arXiv subjects

Haitao Lin

Publications and source records attributed to Haitao Lin.

At least 37 records · Page 2Linked to original sources

arXiv2025

MogaNet: Multi-order Gated Aggregation Network

By contextualizing the kernel as global as possible, Modern ConvNets have shown great potential in computer vision tasks. However, recent progress on multi-order game-theoretic interaction within deep neural networks (DNNs) reveals the representation bottleneck of modern ConvNets, where the expressive interactions have not been effectively encoded with the increased kernel size. To tackle this challenge, we propose a new family of modern ConvNets, dubbed MogaNet, for discriminative visual representation learning in pure ConvNet-based models with favorable complexity-performance trade-offs. MogaNet encapsulates conceptually simple yet effective convolutions and gated aggregation into a compact module, where discriminative features are efficiently gathered and contextualized adaptively. MogaNet exhibits great scalability, impressive efficiency of parameters, and competitive performance compared to state-of-the-art ViTs and ConvNets on ImageNet and various downstream vision benchmarks, including COCO object detection, ADE20K semantic segmentation, 2D&3D human pose estimation, and video prediction. Notably, MogaNet hits 80.0% and 87.8% accuracy with 5.2M and 181M parameters on ImageNet-1K, outperforming ParC-Net and ConvNeXt-L, while saving 59% FLOPs and 17M parameters, respectively. The source code is available at https://github.com/Westlake-AI/MogaNet.

cs.CV↗

arXiv2025

Graph Neural Networks in Modern AI-aided Drug Discovery

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive framework for learning the complex topological and geometric features of drug-like molecules, cementing their role in modern molecular modeling. This review provides a comprehensive overview of the methodological foundations and representative applications of GNNs in drug discovery, spanning tasks such as molecular property prediction, virtual screening, molecular generation, biomedical knowledge graph construction, and synthesis planning. Particular attention is given to recent methodological advances, including geometric GNNs, interpretable models, uncertainty quantification, scalable graph architectures, and graph generative frameworks. We also discuss how these models integrate with modern deep learning approaches, such as self-supervised learning, multi-task learning, meta-learning and pre-training. Throughout this review, we highlight the practical challenges and methodological bottlenecks encountered when applying GNNs to real-world drug discovery pipelines, and conclude with a discussion on future directions.

q-bio.BM↗

arXiv2025

You Only Estimate Once: Unified, One-stage, Real-Time Category-level Articulated Object 6D Pose Estimation for Robotic Grasping

This paper addresses the problem of category-level pose estimation for articulated objects in robotic manipulation tasks. Recent works have shown promising results in estimating part pose and size at the category level. However, these approaches primarily follow a complex multi-stage pipeline that first segments part instances in the point cloud and then estimates the Normalized Part Coordinate Space (NPCS) representation for 6D poses. These approaches suffer from high computational costs and low performance in real-time robotic tasks. To address these limitations, we propose YOEO, a single-stage method that simultaneously outputs instance segmentation and NPCS representations in an end-to-end manner. We use a unified network to generate point-wise semantic labels and centroid offsets, allowing points from the same part instance to vote for the same centroid. We further utilize a clustering algorithm to distinguish points based on their estimated centroid distances. Finally, we first separate the NPCS region of each instance. Then, we align the separated regions with the real point cloud to recover the final pose and size. Experimental results on the GAPart dataset demonstrate the pose estimation capabilities of our proposed single-shot method. We also deploy our synthetically-trained model in a real-world setting, providing real-time visual feedback at 200Hz, enabling a physical Kinova robot to interact with unseen articulated objects. This showcases the utility and effectiveness of our proposed method.

cs.CV↗

arXiv2025

CAP-Net: A Unified Network for 6D Pose and Size Estimation of Categorical Articulated Parts from a Single RGB-D Image

This paper tackles category-level pose estimation of articulated objects in robotic manipulation tasks and introduces a new benchmark dataset. While recent methods estimate part poses and sizes at the category level, they often rely on geometric cues and complex multi-stage pipelines that first segment parts from the point cloud, followed by Normalized Part Coordinate Space (NPCS) estimation for 6D poses. These approaches overlook dense semantic cues from RGB images, leading to suboptimal accuracy, particularly for objects with small parts. To address these limitations, we propose a single-stage Network, CAP-Net, for estimating the 6D poses and sizes of Categorical Articulated Parts. This method combines RGB-D features to generate instance segmentation and NPCS representations for each part in an end-to-end manner. CAP-Net uses a unified network to simultaneously predict point-wise class labels, centroid offsets, and NPCS maps. A clustering algorithm then groups points of the same predicted class based on their estimated centroid distances to isolate each part. Finally, the NPCS region of each part is aligned with the point cloud to recover its final pose and size. To bridge the sim-to-real domain gap, we introduce the RGBD-Art dataset, the largest RGB-D articulated dataset to date, featuring photorealistic RGB images and depth noise simulated from real sensors. Experimental evaluations on the RGBD-Art dataset demonstrate that our method significantly outperforms the state-of-the-art approach. Real-world deployments of our model in robotic tasks underscore its robustness and exceptional sim-to-real transfer capabilities, confirming its substantial practical utility. Our dataset, code and pre-trained models are available on the project page.

cs.CV↗

arXiv2025

Tokenizing Electron Cloud in Protein-Ligand Interaction Learning

The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Most deep-learning-based prediction approaches focus on structures of atoms or fragments. However, quantum chemical properties, such as electronic structures, are the key to unveiling interaction patterns but remain largely underexplored. To bridge this gap, we propose ECBind, a method for tokenizing electron cloud signals into quantized embeddings, enabling their integration into downstream tasks such as binding affinity prediction. By incorporating electron densities, ECBind helps uncover binding modes that cannot be fully represented by atom-level models. Specifically, to remove the redundancy inherent in electron cloud signals, a structure-aware transformer and hierarchical codebooks encode 3D binding sites enriched with electron structures into tokens. These tokenized codes are then used for specific tasks with labels. To extend its applicability to a wider range of scenarios, we utilize knowledge distillation to develop an electron-cloud-agnostic prediction model. Experimentally, ECBind demonstrates state-of-the-art performance across multiple tasks, achieving improvements of 6.42\% and 15.58\% in per-structure Pearson and Spearman correlation coefficients, respectively.

cs.LG↗

arXiv2025

HGCL: Hierarchical Graph Contrastive Learning for User-Item Recommendation

Graph Contrastive Learning (GCL), which fuses graph neural networks with contrastive learning, has evolved as a pivotal tool in user-item recommendations. While promising, existing GCL methods often lack explicit modeling of hierarchical item structures, which represent item similarities across varying resolutions. Such hierarchical item structures are ubiquitous in various items (e.g., online products and local businesses), and reflect their inherent organizational properties that serve as critical signals for enhancing recommendation accuracy. In this paper, we propose Hierarchical Graph Contrastive Learning (HGCL), a novel GCL method that incorporates hierarchical item structures for user-item recommendations. First, HGCL pre-trains a GCL module using cross-layer contrastive learning to obtain user and item representations. Second, HGCL employs a representation compression and clustering method to construct a two-hierarchy user-item bipartite graph. Ultimately, HGCL fine-tunes user and item representations by learning on the hierarchical graph, and then provides recommendations based on user-item interaction scores. Experiments on three widely adopted benchmark datasets ranging from 70K to 382K nodes confirm the superior performance of HGCL over existing baseline models, highlighting the contribution of hierarchical item structures in enhancing GCL methods for recommendation tasks.

cs.IR↗

arXiv2025

PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models

Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins, these methods struggle to generate polymer conformations due to their unique structural characteristics. Meanwhile, the scarcity of polymer conformation datasets further limits the progress, making this important area largely unexplored. In this work, we propose PolyConf, a pioneering tailored polymer conformation generation method that leverages hierarchical generative models to unlock new possibilities. Specifically, we decompose the polymer conformation into a series of local conformations (i.e., the conformations of its repeating units), generating these local conformations through an autoregressive model, and then generating their orientation transformations via a diffusion model to assemble them into the complete polymer conformation. Moreover, we develop the first benchmark with a high-quality polymer conformation dataset derived from molecular dynamics simulations to boost related research in this area. The comprehensive evaluation demonstrates that PolyConf consistently outperforms existing conformation generation methods, thus facilitating advancements in polymer modeling and simulation.

cond-mat.soft↗

arXiv2025

Scaling Function Learning: A sparse aerodynamic data reconstruction method for generalizing aircraft shapes

Accurate and complete aerodynamic data sets are the basis for comprehensive and accurate evaluation of the overall performance of aircraft. However, the sampling cost of full-state aerodynamic data is extremely high, and there are often differences between wind tunnel conditions and actual flight conditions. Conventional scaling parameter extraction methods can solve the problem of aerodynamic state extrapolation, but hard to achieve data migration and shape generalization. In order to realize the low-cost construction of a full-state nonlinear aerodynamic database, this research proposes the Scaling Function Learning (SFL) method. In SFL method, symbolic regression is used to mine the composite function expression of aerodynamic force coefficient for a relatively complete aerodynamic data set of typical aircraft. The inner layer of the function represents a scaling function. The SFL method was validated on the HB-2 by extracting scaling parameters for axial force coefficients and generalizing the scaling function by releasing its constants. The effectiveness and accuracy of the scaling function are verified using different hypersonic aircraft configurations, such as HBS, double ellipsoid, sharp cone, and double cone missile. The results show that the extracted scaling function has the ability to generalize across states and configurations. With only 3-4 state samples, the aerodynamic database construction of variable Mach number, angle of attack and Reynolds number can be realized, which shows great state extrapolation ability with a relative error of about 1-5%. This research also lays a methodological foundation for parameter space dimensionality reduction and small sample modeling of other complex high-dimensional engineering problems.

physics.flu-dyn↗

arXiv2025

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen

The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing computational methods in antibody design often overlook crucial conformational changes that antigens undergo during the binding process, significantly impacting the reliability of the resulting antibodies. To bridge this gap, we introduce dyAb, a flexible framework that incorporates AlphaFold2-driven predictions to model pre-binding antigen structures and specifically addresses the dynamic nature of antigen conformation changes. Our dyAb model leverages a unique combination of coarse-grained interface alignment and fine-grained flow matching techniques to simulate the interaction dynamics and structural evolution of the antigen-antibody complex, providing a realistic representation of the binding process. Extensive experiments show that dyAb significantly outperforms existing models in antibody design involving changing antigen conformations. These results highlight dyAb's potential to streamline the design process for therapeutic antibodies, promising more efficient development cycles and improved outcomes in clinical applications.

q-bio.QM↗

arXiv2025

A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer

The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of functionally promising mutations is challenged by the limited evolutionary accessible regions, i.e., only a small region on the fitness landscape is beneficial. There have been numerous priors used to constrain protein evolution to regions of landscapes with high-fitness variants, among which the change in binding free energy (DDG) of protein complexes upon mutations is one of the most commonly used priors. However, the huge mutation space poses two challenges: (1) how to improve the efficiency of DDG prediction for fast mutation screening; and (2) how to explain mutation preferences and efficiently explore accessible evolutionary regions. To address these challenges, we propose a lightweight DDG predictor (Light-DDG), which adopts a structure-aware Transformer as the backbone and enhances it by knowledge distilled from existing powerful but computationally heavy DDG predictors. Additionally, we augmented, annotated, and released a large-scale dataset containing millions of mutation data for pre-training Light-DDG. We find that such a simple yet effective Light-DDG can serve as a good unsupervised antibody optimizer and explainer. For the target antibody, we propose a novel Mutation Explainer to learn mutation preferences, which accounts for the marginal benefit of each mutation per residue. To further explore accessible evolutionary regions, we conduct preference-guided antibody optimization and evaluate antibody candidates quickly using Light-DDG to identify desirable mutations.

q-bio.QM↗

arXiv2024

An Empirical Study: Extensive Deep Temporal Point Process

Temporal point process as the stochastic process on continuous domain of time is commonly used to model the asynchronous event sequence featuring with occurrence timestamps. Thanks to the strong expressivity of deep neural networks, they are emerging as a promising choice for capturing the patterns in asynchronous sequences, in the context of temporal point process. In this paper, we first review recent research emphasis and difficulties in modeling asynchronous event sequences with deep temporal point process, which can be concluded into four fields: encoding of history sequence, formulation of conditional intensity function, relational discovery of events and learning approaches for optimization. We introduce most of recently proposed models by dismantling them into the four parts, and conduct experiments by remodularizing the first three parts with the same learning strategy for a fair empirical evaluation. Besides, we extend the history encoders and conditional intensity function family, and propose a Granger causality discovery framework for exploiting the relations among multi-types of events. Because the Granger causality can be represented by the Granger causality graph, discrete graph structure learning in the framework of Variational Inference is employed to reveal latent structures of the graph. Further experiments show that the proposed framework with latent graph discovery can both capture the relations and achieve an improved fitting and predicting performance.

cs.LG↗

arXiv2024

Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization

Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design, existing computational methods still encounter several challenges: 1) poor capability of modeling complex CDRs with long sequences due to insufficient contextual information; 2) conditioned on pre-given antigenic epitopes and their static interaction with the target antibody; 3) neglect of specificity during antibody optimization leads to non-specific antibodies. In this paper, we take into account a variety of node features, edge features, and edge relations to include more contextual and geometric information. We propose a novel Relation-Aware Antibody Design (RAAD) framework, which dynamically models antigen-antibody interactions for co-designing the sequences and structures of antigen-specific CDRs. Furthermore, we propose a new evaluation metric to better measure antibody specificity and develop a contrasting specificity-enhancing constraint to optimize the specificity of antibodies. Extensive experiments have demonstrated the superior capability of RAAD in terms of antibody modeling, generation, and optimization across different CDR types, sequence lengths, pre-training strategies, and input contexts.

q-bio.QM↗

arXiv2024

PPFlow: Target-aware Peptide Design with Torsional Flow Matching

Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored. To fill the gap, we propose a target-aware peptide design method called \textsc{PPFlow}, based on conditional flow matching on torus manifolds, to model the internal geometries of torsion angles for the peptide structure design. Besides, we establish a protein-peptide binding dataset named PPBench2024 to fill the void of massive data for the task of structure-based peptide drug design and to allow the training of deep learning methods. Extensive experiments show that PPFlow reaches state-of-the-art performance in tasks of peptide drug generation and optimization in comparison with baseline models, and can be generalized to other tasks including docking and side-chain packing.

q-bio.BM↗

arXiv2024

SparseGrasp: Robotic Grasping via 3D Semantic Gaussian Splatting from Sparse Multi-View RGB Images

Language-guided robotic grasping is a rapidly advancing field where robots are instructed using human language to grasp specific objects. However, existing methods often depend on dense camera views and struggle to quickly update scenes, limiting their effectiveness in changeable environments. In contrast, we propose SparseGrasp, a novel open-vocabulary robotic grasping system that operates efficiently with sparse-view RGB images and handles scene updates fastly. Our system builds upon and significantly enhances existing computer vision modules in robotic learning. Specifically, SparseGrasp utilizes DUSt3R to generate a dense point cloud as the initialization for 3D Gaussian Splatting (3DGS), maintaining high fidelity even under sparse supervision. Importantly, SparseGrasp incorporates semantic awareness from recent vision foundation models. To further improve processing efficiency, we repurpose Principal Component Analysis (PCA) to compress features from 2D models. Additionally, we introduce a novel render-and-compare strategy that ensures rapid scene updates, enabling multi-turn grasping in changeable environments. Experimental results show that SparseGrasp significantly outperforms state-of-the-art methods in terms of both speed and adaptability, providing a robust solution for multi-turn grasping in changeable environment.

cs.RO↗

arXiv2024

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative heterogeneous graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements various cutting-edge methods. Secondly, a single task on \textit{de novo} molecule generation can hardly reflect their capabilities. To broaden the scope, we have adapted these models to a range of tasks essential in drug design, which are considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of \textit{de novo} molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide the pre-trained versions of the state-of-the-art models and deep insights with analysis from empirical studies. The codebase for CBGBench is publicly accessible at \url{https://github.com/Edapinenut/CBGBench}.

cs.LG↗

arXiv2024

Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting

Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). However, most existing GNNs are based on message passing to perform feature aggregation and transformation, where the structural information is explicitly involved in the forward propagation by coupling with node features through graph convolution at each layer. As a result, subtle feature noise or structure perturbation may cause severe error propagation, resulting in extremely poor robustness. In this paper, we rethink the roles played by graph structural information in graph data training and identify that message passing is not the only path to modeling structural information. Inspired by this, we propose a simple but effective Graph Structure Self-Contrasting (GSSC) framework that learns graph structural information without message passing. The proposed framework is based purely on Multi-Layer Perceptrons (MLPs), where the structural information is only implicitly incorporated as prior knowledge to guide the computation of supervision signals, substituting the explicit message propagation as in GNNs. Specifically, it first applies structural sparsification to remove potentially uninformative or noisy edges in the neighborhood, and then performs structural self-contrasting in the sparsified neighborhood to learn robust node representations. Finally, structural sparsification and self-contrasting are formulated as a bi-level optimization problem and solved in a unified framework. Extensive experiments have qualitatively and quantitatively demonstrated that the GSSC framework can produce truly encouraging performance with better generalization and robustness than other leading competitors.

cs.LG↗

arXiv2024

Polaris: Open-ended Interactive Robotic Manipulation via Syn2Real Visual Grounding and Large Language Models

This paper investigates the task of the open-ended interactive robotic manipulation on table-top scenarios. While recent Large Language Models (LLMs) enhance robots' comprehension of user instructions, their lack of visual grounding constrains their ability to physically interact with the environment. This is because the robot needs to locate the target object for manipulation within the physical workspace. To this end, we introduce an interactive robotic manipulation framework called Polaris, which integrates perception and interaction by utilizing GPT-4 alongside grounded vision models. For precise manipulation, it is essential that such grounded vision models produce detailed object pose for the target object, rather than merely identifying pixels belonging to them in the image. Consequently, we propose a novel Synthetic-to-Real (Syn2Real) pose estimation pipeline. This pipeline utilizes rendered synthetic data for training and is then transferred to real-world manipulation tasks. The real-world performance demonstrates the efficacy of our proposed pipeline and underscores its potential for extension to more general categories. Moreover, real-robot experiments have showcased the impressive performance of our framework in grasping and executing multiple manipulation tasks. This indicates its potential to generalize to scenarios beyond the tabletop. More information and video results are available here: https://star-uu-wang.github.io/Polaris/

cs.RO↗

arXiv2024

LAC-Net: Linear-Fusion Attention-Guided Convolutional Network for Accurate Robotic Grasping Under the Occlusion

This paper addresses the challenge of perceiving complete object shapes through visual perception. While prior studies have demonstrated encouraging outcomes in segmenting the visible parts of objects within a scene, amodal segmentation, in particular, has the potential to allow robots to infer the occluded parts of objects. To this end, this paper introduces a new framework that explores amodal segmentation for robotic grasping in cluttered scenes, thus greatly enhancing robotic grasping abilities. Initially, we use a conventional segmentation algorithm to detect the visible segments of the target object, which provides shape priors for completing the full object mask. Particularly, to explore how to utilize semantic features from RGB images and geometric information from depth images, we propose a Linear-fusion Attention-guided Convolutional Network (LAC-Net). LAC-Net utilizes the linear-fusion strategy to effectively fuse this cross-modal data, and then uses the prior visible mask as attention map to guide the network to focus on target feature locations for further complete mask recovery. Using the amodal mask of the target object provides advantages in selecting more accurate and robust grasp points compared to relying solely on the visible segments. The results on different datasets show that our method achieves state-of-the-art performance. Furthermore, the robot experiments validate the feasibility and robustness of this method in the real world. Our code and demonstrations are available on the project page: https://jrryzh.github.io/LAC-Net.

cs.RO↗