Wenbing Huang

Yikai Wang, Xinghao Chen, Lele Cao et al.

Many adaptations of transformers have emerged to address the single-modal vision tasks, where self-attention modules are stacked to handle input sources like images. Intuitively, feeding multiple modalities of data to vision transformers could improve the performance, yet the inner-modal attentive weights may also be diluted, which could thus undermine the final performance. In this paper, we propose a multimodal token fusion method (TokenFusion), tailored for transformer-based vision tasks. To effectively fuse multiple modalities, TokenFusion dynamically detects uninformative tokens and substitutes these tokens with projected and aggregated inter-modal features. Residual positional alignment is also adopted to enable explicit utilization of the inter-modal alignments after fusion. The design of TokenFusion allows the transformer to learn correlations among multimodal features, while the single-modal transformer architecture remains largely intact. Extensive experiments are conducted on a variety of homogeneous and heterogeneous modalities and demonstrate that TokenFusion surpasses state-of-the-art methods in three typical vision tasks: multimodal image-to-image translation, RGB-depth semantic segmentation, and 3D object detection with point cloud and images. Our code is available at https://github.com/yikaiw/TokenFusion.

Chengliang Zhong, Peixing You, Xiaoxue Chen et al.

Detecting 3D keypoints from point clouds is important for shape reconstruction, while this work investigates the dual question: can shape reconstruction benefit 3D keypoint detection? Existing methods either seek salient features according to statistics of different orders or learn to predict keypoints that are invariant to transformation. Nevertheless, the idea of incorporating shape reconstruction into 3D keypoint detection is under-explored. We argue that this is restricted by former problem formulations. To this end, a novel unsupervised paradigm named SNAKE is proposed, which is short for shape-aware neural 3D keypoint field. Similar to recent coordinate-based radiance or distance field, our network takes 3D coordinates as inputs and predicts implicit shape indicators and keypoint saliency simultaneously, thus naturally entangling 3D keypoint detection and shape reconstruction. We achieve superior performance on various public benchmarks, including standalone object datasets ModelNet40, KeypointNet, SMPL meshes and scene-level datasets 3DMatch and Redwood. Intrinsic shape awareness brings several advantages as follows. (1) SNAKE generates 3D keypoints consistent with human semantic annotation, even without such supervision. (2) SNAKE outperforms counterparts in terms of repeatability, especially when the input point clouds are down-sampled. (3) the generated keypoints allow accurate geometric registration, notably in a zero-shot setting. Codes are available at https://github.com/zhongcl-thu/SNAKE

Runfa Chen, Yu Rong, Shangmin Guo et al.

After the great success of Vision Transformer variants (ViTs) in computer vision, it has also demonstrated great potential in domain adaptive semantic segmentation. Unfortunately, straightforwardly applying local ViTs in domain adaptive semantic segmentation does not bring in expected improvement. We find that the pitfall of local ViTs is due to the severe high-frequency components generated during both the pseudo-label construction and features alignment for target domains. These high-frequency components make the training of local ViTs very unsmooth and hurt their transferability. In this paper, we introduce a low-pass filtering mechanism, momentum network, to smooth the learning dynamics of target domain features and pseudo labels. Furthermore, we propose a dynamic of discrepancy measurement to align the distributions in the source and target domains via dynamic weights to evaluate the importance of the samples. After tackling the above issues, extensive experiments on sim2real benchmarks show that the proposed method outperforms the state-of-the-art methods. Our codes are available at https://github.com/alpc91/TransDA

Jie Chen, Zhipeng Chen, Jiapeng Wang et al.

Continual pre-training (CPT) has been an important approach for adapting language models to specific domains or tasks. To make the CPT approach more traceable, this paper presents a technical report for continually pre-training Llama-3 (8B), which significantly enhances the Chinese language ability and scientific reasoning ability of the backbone model. To enhance the new abilities while retaining the original abilities, we design specific data mixture and curriculum strategies by utilizing existing datasets and synthesizing high-quality datasets. Specifically, we synthesize multidisciplinary scientific question and answer (QA) pairs based on related web pages, and subsequently incorporate these synthetic data to improve the scientific reasoning ability of Llama-3. We refer to the model after CPT as Llama-3-SynE (Synthetic data Enhanced Llama-3). We also present the tuning experiments with a relatively small model -- TinyLlama, and employ the derived findings to train the backbone model. Extensive experiments on a number of evaluation benchmarks show that our approach can largely improve the performance of the backbone models, including both the general abilities (+8.81 on C-Eval and +6.31 on CMMLU) and the scientific reasoning abilities (+12.00 on MATH and +4.13 on SciEval), without hurting the original capacities. Our model, data, and codes are available at https://github.com/RUC-GSAI/Llama-3-SynE.

Wenbing Huang, Jiaqi Han, Yu Rong et al.

Learning to reason about relations and dynamics over multiple interacting objects is a challenging topic in machine learning. The challenges mainly stem from that the interacting systems are exponentially-compositional, symmetrical, and commonly geometrically-constrained. Current methods, particularly the ones based on equivariant Graph Neural Networks (GNNs), have targeted on the first two challenges but remain immature for constrained systems. In this paper, we propose Graph Mechanics Network (GMN) which is combinatorially efficient, equivariant and constraint-aware. The core of GMN is that it represents, by generalized coordinates, the forward kinematics information (positions and velocities) of a structural object. In this manner, the geometrical constraints are implicitly and naturally encoded in the forward kinematics. Moreover, to allow equivariant message passing in GMN, we have developed a general form of orthogonality-equivariant functions, given that the dynamics of constrained systems are more complicated than the unconstrained counterparts. Theoretically, the proposed equivariant formulation is proved to be universally expressive under certain conditions. Extensive experiments support the advantages of GMN compared to the state-of-the-art GNNs in terms of prediction accuracy, constraint satisfaction and data efficiency on the simulated systems consisting of particles, sticks and hinges, as well as two real-world datasets for molecular dynamics prediction and human motion capture.

Jiaqi Han, Wenbing Huang, Hengbo Ma et al.

Graph Neural Networks (GNNs) have become a prevailing tool for learning physical dynamics. However, they still encounter several challenges: 1) Physical laws abide by symmetry, which is a vital inductive bias accounting for model generalization and should be incorporated into the model design. Existing simulators either consider insufficient symmetry, or enforce excessive equivariance in practice when symmetry is partially broken by gravity. 2) Objects in the physical world possess diverse shapes, sizes, and properties, which should be appropriately processed by the model. To tackle these difficulties, we propose a novel backbone, Subequivariant Graph Neural Network, which 1) relaxes equivariance to subequivariance by considering external fields like gravity, where the universal approximation ability holds theoretically; 2) introduces a new subequivariant object-aware message passing for learning physical interactions between multiple objects of various shapes in the particle-based representation; 3) operates in a hierarchical fashion, allowing for modeling long-range and complex interactions. Our model achieves on average over 3% enhancement in contact prediction accuracy across 8 scenarios on Physion and 2X lower rollout MSE on RigidFall compared with state-of-the-art GNN simulators, while exhibiting strong generalization and data efficiency.

Lin Ma, Jiangtao Gong, Hao Xu et al.

Assembly sequence planning (ASP) is the essential process for modern manufacturing, proven to be NP-complete thus its effective and efficient solution has been a challenge for researchers in the field. In this paper, we present a graph-transformer based framework for the ASP problem which is trained and demonstrated on a self-collected ASP database. The ASP database contains a self-collected set of LEGO models. The LEGO model is abstracted to a heterogeneous graph structure after a thorough analysis of the original structure and feature extraction. The ground truth assembly sequence is first generated by brute-force search and then adjusted manually to in line with human rational habits. Based on this self-collected ASP dataset, we propose a heterogeneous graph-transformer framework to learn the latent rules for assembly planning. We evaluated the proposed framework in a series of experiment. The results show that the similarity of the predicted and ground truth sequences can reach 0.44, a medium correlation measured by Kendall's $τ$. Meanwhile, we compared the different effects of node features and edge features and generated a feasible and reasonable assembly sequence as a benchmark for further research. Our data set and code is available on https://github.com/AIR-DISCOVER/ICRA\_ASP.

Yang Zhang, Zhewei Wei, Ye Yuan et al.

Predicting the binding sites of target proteins plays a fundamental role in drug discovery. Most existing deep-learning methods consider a protein as a 3D image by spatially clustering its atoms into voxels and then feed the voxelized protein into a 3D CNN for prediction. However, the CNN-based methods encounter several critical issues: 1) defective in representing irregular protein structures; 2) sensitive to rotations; 3) insufficient to characterize the protein surface; 4) unaware of protein size shift. To address the above issues, this work proposes EquiPocket, an E(3)-equivariant Graph Neural Network (GNN) for binding site prediction, which comprises three modules: the first one to extract local geometric information for each surface atom, the second one to model both the chemical and spatial structure of protein and the last one to capture the geometry of the surface via equivariant message passing over the surface atoms. We further propose a dense attention output layer to alleviate the effect incurred by variable protein size. Extensive experiments on several representative benchmarks demonstrate the superiority of our framework to the state-of-the-art methods.

Yuelin Zhang, Sijie Cheng, Chen Li et al.

Accurately estimating task progress is critical for embodied agents to plan and execute long-horizon, multi-step tasks. Despite promising advances, existing Vision-Language Models (VLMs) based methods primarily leverage their video understanding capabilities, while neglecting their complex reasoning potential. Furthermore, processing long video trajectories with VLMs is computationally prohibitive for real-world deployment. To address these challenges, we propose the Recurrent Reasoning Vision-Language Model ($\text{R}^2$VLM). Our model features a recurrent reasoning framework that processes local video snippets iteratively, maintaining a global context through an evolving Chain of Thought (CoT). This CoT explicitly records task decomposition, key steps, and their completion status, enabling the model to reason about complex temporal dependencies. This design avoids the high cost of processing long videos while preserving essential reasoning capabilities. We train $\text{R}^2$VLM on large-scale, automatically generated datasets from ALFRED and Ego4D. Extensive experiments on progress estimation and downstream applications, including progress-enhanced policy learning, reward modeling for reinforcement learning, and proactive assistance, demonstrate that $\text{R}^2$VLM achieves strong performance and generalization, achieving a new state-of-the-art in long-horizon task progress estimation. The models and benchmarks are publicly available at \href{https://huggingface.co/collections/zhangyuelin/r2vlm}{huggingface}.

Ning Lin, Luxi Chen, Huaguan Chen et al.

Generating objects with specific symmetries is essential in various real-world scenarios. However, adapting existing 2D continuous representations to enforce planar group symmetry remains a challenge, as the transformation of non-reflective group elements may disrupt continuity. To overcome this limitation, we propose a symmetrization framework for arbitrary planar groups. Our method transforms any 2D continuous representation into a symmetric one while preserving continuity. We provide the mathematical formulation of this representation, demonstrate its approximation capability for symmetric functions, and detail the construction methodology. We validate our approach through three visual design tasks (pattern design, paper-cutting design and stylized topology design) and one material design task. Experiments confirm that our representation enables effective symmetry control and demonstrate its broader applicability.

Xiangzhe Kong, Wenbing Huang, Yang Liu

Antibody design is valuable for therapeutic usage and biological research. Existing deep-learning-based methods encounter several key issues: 1) incomplete context for Complementarity-Determining Regions (CDRs) generation; 2) incapability of capturing the entire 3D geometry of the input structure; 3) inefficient prediction of the CDR sequences in an autoregressive manner. In this paper, we propose Multi-channel Equivariant Attention Network (MEAN) to co-design 1D sequences and 3D structures of CDRs. To be specific, MEAN formulates antibody design as a conditional graph translation problem by importing extra components including the target antigen and the light chain of the antibody. Then, MEAN resorts to E(3)-equivariant message passing along with a proposed attention mechanism to better capture the geometrical correlation between different components. Finally, it outputs both the 1D sequences and 3D structure via a multi-round progressive full-shot scheme, which enjoys more efficiency and precision against previous autoregressive approaches. Our method significantly surpasses state-of-the-art models in sequence and structure modeling, antigen-binding CDR design, and binding affinity optimization. Specifically, the relative improvement to baselines is about 23% in antigen-binding CDR design and 34% for affinity optimization.

Jiaqi Han, Wenbing Huang, Yu Rong et al.

It has been discovered that Graph Convolutional Networks (GCNs) encounter a remarkable drop in performance when multiple layers are piled up. The main factor that accounts for why deep GCNs fail lies in over-smoothing, which isolates the network output from the input with the increase of network depth, weakening expressivity and trainability. In this paper, we start by investigating refined measures upon DropEdge -- an existing simple yet effective technique to relieve over-smoothing. We term our method as DropEdge++ for its two structure-aware samplers in contrast to DropEdge: layer-dependent sampler and feature-dependent sampler. Regarding the layer-dependent sampler, we interestingly find that increasingly sampling edges from the bottom layer yields superior performance than the decreasing counterpart as well as DropEdge. We theoretically reveal this phenomenon with Mean-Edge-Number (MEN), a metric closely related to over-smoothing. For the feature-dependent sampler, we associate the edge sampling probability with the feature similarity of node pairs, and prove that it further correlates the convergence subspace of the output layer with the input features. Extensive experiments on several node classification benchmarks, including both full- and semi- supervised tasks, illustrate the efficacy of DropEdge++ and its compatibility with a variety of backbones by achieving generally better performance over DropEdge and the no-drop version.

Rui Jiao, Jiaqi Han, Wenbing Huang et al.

Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of characterizing 3D geometry and thus defective for downstream 3D tasks. In this work, we tackle 3D molecular pretraining in a complete and novel sense. In particular, we first propose to adopt an equivariant energy-based model as the backbone for pretraining, which enjoys the merits of fulfilling the symmetry of 3D space. Then we develop a node-level pretraining loss for force prediction, where we further exploit the Riemann-Gaussian distribution to ensure the loss to be E(3)-invariant, enabling more robustness. Moreover, a graph-level noise scale prediction task is also leveraged to further promote the eventual performance. We evaluate our model pretrained from a large-scale 3D dataset GEOM-QM9 on two challenging 3D benchmarks: MD17 and QM9. Experimental results demonstrate the efficacy of our method against current state-of-the-art pretraining approaches, and verify the validity of our design for each proposed component.

Xiangzhe Kong, Wenbing Huang, Yang Liu

Antibody design is an essential yet challenging task in various domains like therapeutics and biology. There are two major defects in current learning-based methods: 1) tackling only a certain subtask of the whole antibody design pipeline, making them suboptimal or resource-intensive. 2) omitting either the framework regions or side chains, thus incapable of capturing the full-atom geometry. To address these pitfalls, we propose dynamic Multi-channel Equivariant grAph Network (dyMEAN), an end-to-end full-atom model for E(3)-equivariant antibody design given the epitope and the incomplete sequence of the antibody. Specifically, we first explore structural initialization as a knowledgeable guess of the antibody structure and then propose shadow paratope to bridge the epitope-antibody connections. Both 1D sequences and 3D structures are updated via an adaptive multi-channel equivariant encoder that is able to process protein residues of variable sizes when considering full atoms. Finally, the updated antibody is docked to the epitope via the alignment of the shadow paratope. Experiments on epitope-binding CDR-H3 design, complex structure prediction, and affinity optimization demonstrate the superiority of our end-to-end framework and full-atom modeling.

Rui Jiao, Wenbing Huang, Peijia Lin et al.

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.

Yikai Wang, TengQi Ye, Lele Cao et al.

3D object detection is a crucial research topic in computer vision, which usually uses 3D point clouds as input in conventional setups. Recently, there is a trend of leveraging multiple sources of input data, such as complementing the 3D point cloud with 2D images that often have richer color and fewer noises. However, due to the heterogeneous geometrics of the 2D and 3D representations, it prevents us from applying off-the-shelf neural networks to achieve multimodal fusion. To that end, we propose Bridged Transformer (BrT), an end-to-end architecture for 3D object detection. BrT is simple and effective, which learns to identify 3D and 2D object bounding boxes from both points and image patches. A key element of BrT lies in the utilization of object queries for bridging 3D and 2D spaces, which unifies different sources of data representations in Transformer. We adopt a form of feature aggregation realized by point-to-patch projections which further strengthen the correlations between images and points. Moreover, BrT works seamlessly for fusing the point cloud with multi-view images. We experimentally show that BrT surpasses state-of-the-art methods on SUN RGB-D and ScanNetV2 datasets.

Peihao Chen, Dongyu Ji, Kunyang Lin et al.

Getting robots to navigate to multiple objects autonomously is essential yet difficult in robot applications. One of the key challenges is how to explore environments efficiently with camera sensors only. Existing navigation methods mainly focus on fixed cameras and few attempts have been made to navigate with active cameras. As a result, the agent may take a very long time to perceive the environment due to limited camera scope. In contrast, humans typically gain a larger field of view by looking around for a better perception of the environment. How to make robots perceive the environment as efficiently as humans is a fundamental problem in robotics. In this paper, we consider navigating to multiple objects more efficiently with active cameras. Specifically, we cast moving camera to a Markov Decision Process and reformulate the active camera problem as a reinforcement learning problem. However, we have to address two new challenges: 1) how to learn a good camera policy in complex environments and 2) how to coordinate it with the navigation policy. To address these, we carefully design a reward function to encourage the agent to explore more areas by moving camera actively. Moreover, we exploit human experience to infer a rule-based camera action to guide the learning process. Last, to better coordinate two kinds of policies, the camera policy takes navigation actions into account when making camera moving decisions. Experimental results show our camera policy consistently improves the performance of multi-object navigation over four baselines on two datasets.

Tian Qin, Fengxiang He, Dingfeng Shi et al.

Designing an incentive-compatible auction mechanism that maximizes the auctioneer's revenue while minimizes the bidders' ex-post regret is an important yet intricate problem in economics. Remarkable progress has been achieved through learning the optimal auction mechanism by neural networks. In this paper, we consider the popular additive valuation and symmetric valuation setting; i.e., the valuation for a set of items is defined as the sum of all items' valuations in the set, and the valuation distribution is invariant when the bidders and/or the items are permutated. We prove that permutation-equivariant neural networks have significant advantages: the permutation-equivariance decreases the expected ex-post regret, improves the model generalizability, while maintains the expected revenue invariant. This implies that the permutation-equivariance helps approach the theoretically optimal dominant strategy incentive compatible condition, and reduces the required sample complexity for desired generalization. Extensive experiments fully support our theory. To our best knowledge, this is the first work towards understanding the benefits of permutation-equivariance in auction mechanisms.

Yikai Wang, Wenbing Huang, Yinpeng Dong et al.

Binary Neural Network (BNN) represents convolution weights with 1-bit values, which enhances the efficiency of storage and computation. This paper is motivated by a previously revealed phenomenon that the binary kernels in successful BNNs are nearly power-law distributed: their values are mostly clustered into a small number of codewords. This phenomenon encourages us to compact typical BNNs and obtain further close performance through learning non-repetitive kernels within a binary kernel subspace. Specifically, we regard the binarization process as kernel grouping in terms of a binary codebook, and our task lies in learning to select a smaller subset of codewords from the full codebook. We then leverage the Gumbel-Sinkhorn technique to approximate the codeword selection process, and develop the Permutation Straight-Through Estimator (PSTE) that is able to not only optimize the selection process end-to-end but also maintain the non-repetitive occupancy of selected codewords. Experiments verify that our method reduces both the model size and bit-wise computational costs, and achieves accuracy improvements compared with state-of-the-art BNNs under comparable budgets.

Tianying Ji, Yu Luo, Fuchun Sun et al.

Designing and analyzing model-based RL (MBRL) algorithms with guaranteed monotonic improvement has been challenging, mainly due to the interdependence between policy optimization and model learning. Existing discrepancy bounds generally ignore the impacts of model shifts, and their corresponding algorithms are prone to degrade performance by drastic model updating. In this work, we first propose a novel and general theoretical scheme for a non-decreasing performance guarantee of MBRL. Our follow-up derived bounds reveal the relationship between model shifts and performance improvement. These discoveries encourage us to formulate a constrained lower-bound optimization problem to permit the monotonicity of MBRL. A further example demonstrates that learning models from a dynamically-varying number of explorations benefit the eventual returns. Motivated by these analyses, we design a simple but effective algorithm CMLO (Constrained Model-shift Lower-bound Optimization), by introducing an event-triggered mechanism that flexibly determines when to update the model. Experiments show that CMLO surpasses other state-of-the-art methods and produces a boost when various policy optimization methods are employed.

Xiangzhe Kong, Wenbing Huang, Yang Liu

Many processes in biology and drug discovery involve various 3D interactions between molecules, such as protein and protein, protein and small molecule, etc. Given that different molecules are usually represented in different granularity, existing methods usually encode each type of molecules independently with different models, leaving it defective to learn the various underlying interaction physics. In this paper, we first propose to universally represent an arbitrary 3D complex as a geometric graph of sets, shedding light on encoding all types of molecules with one model. We then propose a Generalist Equivariant Transformer (GET) to effectively capture both domain-specific hierarchies and domain-agnostic interaction physics. To be specific, GET consists of a bilevel attention module, a feed-forward module and a layer normalization module, where each module is E(3) equivariant and specialized for handling sets of variable sizes. Notably, in contrast to conventional pooling-based hierarchical models, our GET is able to retain fine-grained information of all levels. Extensive experiments on the interactions between proteins, small molecules and RNA/DNAs verify the effectiveness and generalization capability of our proposed method across different domains.

Xueyi Liu, Yu Rong, Tingyang Xu et al.

Graph instance contrastive learning has been proved as an effective task for Graph Neural Network (GNN) pre-training. However, one key issue may seriously impede the representative power in existing works: Positive instances created by current methods often miss crucial information of graphs or even yield illegal instances (such as non-chemically-aware graphs in molecular generation). To remedy this issue, we propose to select positive graph instances directly from existing graphs in the training set, which ultimately maintains the legality and similarity to the target graphs. Our selection is based on certain domain-specific pair-wise similarity measurements as well as sampling from a hierarchical graph encoding similarity relations among graphs. Besides, we develop an adaptive node-level pre-training method to dynamically mask nodes to distribute them evenly in the graph. We conduct extensive experiments on $13$ graph classification and node classification benchmark datasets from various domains. The results demonstrate that the GNN models pre-trained by our strategies can outperform those trained-from-scratch models as well as the variants obtained by existing methods.

Yuliang Zhan, Jian Li, Wenbing Huang et al.

Deep learning has demonstrated remarkable capabilities in simulating complex dynamic systems. However, existing methods require known physical properties as supervision or inputs, limiting their applicability under unknown conditions. To explore this challenge, we introduce Cloth Dynamics Grounding (CDG), a novel scenario for unsupervised learning of cloth dynamics from multi-view visual observations. We further propose Cloth Dynamics Splatting (CloDS), an unsupervised dynamic learning framework designed for CDG. CloDS adopts a three-stage pipeline that first performs video-to-geometry grounding and then trains a dynamics model on the grounded meshes. To cope with large non-linear deformations and severe self-occlusions during grounding, we introduce a dual-position opacity modulation that supports bidirectional mapping between 2D observations and 3D geometry via mesh-based Gaussian splatting in video-to-geometry grounding stage. It jointly considers the absolute and relative position of Gaussian components. Comprehensive experimental evaluations demonstrate that CloDS effectively learns cloth dynamics from visual data while maintaining strong generalization capabilities for unseen configurations. Our code is available at https://github.com/whynot-zyl/CloDS. Visualization results are available at https://github.com/whynot-zyl/CloDS_video}.%\footnote{As in this example.

Peijia Lin, Pin Chen, Rui Jiao et al.

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process.

Ziyang Yu, Wenbing Huang, Yang Liu

Molecular Dynamics (MD) is crucial in various fields such as materials science, chemistry, and pharmacology to name a few. Conventional MD software struggles with the balance between time cost and prediction accuracy, which restricts its wider application. Recently, data-driven approaches based on deep generative models have been devised for time-coarsened dynamics, which aim at learning dynamics of diverse molecular systems over a long timestep, enjoying both universality and efficiency. Nevertheless, most current methods are designed solely to learn from the data distribution regardless of the underlying Boltzmann distribution, and the physics priors such as energies and forces are constantly overlooked. In this work, we propose a conditional generative model called Force-guided Bridge Matching (FBM), which learns full-atom time-coarsened dynamics and targets the Boltzmann-constrained distribution. With the guidance of our delicately-designed intermediate force field, FBM leverages favourable physics priors into the generation process, giving rise to enhanced simulations. Experiments on two datasets consisting of peptides verify our superiority in terms of comprehensive metrics and demonstrate transferability to unseen systems.

Yu Sun, Xingyu Qian, Weiwen Xu et al.

Reasoning-based large language models have excelled in mathematics and programming, yet their potential in knowledge-intensive medical question answering remains underexplored and insufficiently validated in clinical contexts. To bridge this gap, we introduce ReasonMed, the largest medical reasoning dataset to date, comprising 370k high-quality examples distilled from 1.75 million initial reasoning paths generated by complementary LLMs and curated through a cost-efficient easy-medium-difficult (EMD) pipeline. ReasonMed is built through a multi-agent generation, verification, and refinement process, in which an Error Refiner improves reasoning paths by correcting error-prone steps identified by a verifier. Using ReasonMed, we investigate effective strategies for training medical reasoning models and find that integrating detailed CoT reasoning with concise answer summaries yields the most robust fine-tuning results. Models trained on ReasonMed set a new benchmark: ReasonMed-7B surpasses the prior best sub-10B models by 4.17% and even exceeds LLaMA3.1-70B on PubMedQA by 4.60%. When scaled to ReasonMed-14B, it remains highly competitive, underscoring consistent scaling potential. The codes and datasets are available at https://github.com/YuSun-Work/ReasonMed.

Han Zhang, Guo-Hua Yuan, Chaohao Yuan et al.

Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful static representations, but they do not explicitly model the distribution of cellular states for generative simulation. Here, we introduce Lingshu-Cell, a masked discrete diffusion model that learns transcriptomic state distributions and supports conditional simulation under perturbation. By operating directly in a discrete token space that is compatible with the sparse, non-sequential nature of single-cell transcriptomic data, Lingshu-Cell captures complex transcriptome-wide expression dependencies across approximately 18,000 genes without relying on prior gene selection, such as filtering by high variability or ranking by expression level. Across diverse tissues and species, Lingshu-Cell accurately reproduces transcriptomic distributions, marker-gene expression patterns and cell-subtype proportions, demonstrating its ability to capture complex cellular heterogeneity. Moreover, by jointly embedding cell type or donor identity with perturbation, Lingshu-Cell can predict whole-transcriptome expression changes for novel combinations of identity and perturbation. It achieves leading performance on the Virtual Cell Challenge H1 genetic perturbation benchmark and in predicting cytokine-induced responses in human PBMCs. Together, these results establish Lingshu-Cell as a flexible cellular world model for in silico simulation of cell states and perturbation responses, laying the foundation for a new paradigm in biological discovery and perturbation screening.

Zongzhao Li, Zongyang Ma, Mingze Li et al.

Multimodal Large Language Models (MLLMs) have demonstrated remarkable capabilities across diverse tasks, yet they lag significantly behind humans in spatial reasoning. We investigate this gap through Transformation-Driven Visual Reasoning (TVR), a challenging task requiring identification of object transformations across images under varying viewpoints. While traditional Supervised Fine-Tuning (SFT) fails to generate coherent reasoning paths in cross-view settings, sparse-reward Reinforcement Learning (RL) suffers from inefficient exploration and slow convergence. To address these limitations, we propose STAR-R1, a novel framework that integrates a single-stage RL paradigm with a fine-grained reward mechanism tailored for TVR. Specifically, STAR-R1 rewards partial correctness while penalizing excessive enumeration and passive inaction, enabling efficient exploration and precise reasoning. Comprehensive evaluations demonstrate that STAR-R1 achieves state-of-the-art performance across all 11 metrics, outperforming SFT by 23% in cross-view scenarios. Further analysis reveals STAR-R1's anthropomorphic behavior and highlights its unique ability to compare all objects for improving spatial reasoning. Our work provides critical insights in advancing the research of MLLMs and reasoning models. The codes, model weights, and data will be publicly available at https://github.com/zongzhao23/STAR-R1.

Runfa Chen, Ling Wang, Yu Du et al.

Learning policies for multi-entity systems in 3D environments is far more complicated against single-entity scenarios, due to the exponential expansion of the global state space as the number of entities increases. One potential solution of alleviating the exponential complexity is dividing the global space into independent local views that are invariant to transformations including translations and rotations. To this end, this paper proposes Subequivariant Hierarchical Neural Networks (SHNN) to facilitate multi-entity policy learning. In particular, SHNN first dynamically decouples the global space into local entity-level graphs via task assignment. Second, it leverages subequivariant message passing over the local entity-level graphs to devise local reference frames, remarkably compressing the representation redundancy, particularly in gravity-affected environments. Furthermore, to overcome the limitations of existing benchmarks in capturing the subtleties of multi-entity systems under the Euclidean symmetry, we propose the Multi-entity Benchmark (MEBEN), a new suite of environments tailored for exploring a wide range of multi-entity reinforcement learning. Extensive experiments demonstrate significant advancements of SHNN on the proposed benchmarks compared to existing methods. Comprehensive ablations are conducted to verify the indispensability of task assignment and subequivariance.

Liming Wu, Rui Jiao, Qi Li et al.

The design of materials with tailored properties is crucial for technological progress. However, most deep generative models focus exclusively on perfectly ordered crystals, neglecting the important class of disordered materials. To address this gap, we introduce DMFlow, a generative framework specifically designed for disordered crystals. Our approach introduces a unified representation for ordered, Substitutionally Disordered (SD), and Positionally Disordered (PD) crystals, and employs a flow matching model to jointly generate all structural components. A key innovation is a Riemannian flow matching framework with spherical reparameterization, which ensures physically valid disorder weights on the probability simplex. The vector field is learned by a novel Graph Neural Network (GNN) that incorporates physical symmetries and a specialized message-passing scheme. Finally, a two-stage discretization procedure converts the continuous weights into multi-hot atomic assignments. To support research in this area, we release a benchmark containing SD, PD, and mixed structures curated from the Crystallography Open Database. Experiments on Crystal Structure Prediction (CSP) and De Novo Generation (DNG) tasks demonstrate that DMFlow significantly outperforms state-of-the-art baselines adapted from ordered crystal generation. We hope our work provides a foundation for the AI-driven discovery of disordered materials.

Yuelin Zhang, Jiacheng Cen, Jiaqi Han et al.

Equivariant Graph Neural Networks (GNNs) have achieved remarkable success across diverse scientific applications. However, existing approaches face critical efficiency challenges when scaling to large geometric graphs and suffer significant performance degradation when the input graphs are sparsified for computational tractability. To address these limitations, we introduce FastEGNN and DistEGNN, two novel enhancements to equivariant GNNs for large-scale geometric graphs. FastEGNN employs a key innovation: a small ordered set of virtual nodes that effectively approximates the large unordered graph of real nodes. Specifically, we implement distinct message passing and aggregation mechanisms for different virtual nodes to ensure mutual distinctiveness, and minimize Maximum Mean Discrepancy (MMD) between virtual and real coordinates to achieve global distributedness. This design enables FastEGNN to maintain high accuracy while efficiently processing large-scale sparse graphs. For extremely large-scale geometric graphs, we present DistEGNN, a distributed extension where virtual nodes act as global bridges between subgraphs in different devices, maintaining consistency while dramatically reducing memory and computational overhead. We comprehensively evaluate our models across four challenging domains: N-body systems (100 nodes), protein dynamics (800 nodes), Water-3D (8,000 nodes), and our new Fluid113K benchmark (113,000 nodes). Results demonstrate superior efficiency and performance, establishing new capabilities in large-scale equivariant graph learning. Code is available at https://github.com/GLAD-RUC/DistEGNN.

Huaguan Chen, Ning Lin, Luxi Chen et al.

Inverse design with physics-based objectives is challenging because it couples high-dimensional geometry with expensive simulations, as exemplified by aerodynamic shape optimization for drag reduction. We revisit inverse design through two canonical solutions, the optimal design point and the optimal design distribution, and relate them to optimization and guided generation. Building on this view, we propose a new training loss for cost predictors and a density-gradient optimization method that improves objectives while preserving plausible shapes. We further unify existing training-free guided generation methods. To address their inability to approximate conditional covariance in high dimensions, we develop a time- and memory-efficient algorithm for approximate covariance estimation. Experiments on a controlled 2D study and high-fidelity 3D aerodynamic benchmarks (car and aircraft), validated by OpenFOAM simulations and miniature wind-tunnel tests with 3D-printed prototypes, demonstrate consistent gains in both optimization and guided generation. Additional offline RL results further support the generality of our approach.

Zongzhao Li, Xiangzhe Kong, Jiahui Su et al.

This paper introduces the concept of Microscopic Spatial Intelligence (MiSI), the capability to perceive and reason about the spatial relationships of invisible microscopic entities, which is fundamental to scientific discovery. To assess the potential of Vision-Language Models (VLMs) in this domain, we propose a systematic benchmark framework MiSI-Bench. This framework features over 163,000 question-answer pairs and 587,000 images derived from approximately 4,000 molecular structures, covering nine complementary tasks that evaluate abilities ranging from elementary spatial transformations to complex relational identifications. Experimental results reveal that current state-of-the-art VLMs perform significantly below human level on this benchmark. However, a fine-tuned 7B model demonstrates substantial potential, even surpassing humans in spatial transformation tasks, while its poor performance in scientifically-grounded tasks like hydrogen bond recognition underscores the necessity of integrating explicit domain knowledge for progress toward scientific AGI. The datasets are available at https://huggingface.co/datasets/zongzhao/MiSI-bench.

Xixian Liu, Rui Jiao, Zhiyuan Liu et al.

Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising methods rely on oversimplied molecular dynamics that assume atomic motions to be isotropic and homoscedastic. To address these limitations, we propose a novel denoising framework AniDS: Anisotropic Variational Autoencoder for 3D Molecular Denoising. AniDS introduces a structure-aware anisotropic noise generator that can produce atom-specific, full covariance matrices for Gaussian noise distributions to better reflect directional and structural variability in molecular systems. These covariances are derived from pairwise atomic interactions as anisotropic corrections to an isotropic base. Our design ensures that the resulting covariance matrices are symmetric, positive semi-definite, and SO(3)-equivariant, while providing greater capacity to model complex molecular dynamics. Extensive experiments show that AniDS outperforms prior isotropic and homoscedastic denoising models and other leading methods on the MD17 and OC22 benchmarks, achieving average relative improvements of 8.9% and 6.2% in force prediction accuracy. Our case study on a crystal and molecule structure shows that AniDS adaptively suppresses noise along the bonding direction, consistent with physicochemical principles. Our code is available at https://github.com/ZeroKnighting/AniDS.

Yutao Zhu, Kun Zhou, Kelong Mao et al.

Large language models (LLMs) have become the foundation of many applications, leveraging their extensive capabilities in processing and understanding natural language. While many open-source LLMs have been released with technical reports, the lack of training details hinders further research and development. This paper presents the development of YuLan, a series of open-source LLMs with $12$ billion parameters. The base model of YuLan is pre-trained on approximately $1.7$T tokens derived from a diverse corpus, including massive English, Chinese, and multilingual texts. We design a three-stage pre-training method to enhance YuLan's overall capabilities. Subsequent phases of training incorporate instruction-tuning and human alignment, employing a substantial volume of high-quality synthesized data. To facilitate the learning of complex and long-tail knowledge, we devise a curriculum-learning framework throughout across these stages, which helps LLMs learn knowledge in an easy-to-hard manner. YuLan's training is finished on Jan, 2024 and has achieved performance on par with state-of-the-art LLMs across various English and Chinese benchmarks. This paper outlines a comprehensive technical roadmap for developing LLMs from scratch. Our model and codes are available at https://github.com/RUC-GSAI/YuLan-Chat.

Yikai Wang, Fuchun Sun, Wenbing Huang et al.

Multimodal fusion and multitask learning are two vital topics in machine learning. Despite the fruitful progress, existing methods for both problems are still brittle to the same challenge -- it remains dilemmatic to integrate the common information across modalities (resp. tasks) meanwhile preserving the specific patterns of each modality (resp. task). Besides, while they are actually closely related to each other, multimodal fusion and multitask learning are rarely explored within the same methodological framework before. In this paper, we propose Channel-Exchanging-Network (CEN) which is self-adaptive, parameter-free, and more importantly, applicable for multimodal and multitask dense image prediction. At its core, CEN adaptively exchanges channels between subnetworks of different modalities. Specifically, the channel exchanging process is self-guided by individual channel importance that is measured by the magnitude of Batch-Normalization (BN) scaling factor during training. For the application of dense image prediction, the validity of CEN is tested by four different scenarios: multimodal fusion, cycle multimodal fusion, multitask learning, and multimodal multitask learning. Extensive experiments on semantic segmentation via RGB-D data and image translation through multi-domain input verify the effectiveness of CEN compared to state-of-the-art methods. Detailed ablation studies have also been carried out, which demonstrate the advantage of each component we propose. Our code is available at https://github.com/yikaiw/CEN.

Xuefeng Du, Tian Bian, Yu Rong et al.

Teaching Graph Neural Networks (GNNs) to accurately classify nodes under severely noisy labels is an important problem in real-world graph learning applications, but is currently underexplored. Although pairwise training methods have demonstrated promise in supervised metric learning and unsupervised contrastive learning, they remain less studied on noisy graphs, where the structural pairwise interactions (PI) between nodes are abundant and thus might benefit label noise learning rather than the pointwise methods. This paper bridges the gap by proposing a pairwise framework for noisy node classification on graphs, which relies on the PI as a primary learning proxy in addition to the pointwise learning from the noisy node class labels. Our proposed framework PI-GNN contributes two novel components: (1) a confidence-aware PI estimation model that adaptively estimates the PI labels, which are defined as whether the two nodes share the same node labels, and (2) a decoupled training approach that leverages the estimated PI labels to regularize a node classification model for robust node classification. Extensive experiments on different datasets and GNN architectures demonstrate the effectiveness of PI-GNN, yielding a promising improvement over the state-of-the-art methods. Code is publicly available at https://github.com/TianBian95/pi-gnn.

Yikai Wang, Wenbing Huang, Fuchun Sun et al.

Deep multimodal fusion by using multiple sources of data for classification or regression has exhibited a clear advantage over the unimodal counterpart on various applications. Yet, current methods including aggregation-based and alignment-based fusion are still inadequate in balancing the trade-off between inter-modal fusion and intra-modal processing, incurring a bottleneck of performance improvement. To this end, this paper proposes Channel-Exchanging-Network (CEN), a parameter-free multimodal fusion framework that dynamically exchanges channels between sub-networks of different modalities. Specifically, the channel exchanging process is self-guided by individual channel importance that is measured by the magnitude of Batch-Normalization (BN) scaling factor during training. The validity of such exchanging process is also guaranteed by sharing convolutional filters yet keeping separate BN layers across modalities, which, as an add-on benefit, allows our multimodal architecture to be almost as compact as a unimodal network. Extensive experiments on semantic segmentation via RGB-D data and image translation through multi-domain input verify the effectiveness of our CEN compared to current state-of-the-art methods. Detailed ablation studies have also been carried out, which provably affirm the advantage of each component we propose. Our code is available at https://github.com/yikaiw/CEN.

Runfa Chen, Wenbing Huang, Binghui Huang et al.

Unsupervised image-to-image translation is a central task in computer vision. Current translation frameworks will abandon the discriminator once the training process is completed. This paper contends a novel role of the discriminator by reusing it for encoding the images of the target domain. The proposed architecture, termed as NICE-GAN, exhibits two advantageous patterns over previous approaches: First, it is more compact since no independent encoding component is required; Second, this plug-in encoder is directly trained by the adversary loss, making it more informative and trained more effectively if a multi-scale discriminator is applied. The main issue in NICE-GAN is the coupling of translation with discrimination along the encoder, which could incur training inconsistency when we play the min-max game via GAN. To tackle this issue, we develop a decoupled training strategy by which the encoder is only trained when maximizing the adversary loss while keeping frozen otherwise. Extensive experiments on four popular benchmarks demonstrate the superior performance of NICE-GAN over state-of-the-art methods in terms of FID, KID, and also human preference. Comprehensive ablation studies are also carried out to isolate the validity of each proposed component. Our codes are available at https://github.com/alpc91/NICE-GAN-pytorch.

Runhao Zeng, Wenbing Huang, Mingkui Tan et al.

Most state-of-the-art action localization systems process each action proposal individually, without explicitly exploiting their relations during learning. However, the relations between proposals actually play an important role in action localization, since a meaningful action always consists of multiple proposals in a video. In this paper, we propose to exploit the proposal-proposal relations using Graph Convolutional Networks (GCNs). First, we construct an action proposal graph, where each proposal is represented as a node and their relations between two proposals as an edge. Here, we use two types of relations, one for capturing the context information for each proposal and the other one for characterizing the correlations between distinct actions. Then we apply the GCNs over the graph to model the relations among different proposals and learn powerful representations for the action classification and localization. Experimental results show that our approach significantly outperforms the state-of-the-art on THUMOS14 (49.1% versus 42.8%). Moreover, augmentation experiments on ActivityNet also verify the efficacy of modeling action proposal relationships. Codes are available at https://github.com/Alvin-Zeng/PGCN.

Yu Rong, Wenbing Huang, Tingyang Xu et al.

\emph{Over-fitting} and \emph{over-smoothing} are two main obstacles of developing deep Graph Convolutional Networks (GCNs) for node classification. In particular, over-fitting weakens the generalization ability on small dataset, while over-smoothing impedes model training by isolating output representations from the input features with the increase in network depth. This paper proposes DropEdge, a novel and flexible technique to alleviate both issues. At its core, DropEdge randomly removes a certain number of edges from the input graph at each training epoch, acting like a data augmenter and also a message passing reducer. Furthermore, we theoretically demonstrate that DropEdge either reduces the convergence speed of over-smoothing or relieves the information loss caused by it. More importantly, our DropEdge is a general skill that can be equipped with many other backbone models (e.g. GCN, ResGCN, GraphSAGE, and JKNet) for enhanced performance. Extensive experiments on several benchmarks verify that DropEdge consistently improves the performance on a variety of both shallow and deep GCNs. The effect of DropEdge on preventing over-smoothing is empirically visualized and validated as well. Codes are released on~\url{https://github.com/DropEdge/DropEdge}.

Rui Jiao, Wenbing Huang, Yu Liu et al.

Crystals are the foundation of numerous scientific and industrial applications. While various learning-based approaches have been proposed for crystal generation, existing methods seldom consider the space group constraint which is crucial in describing the geometry of crystals and closely relevant to many desirable properties. However, considering space group constraint is challenging owing to its diverse and nontrivial forms. In this paper, we reduce the space group constraint into an equivalent formulation that is more tractable to be handcrafted into the generation process. In particular, we translate the space group constraint into two parts: the basis constraint of the invariant logarithmic space of the lattice matrix and the Wyckoff position constraint of the fractional coordinates. Upon the derived constraints, we then propose DiffCSP++, a novel diffusion model that has enhanced a previous work DiffCSP by further taking space group constraint into account. Experiments on several popular datasets verify the benefit of the involvement of the space group constraint, and show that our DiffCSP++ achieves promising performance on crystal structure prediction, ab initio crystal generation and controllable generation with customized space groups.

Jiaqi Han, Jiacheng Cen, Liming Wu et al.

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Wenda Wang, Yang Zhang, Zhewei Wei et al.

Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle to fully exploit antigen-specific geometric information for optimizing local binding interfaces and global structures. To overcome these limitations, we introduce AbFlow, a flow-matching framework that leverages optimal transport to design full-atom antibodies end-to-end. AbFlow incorporates an extended velocity field network featuring an equivariant Surface Multi-channel Encoder, which uses surface-level antigen interaction data to refine the antibody structure, particularly the CDR-H3 region. Extensive experiments in paratoep-centric antibody design, multi-CDRs and full-atom antibody design, binding affinity optimization, and complex structure prediction show that AbFlow produces superior antigen-antibody complexes, especially at the contact interface, and markedly improves the binding affinity of generated antibodies.

Ziyang Yu, Yi He, Wenbing Huang et al.

Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical computational approaches remain prohibitively expensive due to their reliance on extensive molecular dynamics simulations, while deep learning-based methods are constrained by either less-expressive generative models or input dimensions tied to a specific system, resulting in negligible generalization. To address these challenges, we propose CARD, a generative framework that employs a novel radix-based decomposition to bijectively convert 3D coordinates into mixed discrete-continuous sequences, enabling coarse-to-fine autoregressive modeling with enhanced expressiveness. Notably, the model corresponds to a distribution with zero free energy, serving as a proposal for absolute free energy computation of arbitrary systems without relying on alchemical pathways. Experiments across diverse tasks demonstrate that CARD matches the accuracy of classical computational methods on unseen systems with diverse topologies, while achieving an approximately 40-fold speedup in inference.

Jiacheng Cen, Anyi Li, Ning Lin et al.

Equivariant Graph Neural Networks (GNNs) that incorporate E(3) symmetry have achieved significant success in various scientific applications. As one of the most successful models, EGNN leverages a simple scalarization technique to perform equivariant message passing over only Cartesian vectors (i.e., 1st-degree steerable vectors), enjoying greater efficiency and efficacy compared to equivariant GNNs using higher-degree steerable vectors. This success suggests that higher-degree representations might be unnecessary. In this paper, we disprove this hypothesis by exploring the expressivity of equivariant GNNs on symmetric structures, including $k$-fold rotations and regular polyhedra. We theoretically demonstrate that equivariant GNNs will always degenerate to a zero function if the degree of the output representations is fixed to 1 or other specific values. Based on this theoretical insight, we propose HEGNN, a high-degree version of EGNN to increase the expressivity by incorporating high-degree steerable vectors while maintaining EGNN's efficiency through the scalarization trick. Our extensive experiments demonstrate that HEGNN not only aligns with our theoretical analyses on toy datasets consisting of symmetric structures, but also shows substantial improvements on more complicated datasets such as $N$-body and MD17. Our theoretical findings and empirical results potentially open up new possibilities for the research of equivariant GNNs.

Chaohao Yuan, Kangfei Zhao, Ercan Engin Kuruoglu et al.

Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing. Recent studies have proposed diverse architectures, enhanced explainability, and practical applications for Graph Transformers. In light of these rapid developments, we conduct a comprehensive review of Graph Transformers, covering aspects such as their architectures, theoretical foundations, and applications within this survey. We categorize the architecture of Graph Transformers according to their strategies for processing structural information, including graph tokenization, positional encoding, structure-aware attention and model ensemble. Furthermore, from the theoretical perspective, we examine the expressivity of Graph Transformers in various discussed architectures and contrast them with other advanced graph learning algorithms to discover the connections. Furthermore, we provide a summary of the practical applications where Graph Transformers have been utilized, such as molecule, protein, language, vision, traffic, brain and material data. At the end of this survey, we will discuss the current challenges and prospective directions in Graph Transformers for potential future research.

Zongzhao Li, Jiacheng Cen, Bing Su et al.

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they often fall in leveraging extensive broader information. While direct application of Large Language Models (LLMs) can incorporate external knowledge, they lack the capability for spatial reasoning with guaranteed equivariance. In this paper, we propose EquiLLM, a novel framework for representing 3D physical systems that seamlessly integrates E(3)-equivariance with LLM capabilities. Specifically, EquiLLM comprises four key components: geometry-aware prompting, an equivariant encoder, an LLM, and an equivariant adaptor. Essentially, the LLM guided by the instructive prompt serves as a sophisticated invariant feature processor, while 3D directional information is exclusively handled by the equivariant encoder and adaptor modules. Experimental results demonstrate that EquiLLM delivers significant improvements over previous methods across molecular dynamics simulation, human motion simulation, and antibody design, highlighting its promising generalizability.

Mingze Li, Yu Rong, Songyou Li et al.

The discovery of novel materials is critical for global energy and quantum technology transitions. While deep learning has fundamentally reshaped this landscape, existing predictive or generative models typically operate in isolation, lacking the autonomous orchestration required to execute the full discovery process. Here we present ElementsClaw, an agentic framework for materials discovery that synergizes Large Atomic Models (LAMs) with Large Language Models (LLMs). In response to varied human requirements, ElementsClaw dynamically orchestrates a suite of LAM tools finetuned from our proposed model Elements for atomic-scale numerical computation, while leveraging LLMs for high-level semantic reasoning. This shift moves AI-driven materials science from isolated processes toward integrated and human interactive discovery. In the demanding domain of superconductors, our agentic system guides the experimental synthesis of four new superconductors, including Zr3ScRe8 with a transition temperature of 6.8 K and HfZrRe4 at 6.7 K. At scale, ElementsClaw screens more than 2.4 million stable crystals within only 28 GPU hours, identifying 68,000 high-confidence superconducting candidates and vastly expanding the known superconducting space. These results demonstrate how our agent accelerates materials discovery with high physical fidelity.

Ziyang Yu, Wenbing Huang, Yang Liu

The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods and is strongly competitive with current state-of-the-art learning-based models such as DiffDock-PP and Multimer particularly for antibody-antigen docking.