419 citations · 932 across the 46 of their papers we have counts for
47 papers
APO: Unsupervised Atomic Policy Optimization for 3D Structure Prediction of Atomic Systems
Shentong Mo, Yatao Bian
Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery. While flow-matching models (, FlowDPO) have recently shown promise i…
Advancing Optimal Subset Oracle via Learning Relaxation of Neural Set Functions
Yongquan Shi, Zijing Ou, Shiping Wang +1
Learning neural set functions is pivotal to a wide range of important applications, including compound selection in AI-driven drug discovery and product recommendation. Recent work…
InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization
Yifan Niu, Ziqi Gao, Tingyang Xu +5
Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading…
ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking
Yiqiang Yi, Xu Wan, Yatao Bian +2
Predicting the docking between proteins and ligands is a crucial and challenging task for drug discovery. However, traditional docking methods mainly rely on scoring functions, and…
SAILOR: Structural Augmentation Based Tail Node Representation Learning
Jie Liao, Jintang Li, Liang Chen +3
Graph Neural Networks (GNNs) have achieved state-of-the-art performance in representation learning for graphs recently. However, the effectiveness of GNNs, which capitalize on the…
SGFormer: Simplifying and Empowering Transformers for Large-Graph Representations
Qitian Wu, Wentao Zhao, Chenxiao Yang +5
Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class o…
SyNDock: N Rigid Protein Docking via Learnable Group Synchronization
Yuanfeng Ji, Yatao Bian, Guoji Fu +2
The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional st…
Reweighted Mixup for Subpopulation Shift
Zongbo Han, Zhipeng Liang, Fan Yang +8
Subpopulation shift exists widely in many real-world applications, which refers to the training and test distributions that contain the same subpopulation groups but with different…
Understanding and Improving Feature Learning for Out-of-Distribution Generalization
Yongqiang Chen, Wei Huang, Kaiwen Zhou +3
A common explanation for the failure of out-of-distribution (OOD) generalization is that the model trained with empirical risk minimization (ERM) learns spurious features instead o…
Fairness-guided Few-shot Prompting for Large Language Models
Huan Ma, Changqing Zhang, Yatao Bian +7
Large language models have demonstrated surprising ability to perform in-context learning, i.e., these models can be directly applied to solve numerous downstream tasks by conditio…
Activity Cliff Prediction: Dataset and Benchmark
Ziqiao Zhang, Bangyi Zhao, Ailin Xie +2
Activity cliffs (ACs), which are generally defined as pairs of structurally similar molecules that are active against the same bio-target but significantly different in the binding…
ImDrug: A Benchmark for Deep Imbalanced Learning in AI-aided Drug Discovery
Lanqing Li, Liang Zeng, Ziqi Gao +11
The last decade has witnessed a prosperous development of computational methods and dataset curation for AI-aided drug discovery (AIDD). However, real-world pharmaceutical datasets…
Hierarchical Few-Shot Object Detection: Problem, Benchmark and Method
Lu Zhang, Yang Wang, Jiaogen Zhou +5
Few-shot object detection (FSOD) is to detect objects with a few examples. However, existing FSOD methods do not consider hierarchical fine-grained category structures of objects t…
UMIX: Improving Importance Weighting for Subpopulation Shift via Uncertainty-Aware Mixup
Zongbo Han, Zhipeng Liang, Fan Yang +7
Subpopulation shift widely exists in many real-world machine learning applications, referring to the training and test distributions containing the same subpopulation groups but va…
Can Pre-trained Models Really Learn Better Molecular Representations for AI-aided Drug Discovery?
Ziqiao Zhang, Yatao Bian, Ailin Xie +3
Self-supervised pre-training is gaining increasingly more popularity in AI-aided drug discovery, leading to more and more pre-trained models with the promise that they can extract…
Diversity Boosted Learning for Domain Generalization with Large Number of Domains
Xi Leng, Xiaoying Tang, Yatao Bian
Machine learning algorithms minimizing the average training loss usually suffer from poor generalization performance due to the greedy exploitation of correlations among the traini…
Pareto Invariant Risk Minimization: Towards Mitigating the Optimization Dilemma in Out-of-Distribution Generalization
Yongqiang Chen, Kaiwen Zhou, Yatao Bian +8
Recently, there has been a growing surge of interest in enabling machine learning systems to generalize well to Out-of-Distribution (OOD) data. Most efforts are devoted to advancin…
A Survey of Trustworthy Graph Learning: Reliability, Explainability, and Privacy Protection
Bingzhe Wu, Jintang Li, Junchi Yu +17
Deep graph learning has achieved remarkable progresses in both business and scientific areas ranging from finance and e-commerce, to drug and advanced material discovery. Despite t…
DRFLM: Distributionally Robust Federated Learning with Inter-client Noise via Local Mixup
Bingzhe Wu, Zhipeng Liang, Yuxuan Han +3
Recently, federated learning has emerged as a promising approach for training a global model using data from multiple organizations without leaking their raw data. Nevertheless, di…
Fine-Tuning Graph Neural Networks via Graph Topology induced Optimal Transport
Jiying Zhang, Xi Xiao, Long-Kai Huang +2
Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world…
Hypergraph Convolutional Networks via Equivalency between Hypergraphs and Undirected Graphs
Jiying Zhang, Fuyang Li, Xi Xiao +4
As a powerful tool for modeling complex relationships, hypergraphs are gaining popularity from the graph learning community. However, commonly used frameworks in deep hypergraph le…
Learning Neural Set Functions Under the Optimal Subset Oracle
Zijing Ou, Tingyang Xu, Qinliang Su +3
Learning neural set functions becomes increasingly more important in many applications like product recommendation and compound selection in AI-aided drug discovery. The majority o…
Transformer for Graphs: An Overview from Architecture Perspective
Erxue Min, Runfa Chen, Yatao Bian +7
Recently, Transformer model, which has achieved great success in many artificial intelligence fields, has demonstrated its great potential in modeling graph-structured data. Till n…
Recent Advances in Reliable Deep Graph Learning: Inherent Noise, Distribution Shift, and Adversarial Attack
Jintang Li, Bingzhe Wu, Chengbin Hou +5
Deep graph learning (DGL) has achieved remarkable progress in both business and scientific areas ranging from finance and e-commerce to drug and advanced material discovery. Despit…