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Applications · Robotics

Amber Xie, Oleh Rybkin, Dorsa Sadigh, Chelsea Finn

Recent progress in imitation learning has been enabled by policy architectures that scale to complex visuomotor tasks, multimodal distributions, and large datasets. However, these methods often rely on learning from large amount of expert demonstrations.To address these shortcomings, we propose Latent Diffusion Planning (LDP), a modular approach consisting of a planner which can leverage action-free demonstrations, and an inverse dynamics model which can leverage suboptimal data, that both operate over a learned latent space. First, we learn a compact latent space through a variational autoencoder, enabling effective forecasting of future states in image-based domains. Then, we train a planner and an inverse dynamics model with diffusion objectives. By separating planning from action prediction, LDP can benefit from the denser supervision signals of suboptimal and action-free data.On simulated visual robotic manipulation tasks, LDP outperforms state-of-the-art imitation learning approaches, as they cannot leverage such additional data.

Deep Learning · Large Language Models

Yunzhuo Hao, Jiawei Gu, Huichen Wang, Linjie Li, Zhengyuan Yang, Lijuan Wang, Yu Cheng

The ability to organically reason over and with both text and images is a pillar of human intelligence, yet the ability of Multimodal Large Language Models (MLLMs) to perform such multimodal reasoning remains under-explored. Existing benchmarks often emphasize text-dominant reasoning or rely on shallow visual cues, failing to adequately assess integrated visual and textual reasoning. We introduce EMMA (Enhanced MultiModal reAsoning), a benchmark targeting organic multimodal reasoning across mathematics, physics, chemistry, and coding. EMMA tasks demand advanced cross-modal reasoning that cannot be addressed by reasoning independently in each modality, offering an enhanced test suite for MLLMs' reasoning capabilities. Our evaluation of state-of-the-art MLLMs on EMMA reveals significant limitations in handling complex multimodal and multi-step reasoning tasks, even with advanced techniques like Chain-of-Thought prompting and test-time compute scaling underperforming. These findings underscore the need for improved multimodal architectures and training paradigms to close the gap between human and model reasoning in multimodality.

Reinforcement Learning · Batch/Offline

Minting Pan, Yitao Zheng, Jiajian Li, Yunbo Wang, Xiaokang Yang

Offline reinforcement learning (RL) enables policy optimization using static datasets, avoiding the risks and costs of extensive real-world exploration. However, it struggles with suboptimal offline behaviors and inaccurate value estimation due to the lack of environmental interaction. We present Video-Enhanced Offline RL (VeoRL), a model-based method that constructs an interactive world model from diverse, unlabeled video data readily available online. Leveraging model-based behavior guidance, our approach transfers commonsense knowledge of control policy and physical dynamics from natural videos to the RL agent within the target domain. VeoRL achieves substantial performance gains (over 100% in some cases) across visual control tasks in robotic manipulation, autonomous driving, and open-world video games. Project page: https://panmt.github.io/VeoRL.github.io.

Applications · Chemistry, Physics, and Earth Sciences

Ankit Ghosh, Gargee Kashyap, Sarthak Mittal, Nupur Jain, Raghavan B Sunoj, Abir De

Yield of chemical reactions generally depends on the activation barrier, i.e., the energy difference between the reactant and the transition state. Computing the transition state from the reactant and product graphs requires prior knowledge of the correct node alignment (i.e., atom mapping), which is not available in yield prediction datasets. In this work, we propose YieldNet, a neural yield prediction model, which tackles these challenges. Here, we first approximate the atom mapping between the reactants and products using a differentiable node alignment network. We then use this approximate atom mapping to obtain a noisy realization of the condensed graph of reaction (CGR), which is a supergraph encompassing both the reactants and products. This CGR serves as a surrogate for the transition state graph structure. The CGR embeddings of different steps in a multi-step reaction are then passed into a transformer-guided reaction path encoder.Our experiments show that YieldNet can predict the yield more accurately than the baselines. Furthermore, the model is trained only under the distant supervision of yield values, without requiring fine-grained supervision of atom mapping.

Applications · Chemistry, Physics, and Earth Sciences

Ye DU, Chen Yang, Nanxi Yu, Wanyu LIN, Qian Zhao, Shujun Wang

*De novo* peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models encode the observed mass spectra into latent representations from which peptides are predicted auto-regressively. However, the issue of missing fragmentation, attributable to factors such as suboptimal fragmentation efficiency and instrumental constraints, presents a formidable challenge in practical applications. To tackle this obstacle, we propose a novel computational paradigm called $\underline{\textbf{L}}$atent $\underline{\textbf{I}}$mputation before $\underline{\textbf{P}}$rediction (LIPNovo). LIPNovo is devised to compensate for missing fragmentation information within observed spectra before executing the final peptide prediction. Rather than generating raw missing data, LIPNovo performs imputation in the latent space, guided by the theoretical peak profile of the target peptide sequence. The imputation process is conceptualized as a set-prediction problem, utilizing a set of learnable peak queries to reason about the relationships among observed peaks and directly generate the latent representations of theoretical peaks through optimal bipartite matching. In this way, LIPNovo manages to supplement missing information during inference and thus boosts performance. Despite its simplicity, experiments on three benchmark datasets demonstrate that LIPNovo outperforms state-of-the-art methods by large margins. Code is available at https://github.com/usr922/LIPNovo.

Applications · Everything Else

Mingjun Wang, Yihan Wen, Bin Sun, Jianan Mu, Juan Li, Xiaoyi Wang, Jing Ye, Bei Yu, Huawei Li

Accurate and efficient timing prediction at the register-transfer level (RTL) remains a fundamental challenge in electronic design automation (EDA), particularly in striking a balance between accuracy and computational efficiency. While static timing analysis (STA) provides high-fidelity results through comprehensive physical parameters, its computational overhead makes it impractical for rapid design iterations. Conversely, existing RTL-level approaches sacrifice accuracy due to the limited physical information available. We propose RTLDistil, a novel cross-stage knowledge distillation framework that bridges this gap by transferring precise physical characteristics from a layout-aware teacher model (Teacher GNN) to an efficient RTL-level student model (Student GNN), both implemented as graph neural networks (GNNs). RTLDistil efficiently predicts key timing metrics, such as arrival time (AT), and employs a multi-granularity distillation strategy that captures timing-critical features at node, subgraph, and global levels. Experimental results demonstrate that RTLDistil achieves significant improvement in RTL-level timing prediction error reduction, compared to state-of-the-art prediction models. This framework enables accurate early-stage timing prediction, advancing EDA's ``left-shift'' paradigm while maintaining computational efficiency. Our code and dataset will be publicly available at https://github.com/sklp-eda-lab/RTLDistil.

Theory · Deep Learning

Edward Pearce-Crump

Incorporating permutation equivariance into neural networks has proven to be useful in ensuring that models respect symmetries that exist indata. Symmetric tensors, which naturally appearin statistics, machine learning, and graph theory,are essential for many applications in physics,chemistry, and materials science, amongst others. However, existing research on permutationequivariant models has not explored symmetrictensors as inputs, and most prior work on learningfrom these tensors has focused on equivarianceto Euclidean groups. In this paper, we presenttwo different characterisations of all linear permutation equivariant functions between symmetricpower spaces of $\mathbb{R}^{n}$. We show on two tasks thatthese functions are highly data efficient comparedto standard MLPs and have potential to generalisewell to symmetric tensors of different sizes.

Applications · Chemistry, Physics, and Earth Sciences

Jingxiang Qu, Wenhan Gao, Jiaxing Zhang, Xufeng Liu, Hua Wei, Haibin Ling, Yi Liu

3D Geometric Graph Neural Networks (GNNs) have emerged as transformative tools for modeling molecular data. Despite their predictive power, these models often suffer from limited interpretability, raising concerns for scientific applications that require reliable and transparent insights. While existing methods have primarily focused on explaining molecular substructures in 2D GNNs, the transition to 3D GNNs introduces unique challenges, such as handling the implicit dense edge structures created by a cutoff radius. To tackle this, we introduce a novel explanation method specifically designed for 3D GNNs, which localizes the explanation to the immediate neighborhood of each node within the 3D space. Each node is assigned an radius of influence, defining the localized region within which message passing captures spatial and structural interactions crucial for the model's predictions. This method leverages the spatial and geometric characteristics inherent in 3D graphs. By constraining the subgraph to a localized radius of influence, the approach not only enhances interpretability but also aligns with the physical and structural dependencies typical of 3D graph applications, such as molecular learning.

Applications · Chemistry, Physics, and Earth Sciences

Wenyin Zhou, Christopher I Sprague, Vsevolod Viliuga, Matteo Tadiello, Arne Elofsson, Hossein Azizpour

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design.Recent advances in generative modeling, such as diffusion models and flow matching, have made great progress on these tasks by modeling molecular conformations as a distribution.In this work, we focus on flow matching and adopt an energy-based perspective to improve training and inference of structure generation models. Our view results in a mapping function, represented by a deep network, that is directly learned to \textit{iteratively} map random configurations, i.e. samples from the source distribution, to target structures, i.e. points in the data manifold. This yields a conceptually simple and empirically effective flow matching setup that is theoretically justified and has interesting connections to fundamental properties such as idempotency and stability, as well as the empirically useful techniques such as structure refinement in AlphaFold. Experiments on protein docking as well as protein backbone generation consistently demonstrate the method's effectiveness, where it outperforms recent baselines of task-associated flow matching and diffusion models, using a similar computational budget.

Applications · Chemistry, Physics, and Earth Sciences

Yeyun Chen, Jiangming Shi

The progress in materials science and drug discovery is impeded by the availability of labeled data and the high costs of manual annotation, driving the need for efficient strategies to capture molecular representations and enable accurate predictions. Pretrained Graph Neural Networks have shown promise in capturing universal molecular representations, but adapting them to task-specific applications remains challenging. In this paper, we propose Multilevel Informed Prompt-Tuning (MIPT), a novel framework for effectively tailoring pretrained models to molecule-related tasks. MIPT utilizes a lightweight, multi-level prompt learning module to capture node-level and graph-level task-specific knowledge, ensuring adaptable and efficient tuning. Additionally, a noise penalty mechanism is introduced to address mismatches between pretrained representations and downstream tasks, reducing irrelevant or noisy information. Experimental results show that MIPT surpasses all baselines, aligning graph space and task space while achieving significant improvements in molecule-related tasks, demonstrating its scalability and versatility for molecular tasks.

Applications · Chemistry, Physics, and Earth Sciences

Minghao Xu, Jiaze Song, Keming Wu, Xiangxin Zhou, Bin Cui, Wentao Zhang

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA.

Applications · Chemistry, Physics, and Earth Sciences

Shanda Li, Shinjae Yoo, Yiming Yang

Fourier Neural Operators (FNOs) offer a principled approach for solving complex partial differential equations (PDEs). However, scaling them to handle more complex PDEs requires increasing the number of Fourier modes, which significantly expands the number of model parameters and makes hyperparameter tuning computationally impractical. To address this, we introduce $\mu$**Transfer-FNO**, a zero-shot hyperparameter transfer technique that enables optimal configurations, tuned on smaller FNOs, to be directly applied to billion-parameter FNOs _without_ additional tuning. Building on the Maximum Update Parametrization ($\mu$P) framework, we mathematically derive a parametrization scheme that facilitates the transfer of optimal hyperparameters across models with different numbers of Fourier modes in FNOs, which is validated through extensive experiments on various PDEs. Our empirical study shows that $\mu$Transfer-FNO reduces computational cost for tuning hyperparameters on large FNOs while maintaining or improving accuracy.

Applications · Computer Vision

Fanqing Meng, Jiaqi Liao, Xinyu Tan, Quanfeng Lu, WENQI SHAO, Kaipeng Zhang, Yu Cheng, Dianqi Li, Ping Luo

Text-to-video (T2V) models like Sora have made significant strides in visualizing complex prompts, which is increasingly viewed as a promising path towards constructing the universal world simulator. Cognitive psychologists believe that the foundation for achieving this goal is the ability to understand intuitive physics. However, the capacity of these models to accurately represent intuitive physics remains largely unexplored. To bridge this gap, we introduce PhyGenBench, a comprehensive \textbf{Phy}sics \textbf{Gen}eration \textbf{Ben}chmark designed to evaluate physical commonsense correctness in T2V generation. PhyGenBench comprises 160 carefully crafted prompts across 27 distinct physical laws, spanning four fundamental domains, which could comprehensively assesses models' understanding of physical commonsense. Alongside PhyGenBench, we propose a novel evaluation framework called PhyGenEval. This framework employs a hierarchical evaluation structure utilizing appropriate advanced vision-language models and large language models to assess physical commonsense. Through PhyGenBench and PhyGenEval, we can conduct large-scale automated assessments of T2V models' understanding of physical commonsense, which align closely with human feedback. Our evaluation results and in-depth analysis demonstrate that current models struggle to generate videos that comply with physical commonsense. Moreover, simply scaling up models or employing prompt engineering techniques is insufficient to fully address the challenges presented by PhyGenBench (e.g., dynamic scenarios). We hope this study will inspire the community to prioritize the learning of physical commonsense in these models beyond entertainment applications. We will release the data and codes at https://github.com/OpenGVLab/PhyGenBench

Theory · Learning Theory

Alon Beck, Noam Levi, Yohai Bar-Sinai

We investigate the phenomenon of grokking -- delayed generalization accompanied by non-monotonic test loss behavior -- in a simple binary logistic classification task, for which "memorizing" and "generalizing" solutions can be strictly defined. Surprisingly, we find that grokking arises naturally even in this minimal model when the parameters of the problem are close to a critical point, and provide both empirical and analytical insights into its mechanism.Concretely, by appealing to the implicit bias of gradient descent, we show that logistic regression can exhibit grokking when the training dataset is nearly linearly separable from the origin and there is strong noise in the perpendicular directions.The underlying reason is that near the critical point, "flat" directions in the loss landscape with nearly zero gradient cause training dynamics to linger for arbitrarily long times near quasi-stable solutions before eventually reaching the global minimum.Finally, we highlight similarities between our findings and the recent literature, strengthening the conjecture that grokking generally occurs in proximity to the interpolation threshold, reminiscent of critical phenomena often observed in physical systems.

Deep Learning · Graph Neural Networks

Huayu Deng, Xiangming Zhu, Yunbo Wang, Xiaokang Yang

Graph neural networks have been a powerful tool for mesh-based physical simulation. To efficiently model large-scale systems, existing methods mainly employ hierarchical graph structures to capture multi-scale node relations. However, these graph hierarchies are typically manually designed and fixed, limiting their ability to adapt to the evolving dynamics of complex physical systems. We propose EvoMesh, a fully differentiable framework that jointly learns graph hierarchies and physical dynamics, adaptively guided by physical inputs. EvoMesh introduces anisotropic message passing, which enables direction-specific aggregation of dynamic features between nodes within each hierarchy, while simultaneously learning node selection probabilities for the next hierarchical level based on physical context. This design creates more flexible message shortcuts and enhances the model's capacity to capture long-range dependencies. Extensive experiments on five benchmark physical simulation datasets show that EvoMesh outperforms recent fixed-hierarchy message passing networks by large margins. The project page is available at https://hbell99.github.io/evo-mesh/.

Applications · Chemistry, Physics, and Earth Sciences

Christopher Subich, Syed Husain, Leo Separovic, Jing Yang

Recent advancements in data-driven weather forecasting models have delivered deterministic models that outperform the leading operational forecast systems based on traditional, physics-based models. However, these data-driven models are typically trained with a mean squared error loss function, which causes smoothing of fine scales through a ``double penalty'' effect. We develop a simple, parameter-free modification to this loss function that avoids this problem by separating the loss attributable to decorrelation from the loss attributable to spectral amplitude errors. Fine-tuning the GraphCast model with this new loss function results in sharp deterministic weather forecasts, an increase of the model's effective resolution from 1,250km to 160km, improvements to ensemble spread, and improvements to predictions of tropical cyclone strength and surface wind extremes.

Applications · Chemistry, Physics, and Earth Sciences

Yusheng Zhao, Chi Zhang, Yuxuan Du

Characterizing the ground state properties of quantum systems is fundamental to capturing their behavior but computationally challenging. Recent advances in AI have introduced novel approaches, with diverse machine learning (ML) and deep learning (DL) models proposed for this purpose. However, the necessity and specific role of DL models in these tasks remain unclear, as prior studies often employ varied or impractical quantum resources to construct datasets, resulting in unfair comparisons. To address this, we systematically benchmark DL models against traditional ML approaches across three families of Hamiltonian, scaling up to $127$ qubits in three crucial ground-state learning tasks while enforcing equivalent quantum resource usage. Our results reveal that ML models often achieve performance comparable to or even exceeding that of DL approaches across all tasks. Furthermore, a randomization test demonstrates that measurement input features have minimal impact on DL models' prediction performance. These findings challenge the necessity of current DL models in many quantum system learning scenarios and provide valuable insights into their effective utilization.

Applications · Chemistry, Physics, and Earth Sciences

Wangzhi Zhan, Chen Jianpeng, Dongqi Fu, Dawei Zhou

Metamaterials are artificial materials that are designed to meet unseen properties in nature, such as ultra-stiffness and negative materials indices. In mechanical metamaterial design, three key modalities are typically involved, i.e., 3D topology, density condition, and mechanical property. Real-world complex application scenarios place the demanding requirements on machine learning models to consider all three modalities together. However, a comprehensive literature review indicates that most existing works only consider two modalities, e.g., predicting mechanical properties given the 3D topology or generating 3D topology given the required properties. Therefore, there is still a significant gap for the state-of-the-art machine learning models capturing the whole. Hence, we propose a unified model named UniMate, which consists of a modality alignment module and a synergetic diffusion generation module. Experiments indicate that UniMate outperforms the other baseline models in topology generation task, property prediction task, and condition confirmation task by up to 80.2%, 5.1%, and 50.2%, respectively. We open-source our proposed UniMate model and corresponding results at https://github.com/wzhan24/UniMate.

Applications · Chemistry, Physics, and Earth Sciences

Chenhui Xu, Dancheng Liu, Yuting Hu, Jiajie Li, Ruiyang Qin, Qingxiao Zheng, Jinjun Xiong

Physics-Informed Neural Networks (PINNs) are a kind of deep-learning-based numerical solvers for partial differential equations (PDEs). Existing PINNs often suffer from failure modes of being unable to propagate patterns of initial conditions. We discover that these failure modes are caused by the simplicity bias of neural networks and the mismatch between PDE's continuity and PINN's discrete sampling. We reveal that the State Space Model (SSM) can be a continuous-discrete articulation allowing initial condition propagation, and that simplicity bias can be eliminated by aligning a sequence of moderate granularity. Accordingly, we propose PINNMamba, a novel framework that introduces sub-sequence modeling with SSM. Experimental results show that PINNMamba can reduce errors by up to 86.3\% compared with state-of-the-art architecture. Our code is available at Supplementary Material.

Applications · Chemistry, Physics, and Earth Sciences

Cailong Hua, Sivaraman Rajaganapathy, Rebecca Slick, Joseph Vavra, Joseph Muretta, James Ervasti, Murti Salapaka

Deciphering protein folding and unfolding pathways under tension is essential for deepening our understanding of fundamental biological mechanisms. Such insights hold the promise of developing treatments for a range of debilitating and fatal conditions, including muscular disorders like Duchenne Muscular Dystrophy and neurodegenerative diseases such as Parkinson's disease. Single molecule force spectroscopy (SMFS) is a powerful technique for investigating forces involved in protein domains folding and unfolding. However, SMFS trials often involve multiple protein molecules, necessitating filtering to isolate measurements from single-molecule trials. Currently, manual visual inspection is the primary method for classifying single-molecule data; a process that is both time-consuming and requires significant expertise. Here, we both apply state-of-the-art machine learning models and present a novel deep learning model tailored to SMFS data. The proposed model employs a dual-branch fusion strategy; one branch integrates the physics of protein molecules, and the other operates independently of physical constraints. This model automates the isolation of single-molecule measurements, significantly enhancing data processing efficiency. To train and validate our approach, we developed a physics-based Monte Carlo engine to simulate force spectroscopy datasets, including trials involving single molecules, multiple molecules, and no molecules. Our model achieves state-of-the-art performance, outperforming five baseline methods on both simulated and experimental datasets. It attains nearly 100\% accuracy across all simulated datasets and an average accuracy of $79.6 \pm 5.2$\% on experimental datasets, using only $\sim$30 training samples, surpassing baseline methods by 11.4\%. Notably, even without expert annotations on experimental data, the model achieves an average accuracy of $72.0 \pm 5.9$\% when pre-trained on corresponding simulated datasets. With our deep learning approach, the time required to extract meaningful statistics from single-molecule SMFS trials is reduced from a day to under an hour. This work results in SMFS experimental datasets from four important protein molecules crucial to many biological pathways. To support further research, we have made our datasets publicly available and provided a Python-based toolbox (https://github.com/SalapakaLab-SIMBioSys/SMFS-Identification).