manifold while preserving semantic intent. Experiments demonstrate that PhyScene3D outperforms state-of-the-art approaches in both semantic accuracy and physical validity, achieving a 40\% reduction in collision rate relative to the human-annotated training data.
Applications · Language, Speech and Dialog
Diffusion models have recently set new benchmarks in Speech Enhancement (SE). However, most existing score-based models treat speech spectrograms merely as generic 2D images, applying uniform processing that ignores the intrinsic structural sparsity of audio, which results in inefficient spectral representation and prohibitive computational complexity. To bridge this gap, we propose **DVPD**, an extremely lightweight **D**ual-**V**iew **P**redictive **D**iffusion model, which uniquely exploits the dual nature of spectrograms as both visual textures and physical frequency-domain representations across both training and inference stages. Specifically, during training, we optimize spectral utilization via the Frequency-Adaptive Non-uniform Compression (FANC) encoder, which preserves critical low-frequency harmonics while pruning high-frequency redundancies. Simultaneously, we introduce a Lightweight Image-based Spectro-Awareness (LISA) module to capture features from a visual perspective with minimal overhead. During inference, we propose a Training-free Lossless Boost (TLB) strategy that leverages the same dual-view priors to refine generation quality without any additional fine-tuning. Extensive experiments across various benchmarks demonstrate that DVPD achieves state-of-the-art performance while requiring only **35** of the parameters and **40%** of the inference MACs compared to SOTA lightweight model, PGUSE. These results highlight DVPD's superior ability to balance high-fidelity speech quality with extreme architectural efficiency. Code and audio samples are available at the anonymous website: https://anonymous.4open.science/r/dvpd_demo-E630
Applications · Chemistry, Physics, and Earth Sciences
Current computer-aided synthesis planning (CASP) methods often treat retrosynthesis as solved once a single feasible route is identified, focusing primarily on convergence or shortest-path metrics. This view is misaligned with real-world practice, where chemists must balance competing objectives such as cost, sustainability, toxicity, and overall yield. To address this, we formulate synthesis planning as a multi-objective search problem and introduce MORetro$^\ast$, an algorithm that generates a Pareto front of synthesis routes to explicitly capture trade-offs between user-defined criteria. MORetro$^\ast$ uses weighted scalarization and solution-informed sampling to efficiently navigate the combinatorial search space and prioritize promising trade-offs. Building on multi-objective A$^\ast$-search, we provide optimality guarantees showing that, for a fixed single-step model, MORetro$^\ast$ recovers the true Pareto front. Across multiple retrosynthesis benchmarks, MORetro$^\ast$ produces diverse, high-quality Pareto fronts, uncovering solutions overlooked by single-objective approaches and better aligning CASP outputs with industrial decision-making.
Applications · Neuroscience, Cognitive Science
Multi-compartment Hodgkin–Huxley (HH) models provide a principled framework for predicting neural dynamics and responses to electrical stimulation. However, fitting HH biophysical parameters typically requires intracellular recordings, which are invasive and low-throughput, limiting the ability to capture the geometry and cell-specific properties of many neurons in a given neural circuit. Multi-electrode arrays (MEAs) offer a scalable alternative—high-density extracellular measurements from full neural populations—but HH model complexity has so far precluded reliable biophysical inference from extracellular data alone. Here, we introduce a framework that rapidly infers HH parameters from designed features of extracellular MEA measurements by leveraging differentiable biophysical simulation and simulation-based inference, unlocking a wide range of downstream applications. In this work, we focus on a central goal of translational neuroengineering: predicting neural spiking responses to candidate neurostimulation patterns that would take hours to measure clinically. To validate our approach, we collected hundreds of hours of stimulation and recording data from isolated macaque retina with a 30 µm-pitch 512-electrode array. Our framework predicted previously unseen multi-electrode stimulation responses with 90.4\% accuracy using HH models fit from only a few minutes of recording, replacing hours of stimulus testing.
Deep Learning · Other Representation Learning
Learning from geometrically structured data is central to applications in biology, physics, and computer vision. In many tasks, meaningful comparisons depend on how features are aligned in space. Graph Neural Networks capture local structure but are constrained by message passing. Transformers model long-range dependencies but largely ignore geometry. We introduce the Vector Bundle Attention Transformer (VBA-Transformer), a framework that redefines attention as an intrinsic geometric operator. Each token couples a base manifold coordinate with a fiber feature vector, following vector bundle theory. A principled parallel transport mechanism aligns fiber features across local coordinate systems before similarity is computed. This embeds geometry directly into the attention operator. Unlike prior methods that inject geometry as an external bias or positional encoding, VBA integrates geometry natively inside attention. On challenging single-cell RNA sequencing benchmarks, VBA achieves state-of-the-art accuracy, outperforming Transformer baselines by over 3--5\%. On spatial transcriptomics, it demonstrates superior clustering performance. On 3D point clouds, it achieves competitive accuracy, validating broad generalization across domains. Beyond empirical gains, we provide theoretical analysis of invariance and perturbation stability. We also demonstrate robust transport behavior empirically. Together, these results establish intrinsic geometric alignment as a powerful principle for scalable representation learning.
Computer Vision · Image and Video Generation
Generating realistic 3D Human-Human Interaction (HHI) requires coherent modeling of the physical plausibility of the agents and their interaction semantics. Existing methods compress all motion information into a single latent representation, limiting their ability to capture fine-grained actions and inter-agent interactions. This often leads to semantic misalignment and physically implausible artifacts, such as penetration or missed contact. We propose Disentangled Hierarchical Variational Autoencoder (DHVAE) based latent diffusion for structured and controllable HHI generation. DHVAE explicitly disentangles the global interaction context and individual motion patterns into a decoupled latent structure by employing a CoTransformer module. To mitigate implausible and physically inconsistent contacts in HHI, we incorporate contrastive learning constraints with our DHVAE to promote a more discriminative and physically plausible latent interaction space. For high-fidelity interaction synthesis, DHVAE employs a DDIM-based diffusion denoising process in the hierarchical latent space, enhanced by a skip-connected AdaLN-Transformer denoiser. Extensive evaluations show that DHVAE achieves superior motion fidelity, text alignment, and physical plausibility with greater computational efficiency.
Applications · Climate
Solving primitive equations is essential for accurate weather forecasting. However, traditional numerical weather prediction (NWP) methods often incorporate various simplifications that limit their effectiveness in parameterizing unresolved physical processes. Meanwhile, existing deep learning-based models mostly focus on pure data-driven paradigms, overlooking the fundamental physical principles that govern atmospheric dynamics. To address these challenges, we present DeepPrim, a novel 3D \underline{deep} weather forecaster designed to learn \underline{prim}itive equations of the Earth’s atmosphere. Specifically, DeepPrim aims at accurately modeling 3D atmospheric motion through Navier-Stokes equation in pressure coordinates, and effectively capturing the interactions between the solved advection and key weather variables (e.g., temperature and water vapor) through corresponding equations. By seamlessly integrating fundamental atmospheric physics with advanced data-driven techniques, our model effectively approximates complicated physical processes without relying on empirical simplifications. Experimentally, DeepPrim achieves impressive performance in both short-term global and regional weather forecasting tasks, and exhibits the superior capacity to capture 3D atmospheric dynamics. It is now deployed as part of the Baguan weather forecasting system, especially specializing in short-term forecasting. The code is available at https://github.com/DAMO-DI-ML/DeepPrim.
Applications · Chemistry and Drug Discovery
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational costs, which severely restrict accessible timescales for many biologically relevant processes. Despite the encouraging performance of existing machine learning (ML) methods, they struggle to generate extended biomolecular system trajectories, primarily due to the lack of MD datasets and the large computational demands of modeling long historical trajectories. Here, we introduce BioMD, the first all-atom generative model to simulate long-timescale protein-ligand dynamics using a hierarchical framework of forecasting and interpolation. We demonstrate the effectiveness and versatility of BioMD on the DD-13M (ligand unbinding) and MISATO datasets. For both datasets, BioMD generates highly realistic conformations, showing high physical plausibility and low reconstruction errors. Besides, BioMD successfully generates ligand unbinding paths for 97.1% of the protein-ligand systems within ten attempts, demonstrating its ability to explore critical unbinding pathways. Collectively, these results establish BioMD as a tool for simulating complex biomolecular processes, offering broad applicability for computational chemistry and drug discovery.