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Applications

Taoran Zheng, Yan Yang, Xing Li, Xiang Gu, Jian Sun, Zongben Xu

Medical image reconstruction from measurement data is a vital but challenging inverse problem. Deep learning approaches have achieved promising results, but often requires paired measurement and high-quality images, which is typically simulated through a forward model, i.e., retrospective reconstruction. However, training on simulated pairs commonly leads to performance degradation on real prospective data due to the retrospective-to-prospective gap caused by incomplete imaging knowledge in simulation. To address this challenge, this paper introduces imaging Knowledge-Informed Dynamic Optimal Transport (KIDOT), a novel dynamic optimal transport framework with optimality in the sense of preserving consistency with imaging physics in transport, that conceptualizes reconstruction as finding a dynamic transport path. KIDOT learns from unpaired data by modeling reconstruction as a continuous evolution path from measurements to images, guided by an imaging knowledge-informed cost function and transport equation. This dynamic and knowledge-aware approach enhances robustness and better leverages unpaired data while respecting acquisition physics. Theoretically, we demonstrate that KIDOT naturally generalizes dynamic optimal transport, ensuring its mathematical rationale and solution existence. Extensive experiments on MRI and CT reconstruction demonstrate KIDOT's superior performance. Code is available at https://github.com/TaoranZheng717/KIDOT.

Applications · Health

Yasar Utku Alcalar, Merve Gulle, Mehmet Akcakaya

Physics-driven deep learning (PD-DL) approaches have become popular for improved reconstruction of fast magnetic resonance imaging (MRI) scans. Though PD-DL offers higher acceleration rates than existing clinical fast MRI techniques, their use has been limited outside specialized MRI centers. A key challenge is generalization to rare pathologies or different populations, noted in multiple studies, with fine-tuning on target populations suggested for improvement. However, current approaches for PD-DL training require access to raw k-space measurements, which is typically only available at specialized MRI centers that have research agreements for such data access. This is especially an issue for rural and under-resourced areas, where commercial MRI scanners only provide access to a final reconstructed image. To tackle these challenges, we propose Compressibility-inspired Unsupervised Learning via Parallel Imaging Fidelity (CUPID) for high-quality PD-DL training using only routine clinical reconstructed images exported from an MRI scanner. CUPID evaluates output quality with a compressibility-based approach while ensuring that the output stays consistent with the clinical parallel imaging reconstruction through well-designed perturbations. Our results show CUPID achieves similar quality to established PD-DL training that requires k-space data while outperforming compressed sensing (CS) and diffusion-based generative methods. We further demonstrate its effectiveness in a zero-shot training setup for retrospectively and prospectively sub-sampled acquisitions, attesting to its minimal training burden. As an approach that radically deviates from existing strategies, CUPID presents an opportunity to provide broader access to fast MRI for remote and rural populations in an attempt to reduce the obstacles associated with this expensive imaging modality. Code is available at https://github.com/ualcalar17/CUPID.

Reinforcement Learning · Multi-agent

Zelai Xu, Ruize Zhang, Chao Yu, Huining Yuan, Xiangmin Yi, Shilong Ji, Chuqi Wang, Wenhao Tang, Feng Gao, Wenbo Ding 等

Robot sports, characterized by well-defined objectives, explicit rules, and dynamic interactions, present ideal scenarios for demonstrating embodied intelligence. In this paper, we present VolleyBots, a novel robot sports testbed where multiple drones cooperate and compete in the sport of volleyball under physical dynamics. VolleyBots integrates three features within a unified platform: competitive and cooperative gameplay, turn-based interaction structure, and agile 3D maneuvering.These intertwined features yield a complex problem combining motion control and strategic play, with no available expert demonstrations.We provide a comprehensive suite of tasks ranging from single-drone drills to multi-drone cooperative and competitive tasks, accompanied by baseline evaluations of representative reinforcement learning (RL), multi-agent reinforcement learning (MARL) and game-theoretic algorithms. Simulation results show that on-policy RL methods outperform off-policy methods in single-agent tasks, but both approaches struggle in complex tasks that combine motion control and strategic play.We additionally design a hierarchical policy which achieves 69.5% win rate against the strongest baseline in the 3 vs 3 task, demonstrating its potential for tackling the complex interplay between low-level control and high-level strategy.To highlight VolleyBots’ sim-to-real potential, we further demonstrate the zero-shot deployment of a policy trained entirely in simulation on real-world drones.

Applications · Physics

Xinbiao Wang, Yuxuan Du, Zihan Lou, Yang Qian, Kaining Zhang, Yong Luo, Bo Du, Dacheng Tao

Quantum many-body problems are central to various scientific disciplines, yet their ground-state properties are intrinsically challenging to estimate. Recent advances in deep learning (DL) offer potential solutions in this field, complementing prior purely classical and quantum approaches. However, existing DL-based models typically assume access to a large-scale and noiseless labeled dataset collected by infinite sampling. This idealization raises fundamental concerns about their practical utility, especially given the limited availability of quantum hardware in the near term. To unleash the power of these DL-based models, we propose AiDE-Q (\underline{a}utomat\underline{i}c \underline{d}ata \underline{e}ngine for \underline{q}uantum property estimation), an effective framework that addresses this challenge by iteratively generating high-quality synthetic labeled datasets. Specifically, AiDE-Q utilizes a confidence-check method to assess the quality of synthetic labels and continuously improves the employed DL models with the identified high-quality synthetic dataset. To verify the effectiveness of AiDE-Q, we conduct extensive numerical simulations on a diverse set of quantum many-body and molecular systems, with up to 50 qubits. The results show that AiDE-Q enhances prediction performance for various reference learning models, with improvements of up to $14.2\\%$. Moreover, we exhibit that a basic supervised learning model integrated with AiDE-Q outperforms advanced reference models, highlighting the importance of a synthetic dataset. Our work paves the way for more efficient and practical applications of DL for quantum property estimation.

Deep Learning · Theory

Yuqian Cheng, Zhuo Chen, Qian Lin

The physics-informed neural networks (PINNs) are widely applied in solving differential equations. However, few studies have discussed their consistency. In this paper, we consider the consistency of PINNs when applied to second-order elliptic equations with Dirichlet boundary conditions. We first provide the necessary and sufficient condition for the consistency of the physics-informed kernel gradient flow algorithm, and then as a direct corollary, when the neural network is sufficiently wide, we obtain a necessary and sufficient condition for the consistency of PINNs based on the neural tangent kernel theory. We also estimate the non-asymptotic loss bounds of physics-informed kernel gradient flow and PINN under suitable stronger assumptions. Finally, these results inspires us to construct a notable pathological example where the PINN method is inconsistent.

Computer Vision · Image and Video Generation

Jingjun Yi, Qi Bi, Hao Zheng, Huimin Huang, Yixian Shen, Haolan Zhan, Wei Ji, Yawen Huang, Yuexiang Li, Xian Wu 等

Image restoration is a fundamental task in computer vision and machine learning, which learns a mapping between the clear images and the degraded images under various conditions (e.g., blur, low-light, haze). Yet, most existing image restoration methods are highly restricted by the requirement of degraded and clear image pairs, which limits the generalization and feasibility to enormous real-world scenarios without paired images. To address this bottleneck, we propose a Degradation-aware Dynamic Schr\"{o}dinger Bridge (DDSB) for unpaired image restoration. Its general idea is to learn a Schr\"{o}dinger Bridge between clear and degraded image distribution, while at the same time emphasizing the physical degradation priors to reduce the accumulation of errors during the restoration process. A Degradation-aware Optimal Transport (DOT) learning scheme is accordingly devised. Training a degradation model to learn the inverse restoration process is particularly challenging, as it must be applicable across different stages of the iterative restoration process. A Dynamic Transport with Consistency (DTC) learning objective is further proposed to reduce the loss of image details in the early iterations and therefore refine the degradation model. Extensive experiments on multiple image degradation tasks show its state-of-the-art performance over the prior arts.

Probabilistic Methods · Everything Else

Naoki Kiyohara, Edward Johns, Yingzhen Li

Stochastic differential equations (SDEs) are well suited to modelling noisy and/or irregularly-sampled time series, which are omnipresent in finance, physics, and machine learning applications. Traditional approaches require costly simulation of numerical solvers when sampling between arbitrary time points. We introduce Neural Stochastic Flows (NSFs) and their latent dynamic versions, which learns (latent) SDE transition laws directly using conditional normalising flows, with architectural constraints that preserve properties inherited from stochastic flow. This enables sampling between arbitrary states in a single step, providing up to two orders of magnitude speedup for distant time points. Experiments on synthetic SDE simulations and real-world tracking and video data demonstrate that NSF maintains distributional accuracy comparable to numerical approaches while dramatically reducing computation for arbitrary time-point sampling, enabling applications where numerical solvers remain prohibitively expensive.

Optimization

Gonzalo E. Constante, Hao Chen, Can Li

Deep learning models are increasingly deployed in safety-critical tasks where predictions must satisfy hard constraints, such as physical laws, fairness requirements, or safety limits. However, standard architectures lack built-in mechanisms to enforce such constraints, and existing approaches based on regularization or projection are often limited to simple constraints, computationally expensive, or lack feasibility guarantees. This paper proposes a model-agnostic framework for enforcing input-dependent linear equality and inequality constraints on neural network outputs. The architecture combines a task network trained for prediction accuracy with a safe network trained using decision rules from the stochastic and robust optimization literature to ensure feasibility across the entire input space. The final prediction is a convex combination of the two subnetworks, guaranteeing constraint satisfaction during both training and inference without iterative procedures or runtime optimization. We prove that the architecture is a universal approximator of constrained functions and derive computationally tractable formulations based on linear decision rules. Empirical results on benchmark regression tasks show that our method consistently satisfies constraints while maintaining competitive accuracy and low inference latency.

Applications · Climate

Tung Nguyen, Tuan Pham, Troy Arcomano, Rao Kotamarthi, Ian Foster, Sandeep Madireddy, Aditya Grover

Accurate weather forecasting across time scales is critical for anticipating and mitigating the impacts of climate change. Recent data-driven methods based on deep learning have achieved significant success in the medium range, but struggle at longer subseasonal-to-seasonal (S2S) horizons due to error accumulation in their autoregressive approach. In this work, we propose OmniCast, a scalable and skillful probabilistic model that unifies weather forecasting across timescales. OmniCast consists of two components: a VAE model that encodes raw weather data into a continuous, lower-dimensional latent space, and a diffusion-based transformer model that generates a sequence of future latent tokens given the initial conditioning tokens. During training, we mask random future tokens and train the transformer to estimate their distribution given conditioning and visible tokens using a per-token diffusion head. During inference, the transformer generates the full sequence of future tokens by iteratively unmasking random subsets of tokens. This joint sampling across space and time mitigates compounding errors from autoregressive approaches. The low-dimensional latent space enables modeling long sequences of future latent states, allowing the transformer to learn weather dynamics beyond initial conditions. OmniCast performs competitively with leading probabilistic methods at the medium-range timescale while being 10× to 20× faster, and achieves state-of-the-art performance at the subseasonal-to-seasonal scale across accuracy, physics-based, and probabilistic metrics. Furthermore, we demonstrate that OmniCast can generate stable rollouts up to 100 years ahead. Code and model checkpoints are available at https://github.com/tung-nd/omnicast.

Applications · Time Series

Pengrui Quan, Brian Wang, Kang Yang, Liying Han, Mani Srivastava

Spatiotemporal reasoning plays a key role in Cyber-Physical Systems (CPS). Despite advances in Large Language Models (LLMs) and Large Reasoning Models (LRMs), their capacity to reason about complex spatiotemporal signals remains underexplored. This paper proposes a hierarchical SpatioTemporal reAsoning benchmaRK, STARK, to systematically evaluate LLMs across three levels of reasoning complexity: state estimation (e.g., predicting field variables, localizing and tracking events in space and time), spatiotemporal reasoning over states (e.g., inferring spatial-temporal relationships), and world-knowledge-aware reasoning that integrates contextual and domain knowledge (e.g., intent prediction, landmark-aware navigation). We curate 26 distinct spatiotemporal tasks with diverse sensor modalities, comprising 14,552 challenges where models answer directly or by Python Code Interpreter. Evaluating 3 LRMs and 8 LLMs, we find LLMs achieve limited success in tasks requiring geometric reasoning (e.g., multilateration or triangulation), particularly as complexity increases. Surprisingly, LRMs show robust performance across tasks with various levels of difficulty, often competing or surpassing traditional first-principle-based methods. Our results show that in reasoning tasks requiring world knowledge, the performance gap between LLMs and LRMs narrows, with some LLMs even surpassing LRMs. However, the LRM o3 model continues to achieve leading performance across all evaluated tasks, a result attributed primarily to the larger size of the reasoning models. STARK motivates future innovations in model architectures and reasoning paradigms for intelligent CPS by providing a structured framework to identify limitations in the spatiotemporal reasoning of LLMs and LRMs.

Computer Vision · 3D Rendering & Reconstruction

qigeng duan, Benyun ZHAO, Mingqiao Han, Yijun Huang, Ben Chen

Scene understanding based on 3D Gaussian Splatting (3DGS) has recently achieved notable advances. Although 3DGS related methods have efficient rendering capabilities, they fail to address the inherent contradiction between the anisotropic color representation of gaussian primitives and the isotropic requirements of semantic features, leading to insufficient cross-view feature consistency. To overcome the limitation, we proposes FHGS (Feature-Homogenized Gaussian Splatting), a novel 3D feature distillation framework inspired by physical models, which freezes and distills 2D pre-trained features into 3D representations while preserving the real-time rendering efficiency of 3DGS. Specifically, our FHGS introduces the following innovations: Firstly, a universal feature fusion architecture is proposed, enabling robust embedding of large-scale pre-trained models' semantic features (e.g., SAM, CLIP) into sparse 3D structures. Secondly, a non-differentiable feature fusion mechanism is introduced, which enables semantic features to exhibit viewpoint independent isotropic distributions. This fundamentally balances the anisotropic rendering of gaussian primitives and the isotropic expression of features; Thirdly, a dual-driven optimization strategy inspired by electric potential fields is proposed, which combines external supervision from semantic feature fields with internal primitive clustering guidance. This mechanism enables synergistic optimization of global semantic alignment and local structural consistency. Extensive comparison experiments with other state-of-the-art methods on benchmark datasets demonstrate that our FHGS exhibits superior reconstruction performance in feature fusion, noise suppression, and geometric precision, while maintaining a significantly lower training time. This work establishes a novel Gaussian Splatting data structure, offering practical advancements for real-time semantic mapping, 3D stylization, and Vision-Language Navigation (VLN). Our code and additional results are available on our project page:https://fhgs.cuastro.org/.

Applications · Time Series

Fares Mehouachi, Saif Eddin Jabari

We introduce FlowMixer, a single-layer neural architecture that leverages constrained matrix operations to model structured spatiotemporal patterns with enhanced interpretability. FlowMixer incorporates non-negative matrix mixing layers within a reversible mapping framework—applying transforms before mixing and their inverses afterward. This shape-preserving design enables a Kronecker-Koopman eigenmodes framework that bridges statistical learning with dynamical systems theory, providing interpretable spatiotemporal patterns and facilitating direct algebraic manipulation of prediction horizons without retraining. The architecture's semi-group property enables this single layer to mathematically represent any depth through composition, eliminating depth search entirely. Extensive experiments across diverse domains demonstrate FlowMixer's long-horizon forecasting capabilities while effectively modeling physical phenomena such as chaotic attractors and turbulent flows. Our results achieve performance matching state-of-the-art methods while offering superior interpretability through directly extractable eigenmodes. This work suggests that architectural constraints can simultaneously maintain competitive performance and enhance mathematical interpretability in neural forecasting systems.

Deep Learning · Generative Models and Autoencoders

Gregory Barber, Todd Henry, Mulugeta Haile

We present TIDES, a text informed design approach for generating physically sound designs based on a textual description and a set of physical constraints. TIDES jointly optimizes structural (topology) and visual properties. A pre-trained text-image model is used to measure the design's visual alignment with a text prompt and a differentiable physics simulator is used to measure its physical performance. We evaluate TIDES on a series of structural optimization problems operating under different load and support conditions, at different resolutions, and experimentally in the lab by performing the 3-point bending test on 2D beam designs that are extruded and 3D printed. We find that it can jointly optimize the two objectives and return designs that satisfy engineering design requirements (compliance and density) while utilizing features specified by text.

Applications · Robotics

Pei Zhou, Wanting Yao, Qian Luo, Xunzhe Zhou, Yanchao Yang

Goal-conditioned policy learning for robotic manipulation presents significant challenges in maintaining performance across diverse objectives and environments. We introduce *Hyper-GoalNet*, a framework that generates task-specific policy network parameters from goal specifications using hypernetworks. Unlike conventional methods that simply condition fixed networks on goal-state pairs, our approach separates goal interpretation from state processing -- the former determines network parameters while the latter applies these parameters to current observations. To enhance representation quality for effective policy generation, we implement two complementary constraints on the latent space: (1) a forward dynamics model that promotes state transition predictability, and (2) a distance-based constraint ensuring monotonic progression toward goal states. We evaluate our method on a comprehensive suite of manipulation tasks with varying environmental randomization. Results demonstrate significant performance improvements over state-of-the-art methods, particularly in high-variability conditions. Real-world robotic experiments further validate our method's robustness to sensor noise and physical uncertainties. Our code and trained models will be made publicly available.

Computer Vision · Image and Video Generation

Yutong Bai, Danny Tran, Amir Bar, Yann LeCun, Trevor Darrell, Jitendra Malik

We train models to predict ego-centric video from human actions (PEVA), given the past video and an action represented by the relative 3D body pose. By conditioning on kinematic pose trajectories, structured by the joint hierarchy of the body, our model learns to simulate how physical human actions shape the environment from a first-person point of view. We train an auto-regressive conditional diffusion transformer on Nymeria, a large-scale dataset of real-world egocentric video and body pose capture. We further design a hierarchical evaluation protocol with increasingly challenging tasks, enabling a comprehensive analysis of the model’s embodied prediction and control abilities. Our work represents an initial attempt to tackle the challenges of modeling complex real-world environments and embodied agent behaviors with video prediction from the perspective of a human.

Applications · Robotics

Haotian Chi, Zeyu Feng, Yueming LYU, Chengqi Zheng, Linbo Luo, Yew Soon Ong, Ivor Tsang, Hechang Chen, Yi Chang, Haiyan Yin

Long-horizon planning in robotic manipulation tasks requires translating underspecified, symbolic goals into executable control programs satisfying spatial, temporal, and physical constraints. However, language model-based planners often struggle with long-horizon task decomposition, robust constraint satisfaction, and adaptive failure recovery. We introduce InstructFlow, a multi-agent framework that establishes a symbolic, feedback-driven flow of information for code generation in robotic manipulation tasks. InstructFlow employs a InstructFlow Planner to construct and traverse a hierarchical instruction graph that decomposes goals into semantically meaningful subtasks, while a Code Generator generates executable code snippets conditioned on this graph. Crucially, when execution failures occur, a Constraint Generator analyzes feedback and induces symbolic constraints, which are propagated back into the instruction graph to guide targeted code refinement without regenerating from scratch. This dynamic, graph-guided flow enables structured, interpretable, and failure-resilient planning, significantly improving task success rates and robustness across diverse manipulation benchmarks, especially in constraint-sensitive and long-horizon scenarios.

Applications · Physics

Stephen Zhang, Michael Stumpf

We consider the Schrödinger bridge problem which, given ensemble measurements of the initial and final configurations of a stochastic dynamical system and some prior knowledge on the dynamics, aims to reconstruct the "most likely" evolution of the system compatible with the data. Most existing literature assume Brownian reference dynamics, and are implicitly limited to modelling systems driven by the gradient of a potential energy. We depart from this regime and consider reference processes described by a multivariate Ornstein-Uhlenbeck process with generic drift matrix $\mathbf{A} \in \mathbb{R}^{d \times d}$. When $\mathbf{A}$ is asymmetric, this corresponds to a non-equilibrium system in which non-gradient forces are at play: this is important for applications to biological systems, which naturally exist out-of-equilibrium. In the case of Gaussian marginals, we derive explicit expressions that characterise exactly the solution of both the static and dynamic Schrödinger bridge. For general marginals, we propose mvOU-OTFM, a simulation-free algorithm based on flow and score matching for learning an approximation to the Schrödinger bridge. In application to a range of problems based on synthetic and real single cell data, we demonstrate that mvOU-OTFM achieves higher accuracy compared to competing methods, whilst being significantly faster to train.

Applications · Time Series

Uros Zivanovic, Serafina Di Gioia, Andre Scaffidi, Martín de los Rios, Gabriella Contardo, Roberto Trotta

Applying Transformers to irregular time-series typically requires specializations to their baseline architecture, which can result in additional computational overhead and increased method complexity. We present the Rotary Masked Autoencoder (RoMAE), which utilizes the popular Rotary Positional Embedding (RoPE) method for continuous positions. RoMAE is an extension to the Masked Autoencoder (MAE) that enables interpolation and representation learning with multidimensional continuous positional information while avoiding any time-series-specific architectural specializations. We showcase RoMAE's performance on a variety of modalities including irregular and multivariate time-series, images, and audio, demonstrating that RoMAE surpasses specialized time-series architectures on difficult datasets such as the DESC ELAsTiCC Challenge while maintaining MAE's usual performance across other modalities. In addition, we investigate RoMAE's ability to reconstruct the embedded continuous positions, demonstrating that including learned embeddings in the input sequence breaks RoPE's relative position property.

Applications

Yuanchuan Guo, Jun Liu, Huimin Cheng, Ying Ma

As spatial transcriptomics (ST) datasets increasingly span multiple adjacent or replicated slices, effective joint analysis across slices is needed to reconstruct tissue structures and identify consistent spatial gene expression patterns. This requires resolving spatial correspondences between slices while capturing shared transcriptomic features, two tasks that are typically addressed in isolation. Multi-slice analysis remains challenging due to physical distortions, technical variability, and batch effects. To address these challenges, we introduce Joint Alignment and Deep Embedding for multi-slice ST (JADE), a unified computational framework that simultaneously learns spot-wise alignments and shared low-dimensional embeddings across tissue slices. Unlike existing methods, JADE adopts a roundtrip framework in which each iteration alternates between alignment and embedding refinement. To infer alignment, we employ attention mechanisms that dynamically assess and weight the importance of different embedding dimensions, allowing the model to focus on the most alignment-relevant features while suppressing noise. To the best of our knowledge, JADE is the first method that jointly optimizes alignment and representation learning in a shared latent space, enabling robust multi-slice integration. We demonstrate that JADE outperforms existing alignment and embedding methods across multiple evaluation metrics in the 10x Visium human dorsolateral prefrontal cortex (DLPFC) and Stereo-seq axolotl brain datasets. By bridging spatial alignment and feature integration, JADE provides a scalable and accurate solution for cross-slice analysis of ST data.

Applications · Everything Else

Ori Press, Brandon Amos, Haoyu Zhao, Yikai Wu, Samuel Ainsworth, Dominik Krupke, Patrick Kidger, Touqir Sajed, Bartolomeo Stellato, Jisun Park 等

Despite progress in language model (LM) capabilities, evaluations have thus far focused on models' performance on tasks that humans have previously solved, including in programming (SWE-Bench) and mathematics (FrontierMath). We therefore propose testing models' ability to design and implement algorithms in an open-ended benchmark: We task LMs with writing code that efficiently solves computationally challenging problems in computer science, physics, and mathematics. Our AlgoTune benchmark consists of 120 tasks collected from domain experts and a framework for validating and timing LM-synthesized solution code, which is compared to reference implementations from popular open-source packages.In addition, we develop a baseline LM agent, AlgoTuner, and evaluate its performance across a suite of frontier models.AlgoTuner achieves an average 1.58x speedup against reference solvers, including methods from packages such as SciPy, scikit-learn and CVXPY.However, we find that current models fail to discover algorithmic innovations, instead preferring surface-level optimizations. We hope that AlgoTune catalyzes the development of LM agents exhibiting creative problem solving beyond state-of-the-art human performance.