294 citations · 567 across the 32 of their papers we have counts for
32 papers
Multimodal Regression for Enzyme Turnover Rates Prediction
Bozhen Hu, Cheng Tan, Siyuan Li +4
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most org…
GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype
Changxi Chi, Jun Xia, Jingbo Zhou +3
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Sinc…
Adversarial Curriculum Graph-Free Knowledge Distillation for Graph Neural Networks
Yuang Jia, Xiaojuan Shan, Jun Xia +5
Data-free Knowledge Distillation (DFKD) is a method that constructs pseudo-samples using a generator without real data, and transfers knowledge from a teacher model to a student by…
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…
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning
Sizhe Liu, Jun Xia, Lecheng Zhang +8
Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, th…
NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics
Jingbo Zhou, Shaorong Chen, Jun Xia +6
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning m…
AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information
Jun Xia, Shaorong Chen, Jingbo Zhou +4
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various d…
Advances of Deep Learning in Protein Science: A Comprehensive Survey
Bozhen Hu, Cheng Tan, Lirong Wu +7
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological proces…
A Graph is Worth Words: Euclideanizing Graph using Pure Transformer
Zhangyang Gao, Daize Dong, Cheng Tan +3
Can we model Non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The Non-Euclidean property have posed a long term challenge…
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…
Masked Modeling for Self-supervised Representation Learning on Vision and Beyond
Siyuan Li, Luyuan Zhang, Zedong Wang +8
As the deep learning revolution marches on, self-supervised learning has garnered increasing attention in recent years thanks to its remarkable representation learning ability and…
Graph-level Protein Representation Learning by Structure Knowledge Refinement
Ge Wang, Zelin Zang, Jiangbin Zheng +2
This paper focuses on learning representation on the whole graph level in an unsupervised manner. Learning graph-level representation plays an important role in a variety of real-w…
Progressive Multi-Modality Learning for Inverse Protein Folding
Jiangbin Zheng, Stan Z. Li
While deep generative models show promise for learning inverse protein folding directly from data, the lack of publicly available structure-sequence pairings limits their generaliz…
USTEP: Spatio-Temporal Predictive Learning under A Unified View
Cheng Tan, Jue Wang, Zhangyang Gao +2
Spatio-temporal predictive learning plays a crucial role in self-supervised learning, with wide-ranging applications across a diverse range of fields. Previous approaches for tempo…
Reinforcement Graph Clustering with Unknown Cluster Number
Yue Liu, Ke Liang, Jun Xia +5
Deep graph clustering, which aims to group nodes into disjoint clusters by neural networks in an unsupervised manner, has attracted great attention in recent years. Although the pe…
CONVERT:Contrastive Graph Clustering with Reliable Augmentation
Xihong Yang, Cheng Tan, Yue Liu +7
Contrastive graph node clustering via learnable data augmentation is a hot research spot in the field of unsupervised graph learning. The existing methods learn the sampling distri…
Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?
Jun Xia, Lecheng Zhang, Xiao Zhu +1
Molecular property prediction (MPP) is a crucial task in the drug discovery pipeline, which has recently gained considerable attention thanks to advances in deep neural networks. H…
Dink-Net: Neural Clustering on Large Graphs
Yue Liu, Ke Liang, Jun Xia +4
Deep graph clustering, which aims to group the nodes of a graph into disjoint clusters with deep neural networks, has achieved promising progress in recent years. However, the exis…
CVT-SLR: Contrastive Visual-Textual Transformation for Sign Language Recognition with Variational Alignment
Jiangbin Zheng, Yile Wang, Cheng Tan +5
Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of larg…
Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective
Cheng Tan, Zhangyang Gao, Hanqun Cao +6
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although dee…
Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings
Jiangbin Zheng, Yile Wang, Ge Wang +5
Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an…
A Systematic Survey of Chemical Pre-trained Models
Jun Xia, Yanqiao Zhu, Yuanqi Du +1
Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to…
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…
Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning
Cheng Tan, Zhangyang Gao, Lirong Wu +4
Spatiotemporal predictive learning aims to generate future frames by learning from historical frames. In this paper, we investigate existing methods and present a general framework…