294 citations · 737 across the 61 of their papers we have counts for
39 papers · 1 filter
Tokenizing Electron Cloud in Protein-Ligand Interaction Learning
Haitao Lin, Odin Zhang, Jia Xu +6
The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Mo…
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction
Cheng Tan, Zhenxiao Cao, Zhangyang Gao +6
Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biol…
FlowTS: Time Series Generation via Rectified Flow
Yang Hu, Xiao Wang, Zezhen Ding +7
Diffusion-based models have significant achievements in time series generation but suffer from inefficient computation: solving high-dimensional ODEs/SDEs via iterative numerical s…
Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting
Lirong Wu, Haitao Lin, Guojiang Zhao +2
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 fea…
Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation
Lirong Wu, Yunfan Liu, Haitao Lin +2
To bridge the gaps between powerful Graph Neural Networks (GNNs) and lightweight Multi-Layer Perceptron (MLPs), GNN-to-MLP Knowledge Distillation (KD) proposes to distill knowledge…
The Heterophilic Graph Learning Handbook: Benchmarks, Models, Theoretical Analysis, Applications and Challenges
Sitao Luan, Chenqing Hua, Qincheng Lu +11
Homophily principle, \ie{} nodes with the same labels or similar attributes are more likely to be connected, has been commonly believed to be the main reason for the superiority of…
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin, Guojiang Zhao, Odin Zhang +7
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. How…
A Teacher-Free Graph Knowledge Distillation Framework with Dual Self-Distillation
Lirong Wu, Haitao Lin, Zhangyang Gao +2
Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). Despite their great academic success, Multi-Layer Perceptrons (MLPs) re…
Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks
Tianyu Fan, Lirong Wu, Yufei Huang +4
Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acq…
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
Lirong Wu, Yijun Tian, Yufei Huang +4
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays r…
Deep Manifold Graph Auto-Encoder for Attributed Graph Embedding
Bozhen Hu, Zelin Zang, Jun Xia +3
Representing graph data in a low-dimensional space for subsequent tasks is the purpose of attributed graph embedding. Most existing neural network approaches learn latent represent…
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction
Yufei Huang, Siyuan Li, Jin Su +9
Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimati…
Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs
Lirong Wu, Haitao Lin, Yufei Huang +1
To bridge the gaps between topology-aware Graph Neural Networks (GNNs) and inference-efficient Multi-Layer Perceptron (MLPs), GLNN proposes to distill knowledge from a well-trained…
Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting it into MLPs: An Effective GNN-to-MLP Distillation Framework
Lirong Wu, Haitao Lin, Yufei Huang +2
Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial a…
Towards Reasonable Budget Allocation in Untargeted Graph Structure Attacks via Gradient Debias
Zihan Liu, Yun Luo, Lirong Wu +2
It has become cognitive inertia to employ cross-entropy loss function in classification related tasks. In the untargeted attacks on graph structure, the gradients derived from the…
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy
Yufei Huang, Lirong Wu, Haitao Lin +3
Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein se…
Rethinking Explaining Graph Neural Networks via Non-parametric Subgraph Matching
Fang Wu, Siyuan Li, Xurui Jin +4
The success of graph neural networks (GNNs) provokes the question about explainability: ``Which fraction of the input graph is the most determinant of the prediction?'' Particularl…
A Survey on Protein Representation Learning: Retrospect and Prospect
Lirong Wu, Yufei Huang, Haitao Lin +1
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physi…
Non-equispaced Fourier Neural Solvers for PDEs
Haitao Lin, Lirong Wu, Yongjie Xu +4
Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced sp…
Automated Graph Self-supervised Learning via Multi-teacher Knowledge Distillation
Lirong Wu, Yufei Huang, Haitao Lin +3
Self-supervised learning on graphs has recently achieved remarkable success in graph representation learning. With hundreds of self-supervised pretext tasks proposed over the past…
Teaching Yourself: Graph Self-Distillation on Neighborhood for Node Classification
Lirong Wu, Jun Xia, Haitao Lin +4
Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). Despite their great academic success, Multi-Layer Perceptrons (MLPs) re…
Exploring Generative Neural Temporal Point Process
Haitao Lin, Lirong Wu, Guojiang Zhao +2
Temporal point process (TPP) is commonly used to model the asynchronous event sequence featuring occurrence timestamps and revealed by probabilistic models conditioned on historica…
CoSP: Co-supervised pretraining of pocket and ligand
Zhangyang Gao, Cheng Tan, Lirong Wu +1
Can we inject the pocket-ligand interaction knowledge into the pre-trained model and jointly learn their chemical space? Pretraining molecules and proteins has attracted considerab…
Hyperspherical Consistency Regularization
Cheng Tan, Zhangyang Gao, Lirong Wu +2
Recent advances in contrastive learning have enlightened diverse applications across various semi-supervised fields. Jointly training supervised learning and unsupervised learning…