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Applications · Chemistry, Physics, and Earth Sciences

Mohammad Rashed, Duarte Filipe Valoroso Madeira, Babak Gholami, Caglar Guerbuez, Yunjia Yang, Nils Thuerey

Surrogate models for topology optimization (TO) exhibit highly variable out-of-distribution (OOD) generalization under distribution shifts such as changing loads or boundary conditions, yet the source of this variability remains unclear. We hypothesize that OOD performance is governed by how much information the conditioning signal preserves about the adjoint sensitivity (reduced gradient) that drives classical TO. Modeling the TO pipeline as a causal Markov chain, the Data Processing Inequality establishes that, under this abstraction, the sensitivity field is an information-theoretically optimal conditioning signal for topology prediction. However, computing exact adjoint sensitivities can be expensive or unavailable in practice; we observe that certain physical fields can approximate sensitivities through monotone transformations. To formalize this, we introduce \textbf{pseudo-sensitivities} to characterize which fields enable generalization versus those that are information-poor. We then show that a sensitivity-conditioned Bernoulli flow-matching generator empirically confirms these predictions: conditioning on sensitivities yields state-of-the-art OOD performance, while increasingly distant physical fields degrade toward raw parameter conditioning. We further benchmark against competitive baselines, and find the same ordering of conditioning signals and the same OOD trends. Results hold across structural TO benchmarks under load shifts and our new CFD-TO dataset under boundary-condition shifts such as multi-outlet configurations.

Applications · Time Series

Hunjae Lee, Corey Clark

Standard attention mechanisms in transformers employ static token representations that remain unchanged across all pair-wise computations in each layer. This limits their representational alignment with the potentially diverse dynamics of each token-pair interaction. While they excel in domains with relatively homogeneous relationships, standard attention may be inadequate in capturing heterogeneous inter-channel dependencies of multivariate time series (MTS) data where different channel-pair interactions within a single system may be governed by entirely different physical laws or temporal dynamics. To better align the attention mechanism for such domain phenomena, we propose attention with dynamic relational priming (prime attention). Prime attention modulates token representations for each token-pair, optimizing each pair-wise interaction for that specific relationship. Our results demonstrate that prime attention consistently outperforms standard attention across benchmarks, achieving up to 6.5\% improvement in forecasting accuracy. In addition, prime attention achieves comparable performance using up to 40\% less sequence length compared to standard attention, demonstrating its superior relational modeling capabilities and potential for data efficiency.

Applications · Chemistry, Physics, and Earth Sciences

Sung Moon Ko, Jaewan Lee, Sumin Lee, Soorin Yim, Sehui Han

Geometrical interpretations of deep learning models offer insightful perspectives into their underlying mathematical structures. In this work, we introduce a novel approach that leverages differential geometry, particularly concepts from Riemannian geometry, to integrate multiple models into a unified transfer learning framework. By aligning the Ricci curvature of latent space of individual models, we construct an interrelated architecture, namely Geometric Embedding Alignment via cuRvature matching in transfer learning (GEAR), which ensures comprehensive geometric representation across datapoints. This framework enables the effective aggregation of knowledge from diverse sources, thereby improving performance on target tasks. We evaluate our model on 23 molecular task pairs and demonstrate significant performance gains over existing benchmark models—achieving improvements of at least 14.4% under random splits and 8.3% under scaffold splits.

Deep Learning · Large Language Models

Fedor Rodionov, Abdelrahman Eldesokey, Michael Birsak, John Femiani, Bernard Ghanem, Peter Wonka

We introduce FloorplanQA, a diagnostic benchmark for evaluating spatial reasoning in large-language models (LLMs). FloorplanQA is grounded in structured representations of indoor scenes (e.g., kitchens, living rooms, bedrooms, bathrooms, and others), encoded symbolically in JSON or XML layouts. The benchmark covers core spatial tasks, including distance measurement, visibility, path finding, and object placement within constrained spaces. Our results across a variety of frontier open-source and commercial LLMs reveal that while models may succeed on shallow queries, they often fail to respect physical constraints and preserve spatial coherence, though they remain mostly robust to small spatial perturbations. FloorplanQA uncovers a blind spot in today’s LLMs: inconsistent reasoning about indoor layouts. We hope this benchmark inspires new work on language models that can accurately infer and manipulate spatial and geometric properties in practical settings.

Applications · Chemistry, Physics, and Earth Sciences

Jacopo Teneggi, SM Turzo, Tanya Marwah, Alberto Bietti, P. Douglas Renfrew, Vikram Mulligan, Siavash Golkar

Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML) methods achieve strong results, these are largely restricted to canonical amino acids and narrow objectives, leaving unfilled need for a generalist tool for broad design pipelines. We introduce Agent Rosetta, an LLM agent paired with a structured environment for operating Rosetta, the leading physics-based heteropolymer design software, capable of modeling non-canonical building blocks and geometries. Agent Rosetta iteratively refines designs to achieve user-defined objectives, combining LLM reasoning with Rosetta's generality. We evaluate Agent Rosetta on design with canonical amino acids, matching specialized models and expert baselines, and with non-canonical residues-where ML approaches fail-achieving comparable performance. Critically, prompt engineering alone often fails to generate Rosetta actions, demonstrating that environment design is essential for integrating LLM agents with specialized software. Our results show that properly designed environments enable LLM agents to make scientific software accessible while matching specialized tools and human experts.

Applications · Robotics

Jiaxu Wang, Junhao He, Jingkai SUN, Yi Gu, Yunyang Mo, Jiahang Cao, Qiang Zhang, Renjing Xu

Learning real-world dynamics from visual observations is crucial for various domains. A common strategy is to calibrate simulators by estimating physical parameters, yet accuracy is ultimately bounded by the underlying physical models, which often assume materials are homogeneous and isotropic. Even if reasonable, real-world objects typically exhibit mild anisotropy and heterogeneity. After the near-isotropic backbone is well calibrated, these residual effects become the key bottleneck for further closing the real-to-sim gap. Although neural networks can fit dynamics end-to-end, such black-box modeling discards strong physical priors, leading to poor data efficiency and overfitting. Therefore, we propose MoSA, a motion-constrained stress adaptation framework that targets these residual effects to further improve real-to-sim dynamics learning. MoSA uses an isotropic model as a physics prior and learns residual stress operators to capture mild anisotropy and heterogeneity. It progressively adapts stresses via microplane-constrained redistribution in a physics-informed cascaded network. We further impose motion constraints by supervising temporal and spatial derivatives of the deformation field. Experimentally, our learned dynamics achieves superior accuracy, generalization, and robustness, while learning physically meaningful residual anisotropy. Finally, we validate MoSA in a robot manipulation setting, showing that better real-to-sim dynamics modeling translates into more reliable sim-to-real transfer.

Jeong Woon Lee, Kyoleen Kwak, Daeho Kim, Hyoseok Hwang

Policies learned via continuous actor-critic methods often exhibit erratic, high-frequency oscillations, making them unsuitable for physical deployment. Current approaches attempt to enforce smoothness by directly regularizing the policy's output. We argue that this approach treats the symptom rather than the cause. In this work, we theoretically establish that policy non-smoothness is fundamentally governed by the differential geometry of the critic. By applying implicit differentiation to the actor-critic objective, we prove that the sensitivity of the optimal policy is bounded by the ratio of the Q-function's mixed-partial derivative (noise sensitivity) to its action-space curvature (signal distinctness). To empirically validate this theoretical insight, we introduce PAVE (Policy-Aware Value-field Equalization), a critic-centric regularization framework that treats the critic as a scalar field and stabilizes its induced action-gradient field. PAVE rectifies the learning signal by minimizing the Q-gradient volatility while preserving local curvature. Experimental results demonstrate that PAVE achieves smoothness and robustness comparable to policy-side smoothness regularization methods, while maintaining competitive task performance, without modifying the actor.

Deep Learning · Graph Neural Networks

Jintao Li, Yong-Yi Wang, Zheng-An Wang, Heng Fan

Diffusion-based neural solvers for combinatorial optimization repeatedly re-evaluate dense edge/factor interactions, making inference expensive in wall-clock time and often memory-bound at scale. We introduce LoRe, a training-free, inference-time drop-in wrapper that enforces per-step interaction-evaluation budgeting: at each iteration, it evaluates only a fixed fraction of interactions by dynamically routing computation to high-conflict or high-uncertainty interactions, instead of using a fixed sparsification (e.g., static kNN graphs or static masks). Under fully inclusive end-to-end wall-clock accounting, LoRe substantially improves scalability on maximum independent set, pushing feasible inference beyond the baseline out-of-memory boundary by $2.5\times$ while delivering $4$--$5\times$ speedup, about 81% peak-memory reduction, and 86.9% MIS-size retention. As an auxiliary study on large-scale TSP, LoRe achieves $7.5\times$ median speedup at $n=1000$ with 97% median memory reduction and a median gap difference of $-0.22$ percentage points versus the baseline, supporting its generality across problem families.

Applications · Chemistry, Physics, and Earth Sciences

Liao Chang, Luotian Yuan, Yiping Ke, Ying Wei

Multi-step retrosynthesis planning is a fundamental challenge in organic chemistry, defined by its enormous search space. Existing methods typically formulate it as a Markov Decision Process (MDP) with a fixed choice of transition model (i.e., a single-step retrosynthesis model), and focus on improving *how to search* through better policies and value functions. However, *how the transition space itself is navigated* remains largely unexplored. This limitation is particularly urgent given our observation of pronounced *skill disparity* among single-step prediction models: different models exhibit substantially different performance across molecule states. Motivated by this observation, we introduce RetrOrchestrator, an LLM-powered agent that explicitly accounts for model skill disparity by reframing retrosynthesis planning as a Partially Observable Markov Decision Process (POMDP). By regarding each single-step prediction model as a tool, we further propose a scaffold-aware reinforcement learning algorithm to optimize navigation policy within the transition space. As a result, RetrOrchestrator jointly searches which molecule to expand and which single-step model to apply for the molecule at the current step. Empirically, RetrOrchestrator significantly outperforms static baselines on the Retro*-190 benchmark, achieving a state-of-the-art 94.21\% success rate as well as a Pareto front in both wallclock time and number of model queries.

Applications · Chemistry, Physics, and Earth Sciences

Mujie Lin, Yutian Liu, Yudi Guo, Yanzhen Hou, Yiheng Tao, Ruochong Zheng, Kaiwen Cheng, Xin Shan, Youdong Mao, Jie Chen

Generating long-horizon, all-atom molecular dynamics (MD) is difficult due to error accumulation in time-domain autoregressive models (causing drift) and fixed step-size constraints on temporal resolution. We propose **BioDynaSpec**, which reformulates protein dynamics as spatio-spectral generation: **Independent Windowed Fourier Decomposition (IWFD)** decomposes trajectories into independent windowed frequency representations, and a generator combines low-to-high frequency autoregression with diffusion denoising to reconstruct continuous motion. We introduce **Inter-Residue Frequency Coupling (IRFC)** bias, a learnable Gaussian distance bias in attention that injects a resonance-inspired structural prior to stabilize training and improve cross-residue, cross-frequency consistency. On ATLAS, BioDynaSpec improves 250-frame trajectory generation with $R_{250}=1.509$ Å (where $R_s$ denotes the mean per-frame C$\alpha$-RMSE over the first $s$ frames after alignment), reducing error by 60.4\% vs. MDGEN and 57.2\% vs. ProAR, and achieves the best PCA-2D displacement-profile correlation and stepwise distribution matching. For equilibrium conformational sampling, it achieves Root Mean $W_2=1.31$, MD PCA $W_2=0.90$, and Joint PCA $W_2=1.19$ (50.03\%, 35.25\%, and 47.58\% lower than the next best), while ablations show removing IRFC severely degrades RMSE/MAE and correlation.

Applications · Computer Vision

Zijie Lou, Xiangwei Feng, Jiaxin Wang, Jiangtao Yao, Fei Che, Tianbao Liu, WU CHENGJING, Xiaochao Qu, Luoqi Liu, Ting Liu

Existing video object removal methods predominantly rely on diffusion models following a noise-to-data paradigm, where generation starts from uninformative Gaussian noise. This approach discards the rich structural and contextual priors present in the original input video. Consequently, such methods often lack sufficient guidance, leading to incomplete object erasure or the synthesis of implausible content that conflicts with the scene's physical logic. In this paper, we reformulate video object removal as a video-to-video translation task via a stochastic bridge model. Unlike noise-initialized methods, our framework establishes a direct stochastic path from the source video (with objects) to the target video (objects removed). This bridge formulation effectively leverages the input video as a strong structural prior, guiding the model to perform precise removal while ensuring that the filled regions are logically consistent with the surrounding environment. To address the trade-off where strong bridge priors hinder the removal of large objects, we propose a novel adaptive mask modulation strategy. This mechanism dynamically modulates input embeddings based on mask characteristics, balancing background fidelity with generative flexibility. Extensive experiments demonstrate that our approach significantly outperforms existing methods in both visual quality and temporal consistency. The project page is https://bridgeremoval.github.io/.

Applications · Chemistry, Physics, and Earth Sciences

Shrimon Mukherjee, KISHALAY DAS, Partha Basuchowdhuri, Pawan Goyal, Niloy Ganguly

Fast and accurate prediction of crystal properties is a central challenge in new materials design. Graph Neural Networks and transformer-based models have emerged as powerful tools for this task due to their ability to encode the local structural environment of atoms within a crystal. However, these models are data hungry and in practice labeled data for crystal properties are very scarce. Pretrain–finetuning strategies, particularly those based on diffusion models, have shown promise in addressing these limitations. In this work, we introduce a novel latent-diffusion based pretraining framework CrysLDNet designed to mitigate the data scarcity issue. Our approach integrates a Variational Autoencoder (VAE) with a diffusion model during the pretraining stage. The VAE encoder maps 3D crystal structures into a smooth latent space, within which the diffusion process is applied. This latent diffusion pretraining enables the graph encoder to effectively capture structural and chemical semantics from large-scale unlabeled data, which can then be finetuned for specific property prediction tasks. Comprehensive experiments on popular DFT datasets for property prediction reveal that CrysLDNet significantly outperforms both training-from-scratch and pretrained baselines, with improvements of 4.26% and 4.90% on JARVIS and MP datasets. Additionally, the learned representations remain robust under sparse data conditions and are expressive enough to correct DFT errors when finetuned with limited experimental data.

Applications · Computer Vision

Weilun Feng, Guoxin Fan, Haotong Qin, Chuanguang Yang, Mingqiang Wu, Yuqi Li, Xiangqi Li, Zhulin An, Libo Huang, Dingrui Wang 等

Diffusion-based world models have shown strong potential for unified world simulation, but the iterative denoising remains too costly for interactive use and long-horizon rollouts. While feature caching can accelerate inference without training, we find that policies designed for single-modal diffusion transfer poorly to world models due to two world-model-specific obstacles: *token heterogeneity* from multi-modal coupling and spatial variation, and *non-uniform temporal dynamics* where a small set of hard tokens drives error growth, making uniform skipping either unstable or overly conservative. We propose **WorldCache**, a caching framework tailored to diffusion world models. We introduce *Curvature-guided Heterogeneous Token Prediction*, which uses a physics-grounded curvature score to estimate token predictability and applies a Hermite-guided damped predictor for chaotic tokens with abrupt direction changes. We also design *Chaotic-prioritized Adaptive Skipping*, which accumulates a curvature-normalized, dimensionless drift signal and recomputes only when bottleneck tokens begin to drift. Experiments on diffusion world models show that WorldCache delivers up to **3.7$\times$** end-to-end speedups while maintaining **98\%** rollout quality, demonstrating the vast advantages and practicality of WorldCache in resource-constrained scenarios.

Applications · Computer Vision

Yixing Yong, Jian Wang, Ming Lei, Lijun He, Fan Li

Infrared object detection is crucial for perception in autonomous driving and surveillance but remains vulnerable to physical adversarial attacks. Unlike in the RGB domain, where attacks rely on color texture, infrared attacks must manipulate thermal signatures, making the geometry shape of heat-blocking materials the primary adversarial information carrier. Current shape-based methods suffer from a fundamental trade-off between representational capability and optimization power, limiting their attack effectiveness. In this work, we overcome this dilemma by introducing learnable Fourier shapes to the infrared domain. We utilize an end-to-end differentiable framework where a compact set of Fourier coefficients, defining the shape boundary, is analytically mapped to a pixel-space mask via the winding number theorem. This enables efficient gradient-based optimization to generate potent shapes that cause human targets to evade detection. Extensive digital and physical experiments provide a comprehensive evaluation and validate our superior performance. Our resulting physical patch achieves striking robustness, successfully evading detectors across diverse distances, angles, poses, and individuals, and achieves over 88% attack success rate at distances greater than 25m (conf.=0.5).Video demo and source code are available in the supplementary material.

Applications · Chemistry, Physics, and Earth Sciences

Zipeng Sun, Can Chen, Ye Yuan, Haolun Wu, Jiayao Gu, Christopher Pal, Xue Liu

We study offline black-box optimization (BBO), aiming to discover improved designs from an offline dataset of designs and labels, a problem common in robotics, DNA, and materials science with limited labeled samples. While recent work applies autoregressive LLMs to BBO by formatting tasks as natural-language prompts, their left-to-right design generation struggles to capture the strong bidirectional dependencies inherent in design problems. To address this, we propose adapting diffusion LLMs to offline BBO to leverage their bidirectional modeling capabilities. However, a domain gap exists between the natural text pre-training of diffusion LLMs and the heterogeneous signals in BBO (prompts, designs, and labels). To bridge this gap, we construct a unified prompt–response corpus and introduce delimiter tokens to explicitly mark field boundaries for *domain adaptation*. We further propose a two-stage *post-training* framework to align the diffusion LLM generation with high-label designs. The first stage performs supervised fine-tuning on the unified dataset via masked-response prediction, and the second stage adopts reinforcement learning with rewards defined by label improvements. Our method achieves state-of-the-art results on Design-Bench small-data settings. Code for our work is available here: https://anonymous.4open.science/r/Anonymous-dllm4bbo-D78A/README.md.

Deep Learning · Generative Models and Autoencoders

Xiaochao Deng, Jie Chen, Xiaogang Deng

Accurately modeling the full distributions of possible states is crucial for understanding statistical properties and enabling reliable predictions in complex, unsteady physical systems. Recently, diffusion models and flow matching have shown promise in these tasks. However, they remain limited in uncovering the general principles of systems from multiple short trajectories across condition space. In addition, they exhibit inferior adaptability to large irregular geometries, particularly in regions with sharp gradients. In this paper, we propose a condition-aware graph flow matching (CGFM) method that combines condition-aware flow matching with a hierarchical graph structure to learn the full distributions of physical systems from incomplete training data. Specifically, CGFM constructs a flow enabling smooth interpolation across physical conditions and parameterizes the graph-conditioned vector field through HieraGraphNet. HieraGraphNet performs message passing across multilevel graphs to capture multi-scale dynamics and facilitate long-range information interactions in physical systems. Moreover, we introduce a topology- and geometry-aware graph coarsening scheme that incorporates topological connectivity and local geometric density to construct reliable coarse graphs. We validate the effectiveness of CGFM on three canonical scenarios across both 2D and 3D dynamics, which demonstrate its superior performance compared with that of state-of-the-art baselines.

Deep Learning · Generative Models and Autoencoders

Andrew Millard, Fredrik Lindsten, Zheng Zhao

We introduce a guided stochastic sampling method that augments sampling from diffusion models with physics-based guidance derived from partial differential equation (PDE) residuals and observational constraints, ensuring generated samples remain physically admissible. We embed this sampling procedure within a new Sequential Monte Carlo (SMC) framework, yielding a scalable generative PDE solver. Across multiple benchmark PDE systems as well as multiphysics and interacting PDE systems, our method produces solution fields with lower numerical error than existing state-of-the-art generative methods.

Deep Learning · Generative Models and Autoencoders

Gyeonghoon Ko, Juho Lee

Riemannian diffusion models generalize score-based generative modeling to manifold-supported data via stochastic diffusion equations on the manifold. However, training requires sampling from and differentiating the manifold heat kernel, which is rarely available in closed form beyond a few highly symmetric manifolds. We propose a general approach that approximates the heat kernel by directly solving the manifold heat equation with a physics-informed neural network (PINN). Given an explicit manifold specification, we choose a coordinate system, derive the corresponding heat (Fokker--Planck) equation and a short-time asymptotic approximation, and then train a PINN to learn the log heat kernel. The resulting surrogate enables both forward noising (heat-kernel sampling) and conditional-score evaluation for denoising score matching. We demonstrate the method on diverse manifolds including $S^2$, $SO(3)$, $\mathrm{SPD}(n)$, and permutation-quotiented point clouds.

Applications · Time Series

Yangyou Liu, Zezhi Shao, Xinyu Chen, Hu Chen, Fei Wang, Yuankai Wu

Time series forecasting under non-stationarity faces a fundamental tension between capturing stable representations and adapting to distribution shifts. Existing methods implicitly rely on static historical assumptions, leading to a critical failure mode we term Phase Amnesia, where models become blind to the evolving global context. To resolve this, we formalize non-stationary dynamics through three physical hypotheses: Wold decomposition, dynamical phase evolution, and heteroscedastic manifold generation. These principles inspire PULSE, a physics-informed, plug-and-play framework adopting a Disentangle--Evolve--Simulate design philosophy. Specifically, PULSE utilizes phase-anchored disentanglement to resolve optimization interference caused by dominant trends, employs a Phase Router to actively generate future trajectories, and introduces Statistic-Aware Mixup (SAM) to ensure robustness against out-of-distribution volatility. Empirically, PULSE enables a simple MLP backbone to consistently outperform state-of-the-art Transformers across 12 real-world benchmarks. This validates that a correct physics-informed inductive bias is far more critical than raw architectural complexity for non-stationary forecasting.

Reinforcement Learning · Everything Else

Bosun Liang, Shuo Pei, Zirui Chen, Chuanzhi Fan, Chen Sun, Yuankai Wu, Huachun Tan, Yong Wang

Reinforcement learning often produces high-frequency oscillatory control signals that undermine the safety and stability required for physical deployment. Explicit action chunking addresses this by predicting fixed-horizon trajectories but increases the policy output dimension to R^hd, leading to optimization difficulties and incompatibility with standard step-wise interaction. To overcome these challenges, this paper proposes Dual-Window Smoothing (DWS), an implicit action chunking framework for smooth continuous control. Unlike explicit methods, DWS enforces temporal coherence without expanding the action space. It uses a dual-window design: an execution window that ensures physical smoothness through deterministic modulation, and a value window that aligns temporal-difference targets over the horizon to correct critic bias caused by open-loop execution. DWS also includes a lightweight actor-side temporal regularizer based on first-order action differences to promote global continuity. This design effectively bridges the gap between temporal abstraction and reactive step-wise control. Experiments on benchmarks including the DeepMind Control Suite and industrial energy management tasks with vector states show that DWS outperforms state-of-the-art (SOTA) baselines such as LipsNet++ and SmODE. In complex vision-based autonomous driving tasks, DWS achieves smoother control, safer behavior with reduced jitter, and attains a 100% success rate.