73 accepted papers
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 …
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…
Generating objects with specific symmetries is essential in various real-world scenarios, with the creation of patterns exhibiting planar group symmetries being a representative task. However, adapting existing 2D continuous representations to enforce symmetry remains a significant challenge, as the…
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
Equivariant Neural Networks (ENNs) have empowered numerous applications in scientific fields. Despite their remarkable capacity for representing geometric structures, ENNs suffer from degraded expressivity when processing symmetric inputs: the output representations are invariant to transformations…
Multimodal Large Language Models (MLLMs) remain far from human-level performance in multi-view spatial reasoning, where models must establish object correspondences across view and infer coherent scene semantics. We analyze this limitation through the Transformation-Driven Visual Reasoning (TVR) tas
Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by the computational cost. To address this, a surge of deep generative models has recently emerged to learn dynamics at coar…
Denoising learning of 3D molecules learns molecular representations by imposing noises into the equilibrium conformation and predicting the added noises to recover the equilibrium conformation, which essentially captures the information of molecular force fields. Due to the specificity of Potential…
Accurate prediction of ionic conductivity in electrolyte systems is crucial for advancing numerous scientific and technological applications. While significant progress has been made, current research faces two fundamental challenges: (1) the lack of high-quality standardized benchmarks, and (2) ina…
Understanding and leveraging the 3D structures of proteins is central to a variety of biological and drug discovery tasks. While deep learning has been applied successfully for structure-based protein function prediction tasks, current methods usually employ distinct training for each task. However,…
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 fail in leveraging extensive broader information. While…
Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current structure-based generative models are limited in generating nterfaces with sufficient rationality and interpretability.…
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 addres…
Metal-Organic Frameworks (MOFs) have attracted considerable attention due to their unique properties including high surface area and tunable porosity, and promising applications in catalysis, gas storage, and drug delivery. Structure prediction for MOFs is a challenging task, as these frameworks are…
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 reasonin
Understanding the 3D structure of RNA is essential for deciphering its function and developing RNA-based therapeutics. Geometric Graph Neural Networks (GeoGNNs) that conform to the $\mathrm{E}(3)$-symmetry have advanced RNA structure evaluation, a crucial step toward RNA structure prediction. Howeve…
The rapid advancement of large language models (LLMs) has spurred significant interest in tool learning, where LLMs are augmented with external tools to tackle complex tasks. However, existing tool environments face challenges in balancing stability, scale, and realism, particularly for benchmarking…
Modeling human-like action-to-reaction generation has significant real-world applications, like human-robot interaction and games. Despite recent advancements in single-person motion generation, it is still challenging to well handle action-to-reaction generation, due to the difficulty of directly p…
Continual pre-training (CPT) has been an important approach for adapting language models to specific domains or tasks. In this paper, we comprehensively study its key designs to balance the new abilities while retaining the original abilities, and present an effective CPT method that can greatly imp…
Multi-person interactive motion generation, a critical yet under-explored domain in computer character animation, poses significant challenges such as intricate modeling of inter-human interactions beyond individual motions and generating two motions with huge differences from one text condition. Cu…
The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address versatile therapeutic needs or utilize cross-domain transferability…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off between accuracy and efficiency, while recent deep learning-based…
Equivariant Graph Neural Networks (GNNs) have demonstrated significant success across various applications. To achieve completeness---that is, the universal approximation property over the space of equivariant functions---the network must effectively capture the intricate multi-body interactions amo…
Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical needs. However, designing target-specific cyclic peptides remains underexplored due to limited training data. To bridge the…
Predicting high-fidelity 3D structures of atomic systems is a fundamental yet challenging problem in scientific domains. While recent work demonstrates the advantage of generative models in this realm, the exploration of different probability paths are still insufficient, and hallucinations during s…
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.…
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 meth…
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 durin…
Peptide design plays a pivotal role in therapeutics, allowing brand new possibility to leverage target binding sites that are previously undruggable. Most existing methods are either inefficient or only concerned with the target-agnostic design of 1D sequences. In this paper, we propose a generative…
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 indepe…
Equivariant Graph Neural Networks (GNNs) have made remarkable success in a variety of scientific applications. However, existing equivariant GNNs encounter the efficiency issue for large geometric graphs and perform poorly if the input is reduced to sparse local graph for speed acceleration. In this…
Superconductivity is a fascinating phenomenon observed in certain materials under certain conditions. However, some critical aspects of it, such as the relationship between superconductivity and materials' chemical/structural features, still need to be understood. Recent successes of data-driven app…
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 pro…
Crystals are the foundation of numerous scientific and industrial applications. While various learning-based approaches have been proposed for crystal generation, existing methods neglect the spacegroup constraint which is crucial in describing the geometry of crystals and closely relevant to many d…
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 glob…
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 clu…
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…
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 o…
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 ei…
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.…
Learning to represent and simulate the dynamics of physical systems is a crucial yet challenging task. Existing equivariant Graph Neural Network (GNN) based methods have encapsulated the symmetry of physics, \emph{e.g.}, translations, rotations, etc, leading to better generalization ability. Neverth…
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…
Learning a shared policy that guides the locomotion of different agents is of core interest in Reinforcement Learning (RL), which leads to the study of morphology-agnostic RL. However, existing benchmarks are highly restrictive in the choice of starting point and target point, constraining the movem…
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…
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 fe…
Equivariant Graph neural Networks (EGNs) are powerful in characterizing the dynamics of multi-body physical systems. Existing EGNs conduct flat message passing, which, yet, is unable to capture the spatial/dynamical hierarchy for complex systems particularly, limiting substructure discovery and glob…
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, particular…
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 na…
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. Exis…
Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external subgraph construction, and the subgraph assembling depends solel…
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 w…
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 keypoi…
Keypoint detection and description play a central role in computer vision. Most existing methods are in the form of scene-level prediction, without returning the object classes of different keypoints. In this paper, we propose the object-centric formulation, which, beyond the conventional setting, r…
Audio-visual navigation task requires an agent to find a sound source in a realistic, unmapped 3D environment by utilizing egocentric audio-visual observations. Existing audio-visual navigation works assume a clean environment that solely contains the target sound, which, however, would not be suita…
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 alg…
It has been a challenge to learning skills for an agent from long-horizon unannotated demonstrations. Existing approaches like Hierarchical Imitation Learning(HIL) are prone to compounding errors or suboptimal solutions. In this paper, we propose Option-GAIL, a novel method to learn skills at long h…
Knowledge representation learning (KRL) has been used in plenty of knowledge-driven tasks. Despite fruitfully progress, existing methods still suffer from the immaturity on tackling potentially-imperfect knowledge graphs and highly-imbalanced positive-negative instances during training, both of whic…
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…
We address the problem of video grounding from natural language queries. The key challenge in this task is that one training video might only contain a few annotated starting/ending frames that can be used as positive examples for model training. Most conventional approaches directly train a binary…
Over-fitting and 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…
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 pr…
How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation learning. Nevertheless, two issues impede the usage of GNNs in…
We propose a simple, fast, and accurate one-stage approach to visual grounding, inspired by the following insight. The performances of existing propose-and-rank two-stage methods are capped by the quality of the region candidates they propose in the first stage --- if none of the candidates could co…
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 mu…
This paper studies Learning from Observations (LfO) for imitation learning with access to state-only demonstrations. In contrast to Learning from Demonstration (LfD) that involves both action and state supervisions, LfO is more practical in leveraging previously inapplicable resources (e.g., videos)…
We introduce the Neural Collaborative Subspace Clustering, a neural model that discovers clusters of data points drawn from a union of low-dimensional subspaces. In contrast to previous attempts, our model runs without the aid of spectral clustering. This makes our algorithm one of the kinds that ca…
Unsupervised domain adaptation (UDA) transfers knowledge from a label-rich source domain to a fully-unlabeled target domain. To tackle this task, recent approaches resort to discriminative domain transfer in virtue of pseudo-labels to enforce the class-level distribution alignment across the source…
Graph Convolutional Networks (GCNs) have become a crucial tool on learning representations of graph vertices. The main challenge of adapting GCNs on large-scale graphs is the scalability issue that it incurs heavy cost both in computation and memory due to the uncontrollable neighborhood expansion a…
State-of-the-art object detectors usually learn multi-scale representations to get better results by employing feature pyramids. However, the current designs for feature pyramids are still inefficient to integrate the semantic information over different scales. In this paper, we begin by investigati…
Despite the recent success of end-to-end learned representations, hand-crafted optical flow features are still widely used in video analysis tasks. To fill this gap, we propose TVNet, a novel end-to-end trainable neural network, to learn optical-flow-like features from data. TVNet subsumes a specifi…
Dense event captioning aims to detect and describe all events of interest contained in a video. Despite the advanced development in this area, existing methods tackle this task by making use of dense temporal annotations, which is dramatically source-consuming. This paper formulates a new problem: w…
Linear Dynamical Systems (LDSs) are fundamental tools for modeling spatio-temporal data in various disciplines. Though rich in modeling, analyzing LDSs is not free of difficulty, mainly because LDSs do not comply with Euclidean geometry and hence conventional learning techniques can not be applied d…
Linear Dynamical Systems (LDSs) are the fundamental tools for encoding spatio-temporal data in various disciplines. To enhance the performance of LDSs, in this paper, we address the challenging issue of performing sparse coding on the space of LDSs, where both data and dictionary atoms are LDSs. Rat…