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Applications · Genetics, Cell Biology, etc

Stephen Zhang, Suryanarayana Maddu, Xiaojie Qiu, Victor Chardès

Time-resolved single-cell omics data offers high-throughput, genome-wide measurements of cellular states, which are instrumental to reverse-engineer the processes underpinning cell fate. Such technologies are inherently destructive, allowing only cross-sectional measurements of the underlying stochastic dynamical system. Furthermore, cells may divide or die in addition to changing their molecular state. Collectively these present a major challenge to inferring realistic biophysical models. We present a novel approach, unbalanced probability flow inference, that addresses this challenge for biological processes modelled as stochastic dynamics with growth. By leveraging a Lagrangian formulation of the Fokker-Planck equation, our method accurately disentangles drift from intrinsic noise and growth. We showcase the applicability of our approach through evaluation on a range of simulated and real single-cell RNA-seq datasets. Comparing to several existing methods, we find our method achieves higher accuracy while enjoying a simple two-step training scheme.

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.

Deep Learning · Attention Mechanisms

Satoshi Noguchi, Yoshinobu Kawahara

Transformers have achieved remarkable success across natural language processing (NLP) and computer vision (CV). However, deep transformer models often suffer from an over-smoothing issue, in which token representations converge to similar values as they pass through successive transformer blocks. In this paper, we establish an equivalence between the hidden-state dynamics induced by stacked attention layers and graph neural diffusion on a complete graph. From this perspective, over-smoothing can be interpreted as a consequence of the dissipative nature of the underlying diffusion dynamics. Motivated by this physical interpretation, we propose Wavy Transformer, which consists of a novel attention layer based on second-order wavy dynamics. We also introduce a feed-forward network and a normalization layer designed to preserve the physical state-velocity relationship under the chain rule, thereby extending the transformer architecture. We further validate our proposed techniques on various transformer models for NLP and CV tasks. The results consistently demonstrate that Wavy Transformer improves performance with minimal additional parameters and no extra hyperparameter tuning.

Probabilistic Methods · Bayesian Models and Methods

Fuyuan Xiao, Yu Zhou, Witold Pedrycz

In pattern classification, efficient uncertainty reasoning plays a critical role, particularly in real-time applications involving noisy data, ambiguous class boundaries, or overlapping categories. Leveraging the advanced computational power of quantum computing, an Adaptive Quantum Circuit for Dempster’s Rule of Combination (AQC-DRC) is proposed to address efficient classification under uncertain environments. The AQC-DRC is developed within the framework of quantum evidence theory (QET) and facilitates decision-making based on quantum basic probability and plausibility levels, which is a generalized Bayesian inference method. The AQC-DRC provides a deterministic computation of DRC, ensuring that quantum fusion outcomes in uncertain pattern classification are exactly aligned with those of the classical method, while simultaneously achieving exponential reductions in the computational complexity of evidence combination and significantly improving fusion efficiency. It is founded that the quantum basic probability amplitude function in QET, as a generalized quantum probability amplitude, can be naturally utilized to express the quantum amplitude encoding. In addition, the quantum basic probability in QET, as a generalized quantum probability, naturally forms a quantum basic probability distribution and can be used to represent quantum measurement outcomes for quantum basic probability level decision-making. Furthermore, the quantum plausibility function in QET also can be naturally used to express the quantum measurement outcomes for quantum plausibility level decision-making. These findings enrich the physical understanding of quantum amplitude encoding and quantum measurement outcomes, offering broad application prospects for representing and processing uncertain knowledge in pattern classification.

Computer Vision · Image and Video Generation

Lingwei Dang, Ruizhi Shao, Hongwen Zhang, Wei MIN, Yebin Liu, Qingyao Wu

Hand-Object Interaction (HOI) generation has significant application potential. However, current 3D HOI motion generation approaches heavily rely on predefined 3D object models and lab-captured motion data, limiting generalization capabilities. Meanwhile, HOI video generation methods prioritize pixel-level visual fidelity, often sacrificing physical plausibility. Recognizing that visual appearance and motion patterns share fundamental physical laws in the real world, we propose a novel framework that combines visual priors and dynamic constraints within a synchronized diffusion process to generate the HOI video and motion simultaneously. To integrate the heterogeneous semantics, appearance, and motion features, our method implements tri-modal adaptive modulation for feature aligning, coupled with 3D full-attention for modeling inter- and intra-modal dependencies. Furthermore, we introduce a vision-aware 3D interaction diffusion model that generates explicit 3D interaction sequences directly from the synchronized diffusion outputs, then feeds them back to establish a closed-loop feedback cycle. This architecture eliminates dependencies on predefined object models or explicit pose guidance while significantly enhancing video-motion consistency. Experimental results demonstrate our method's superiority over state-of-the-art approaches in generating high-fidelity, dynamically plausible HOI sequences, with notable generalization capabilities in unseen real-world scenarios. Project page at [https://droliven.github.io/SViMo_project](https://droliven.github.io/SViMo_project).

Applications · Chemistry and Drug Discovery

Filippo Bigi, Sanggyu Chong, Agustinus Kristiadi, Michele Ceriotti

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD by providing inexpensive predictions of the forces, but they remain constrained to minuscule time integration steps, which are required by the fast time scale of atomic motion. In this work, we propose FlashMD, a method to predict the evolution of positions and momenta over strides that are between one and two orders of magnitude longer than typical MD time steps. We incorporate considerations on the mathematical and physical properties of Hamiltonian dynamics in the architecture, generalize the approach to allow the simulation of any thermodynamic ensemble, and carefully assess the possible failure modes of a direct MD approach. We validate FlashMD’s accuracy in reproducing equilibrium and time‐dependent properties, using both system‐specific and general-purpose models, extending the ability of MD simulation to reach the long time scales needed to model microscopic processes of high scientific and technological relevance.

Applications · Physics

Zhichao Wang, Xinhai Chen, Qinglin Wang, Xiang Gao, Qingyang Zhang, Menghan Jia, Xiang Zhang, Jie Liu

Partial differential equations (PDEs) form the mathematical foundation for modeling physical systems in science and engineering, where numerical solutions demand rigorous accuracy-efficiency tradeoffs. Mesh movement techniques address this challenge by dynamically relocating mesh nodes to rapidly-varying regions, enhancing both simulation accuracy and computational efficiency. However, traditional approaches suffer from high computational complexity and geometric inflexibility, limiting their applicability, and existing supervised learning-based approaches face challenges in zero-shot generalization across diverse PDEs and mesh topologies. In this paper, we present an $\textbf{U}$nsupervised and $\textbf{G}$eneralizable $\textbf{M}$esh $\textbf{M}$ovement $\textbf{N}$etwork (UGM2N). We first introduce unsupervised mesh adaptation through localized geometric feature learning, eliminating the dependency on pre-adapted meshes. We then develop a physics-constrained loss function, M-Uniform loss, that enforces mesh equidistribution at the nodal level. Experimental results demonstrate that the proposed network exhibits equation-agnostic generalization and geometric independence in efficient mesh adaptation. It demonstrates consistent superiority over existing methods, including robust performance across diverse PDEs and mesh geometries, scalability to multi-scale resolutions and guaranteed error reduction without mesh tangling.

Applications · Chemistry and Drug Discovery

J. Thorben Frank, Winfried Ripken, Gregor Lied, Klaus-Robert Müller, Oliver Unke, Stefan Chmiela

Diffusion Transformers (DiTs) have demonstrated strong performance in generative modeling, particularly in image synthesis, making them a compelling choice for molecular conformer generation. However, applying DiTs to molecules introduces novel challenges, such as integrating discrete molecular graph information with continuous 3D geometry, handling Euclidean symmetries, and designing conditioning mechanisms that generalize across molecules of varying sizes and structures. We propose DiTMC, a framework that adapts DiTs to address these challenges through a modular architecture that separates the processing of 3D coordinates from conditioning on atomic connectivity. To this end, we introduce two complementary graph-based conditioning strategies that integrate seamlessly with the DiT architecture. These are combined with different attention mechanisms, including both standard non-equivariant and SO(3)-equivariant formulations, enabling flexible control over the trade-off between between accuracy and computational efficiency. Experiments on standard conformer generation benchmarks (GEOM-QM9, -DRUGS, -XL) demonstrate that DiTMC achieves state-of-the-art precision and physical validity. Our results highlight how architectural choices and symmetry priors affect sample quality and efficiency, suggesting promising directions for large-scale generative modeling of molecular structures. Code is available at [https://github.com/ML4MolSim/dit_mc](https://github.com/ML4MolSim/dit_mc).

Applications · Physics

Andrea Bonfanti, Ismael Medina, Roman List, Björn Staeves, Roberto Santana, Marco Ellero

Recent advances in Scientific Machine Learning have shown that second-order methods can enhance the training of Physics-Informed Neural Networks (PINNs), making them a suitable alternative to traditional numerical methods for Partial Differential Equations (PDEs). However, second-order methods induce large memory requirements, making them scale poorly with the model size. In this paper, we define a local Mixture of Experts (MoE) combining the parameter-efficiency of ensemble models and sparse coding to enable the use of second-order training. Our model -- PINN Balls -- also features a fully learnable domain decomposition structure, achieved through the use of Adversarial Adaptive Sampling (AAS), which adapts the DD to the PDE and its domain. PINN Balls achieves better accuracy than the state-of-the-art in scientific machine learning, while maintaining invaluable scalability properties and drawing from a sound theoretical background.

Applications · Physics

Fan Xu, Hao Wu, Nan Wang, Lilan Peng, Kun Wang, Wei Gong, Xibin Zhao

The modeling of complicated time-evolving physical dynamics from partial observations is a long-standing challenge. Particularly, observations can be sparsely distributed in a seemingly random or unstructured manner, making it difficult to capture highly nonlinear features in a variety of scientific and engineering problems. However, existing data-driven approaches are often constrained by fixed spatial and temporal discretization. While some researchers attempt to achieve spatio-temporal continuity by designing novel strategies, they either overly rely on traditional numerical methods or fail to truly overcome the limitations imposed by discretization. To address these, we propose CoPS, a purely data-driven methods, to effectively model continuous physics simulation from partial observations. Specifically, we employ multiplicative filter network to fuse and encode spatial information with the corresponding observations. Then we customize geometric grids and use message-passing mechanism to map features from original spatial domain to the customized grids. Subsequently, CoPS models continuous-time dynamics by designing multi-scale graph ODEs, while introducing a Markov-based neural auto-correction module to assist and constrain the continuous extrapolations. Comprehensive experiments demonstrate that CoPS advances the state-of-the-art methods in space-time continuous modeling across various scenarios. The source code is available at~\url{https://github.com/Sunxkissed/CoPS}.

Applications · Robotics

Chunru Lin, Haotian Yuan, Yian Wang, Xiaowen Qiu, Tsun-Hsuan Johnson Wang, Minghao Guo, Bohan Wang, Yashraj Narang, Dieter Fox, Chuang Gan

Endowing robots with tool design abilities is critical for enabling them to solve complex manipulation tasks that would otherwise be intractable. While recent generative frameworks can automatically synthesize task settings—such as 3D scenes and reward functions—they have not yet addressed the challenge of tool-use scenarios. Simply retrieving human-designed tools might not be ideal since many tools (e.g., a rolling pin) are difficult for robotic manipulators to handle. Furthermore, existing tool design approaches either rely on predefined templates with limited parameter tuning or apply generic 3D generation methods that are not optimized for tool creation. To address these limitations, we propose **RobotSmith**, an automated pipeline that leverages the implicit physical knowledge embedded in vision-language models (VLMs) alongside the more accurate physics provided by physics simulations to design and use tools for robotic manipulation. Our system (1) iteratively proposes tool designs using collaborative VLM agents, (2) generates low-level robot trajectories for tool use, and (3) jointly optimizes tool geometry and usage for task performance. We evaluate our approach across a wide range of manipulation tasks involving rigid, deformable, and fluid objects. Experiments show that our method consistently outperforms strong baselines in both task success rate and overall performance. Notably, our approach achieves a 50.0\% average success rate, significantly surpassing other baselines such as 3D generation (21.4\%) and tool retrieval (11.1\%). Finally, we deploy our system in real-world settings, demonstrating that the generated tools and their usage plans transfer effectively to physical execution, validating the practicality and generalization capabilities of our approach.

Applications · Time Series

Xukai Zhang, Shuliang Wang, Guangyin Jin, Ziqiang Yuan, Hanning Yuan, Sijie Ruan

Air pollution remains one of the most critical environmental challenges globally, posing severe threats to public health, ecological sustainability, and climate governance. While existing physics-based and data-driven models have made progress in air quality forecasting, they often struggle to jointly capture the complex spatiotemporal dynamics and ensure spatial continuity of pollutant distributions. In this study, we introduce CTENet, a novel chemical transport deep learning model that embeds the Advection-Diffusion-Reaction equation into a Physics-Informed Neural Network (PINN) framework using an Eulerian representation to model the spatiotemporal evolution of pollutants. Extensive experiments on two real-world datasets demonstrate that CTENet consistently outperforms state-of-the-art (SOTA) baselines, achieving a remarkable RMSE improvement of 45.8% on the USA dataset and 21.0% on the China dataset.

Social Aspects · Fairness, Equity, Justice and Safety

Luyang Zhang, Cathy Jiao, Beibei Li, Chenyan Xiong

Training data is the backbone of large language models (LLMs), yet today’s data markets often operate under exploitative pricing -- sourcing data from marginalized groups with little pay or recognition. This paper introduces a theoretical framework for LLM data markets, modeling the strategic interactions between buyers (LLM builders) and sellers (human annotators). We begin with theoretical and empirical analysis showing how exploitative pricing drives high-quality sellers out of the market, degrading data quality and long-term model performance. Then we introduce fairshare, a pricing mechanism grounded in data valuation that quantifies each data’s contribution. It aligns incentives by sustaining seller participation and optimizing utility for both buyers and sellers. Theoretically, we show that fairshare yields mutually optimal outcomes: maximizing long-term buyer utility and seller profit while sustaining market participation. Empirically when training open-source LLMs on complex NLP tasks, including math problems, medical diagnosis, and physical reasoning, fairshare boosts seller earnings and ensures a stable supply of high-quality data, while improving buyers’ performance-per-dollar and long-term welfare. Our findings offer a concrete path toward fair, transparent, and economically sustainable data markets for LLM. Our code will be open sourced.

Applications · Physics

Sheikh Md Shakeel Hassan, Xianwei Zou, Akash Dhruv, Aparna Chandramowlishwaran

Modeling boiling---an inherently chaotic, multiphase process central to energy and thermal systems---remains a significant challenge for neural PDE surrogates. Existing models require future input (e.g., bubble positions) during inference because they fail to learn nucleation from past states, limiting their ability to autonomously forecast boiling dynamics. They also fail to model flow boiling velocity fields, where sharp interface–momentum coupling demands long-range and directional inductive biases. We introduce Bubbleformer, a transformer-based spatiotemporal model that forecasts stable and long-range boiling dynamics including nucleation, interface evolution, and heat transfer without dependence on simulation data during inference. Bubbleformer integrates factorized axial attention, frequency-aware scaling, and conditions on thermophysical parameters to generalize across fluids, geometries, and operating conditions.To evaluate physical fidelity in chaotic systems, we propose interpretable physics-based metrics that evaluate heat flux consistency, interface geometry, and mass conservation. We also release BubbleML 2.0, a high-fidelity dataset that spans diverse working fluids (cryogens, refrigerants, dielectrics), boiling configurations (pool and flow boiling), flow regimes (bubbly, slug, annular), and boundary conditions. Bubbleformer sets new benchmark results in both prediction and forecasting of two-phase boiling flows.

Applications · Time Series

Xinghong Chen, Weilin Wu, Kunping Yang, Guannan Chen

Forecasting real-world time series requires modeling both short-term fluctuations and long-term evolutions, as these signals typically exhibit multiscale temporal structures. A core challenge lies in reconciling such dynamics: high-frequency seasonality demands local precision, while low-frequency trends require global robustness. However, most existing methods adopt a unified loss function across all temporal components, overlooking their structural differences. This misalignment often causes overfitting to seasonal noise or underfitting of long-term trends, leading to suboptimal forecasting performance. To address this issue, we propose a Physics-guided Multiscale Loss Framework (PMLF) that decomposes time series into seasonal and trend components and assigns component-specific objectives grounded in the distinct energy responses of oscillatory and drift dynamics. Specifically, we assign a quadratic loss to seasonal components, reflecting the quadratic potential energy profile of molecular vibration, while a logarithmic loss is used for trend components to capture the sublinear energy profile of molecular drift under sustained external forces. Furthermore, we introduce a softmax-based strategy that adaptively balances the unequal energetic responses of these two physical processes. Experiments on different public benchmarks show that PMLF improves the performance of diverse baselines, demonstrating the effectiveness of physics-guided loss design in modeling structural heterogeneity in time series forecasting.

Applications · Physics

Ortal Senouf, Antoine Wehenkel, Cédric Vincent-Cuaz, Emmanuel Abbe, Pascal Frossard

Simulation-based inference (SBI) of latent parameters in physical systems is often hindered by model misspecification--the mismatch between simulated and real-world observations caused by inherent modeling simplifications. RoPE, a recent SBI approach, addresses this challenge through a two-stage domain transfer process that combines semi-supervised calibration with optimal transport (OT)-based distribution alignment. However, RoPE operates in a fully transductive setting, requiring access to a batch of test samples at inference time, which limits scalability and generalization. We propose a fully inductive and amortized SBI framework that integrates calibration and distributional alignment into a single, end-to-end trainable model. Our method leverages mini-batch OT with a closed-form coupling to align real and simulated observations that correspond to the same latent parameters, using both paired calibration data and unpaired samples. A conditional normalizing flow is then trained to approximate the OT-induced posterior, enabling efficient inference without simulation access at test time. Across a range of synthetic and real-world benchmarks--including complex medical biomarker estimation--our approach matches or exceeds the performance of RoPE, while offering improved scalability and applicability in challenging, misspecified environments.

Computer Vision · Image and Video Generation

Chenhui Zhu, Yilu Wu, Shuai Wang, Gangshan Wu, Limin Wang

Image-to-video generation has made remarkable progress with the advancements in diffusion models, yet generating videos with realistic motion remains highly challenging. This difficulty arises from the complexity of accurately modeling motion, which involves capturing physical constraints, object interactions, and domain-specific dynamics that are not easily generalized across diverse scenarios. To address this, we propose MotionRAG, a retrieval-augmented framework that enhances motion realism by adapting motion priors from relevant reference videos through Context-Aware Motion Adaptation (CAMA). The key technical innovations include: (i) a retrieval-based pipeline extracting high-level motion features using video encoder and specialized resamplers to distill semantic motion representations; (ii) an in-context learning approach for motion adaptation implemented through a causal transformer architecture; (iii) an attention-based motion injection adapter that seamlessly integrates transferred motion features into pretrained video diffusion models. Extensive experiments demonstrate that our method achieves significant improvements across multiple domains and various base models, all with negligible computational overhead during inference. Furthermore, our modular design enables zero-shot generalization to new domains by simply updating the retrieval database without retraining any components. This research enhances the core capability of video generation systems by enabling the effective retrieval and transfer of motion priors, facilitating the synthesis of realistic motion dynamics.

Computer Vision · Image and Video Generation

Yunuo Chen, Junli Cao, Vidit Goel, Sergei Korolev, Chenfanfu Jiang, Jian Ren, Sergey Tulyakov, Anil Kag

We present a novel video generation framework that integrates 3-dimensional geometry and dynamic awareness. To achieve this, we augment 2D videos with 3D point trajectories and align them in pixel space. The resulting 3D-aware video dataset, PointVid, is then used to fine-tune a latent diffusion model, enabling it to track 2D objects with 3D Cartesian coordinates. Building on this, we regularize the shape and motion of objects in the video to eliminate undesired artifacts, e.g., non-physical deformation. Consequently, we enhance the quality of generated RGB videos and alleviate common issues like object morphing, which are prevalent in current video models due to a lack of shape awareness. With our 3D augmentation and regularization, our model is capable of handling contact-rich scenarios such as task-oriented videos, where 3D information is essential for perceiving shape and motion of interacting solids. Our method can be seamlessly integrated into existing video diffusion models to improve their visual plausibility.

Computer Vision · Everything Else

Jiaxin Huang, Ziwen Li, Hanlue Zhang, Runnan Chen, Zhengqing Gao, Xiao He, Yandong Guo, Wenping Wang, Tongliang Liu, Mingming Gong

The integration of language and 3D perception is critical for embodied AI and robotic systems to perceive, understand, and interact with the physical world. Spatial reasoning, a key capability for understanding spatial relationships between objects, remains underexplored in current 3D vision-language research. Existing datasets often mix semantic cues (e.g., object name) with spatial context, leading models to rely on superficial shortcuts rather than genuinely interpreting spatial relationships. To address this gap, we introduce Surprise3D, a novel dataset designed to evaluate language-guided spatial reasoning segmentation in complex 3D scenes. Surprise3D consists of more than 200k vision language pairs across 900+ detailed indoor scenes from ScanNet++ v2, including more than 2.8k unique object classes. The dataset contains 89k+ human-annotated spatial queries deliberately crafted without object name, thereby mitigating shortcut biases in spatial understanding. These queries comprehensively cover various spatial reasoning skills, such as relative position, narrative perspective, parametric perspective, and absolute distance reasoning. Initial benchmarks demonstrate significant challenges for current state-of-the-art expert 3D visual grounding methods and 3D-LLMs, underscoring the necessity of our dataset and the accompanying 3D Spatial Reasoning Segmentation (3D-SRS) benchmark suite. Surprise3D and 3D-SRS aim to facilitate advancements in spatially aware AI, paving the way for effective embodied interaction and robotic planning.