Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. - Yuedong Yang; Haiyan Liu (J. Comput. Chem., 2006)

DTW-Curve for Classification of Logically Similar Motions. - Yuedong Yang; Qinping Zhao; Aimin Hao; Weihe Wu (GRAPP, 2008)

View-invariant action recognition using interest points. - Yuedong Yang; Aimin Hao; Qinping Zhao (Multimedia Information Retrieval, 2008)

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. - Huiying Zhao; Yuedong Yang; Yaoqi Zhou (Bioinform., 2010)

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. - Yuedong Yang; Eshel Faraggi; Huiying Zhao; Yaoqi Zhou (Bioinform., 2011)

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. - Eshel Faraggi; Tuo Zhang; Yuedong Yang; Lukasz A. Kurgan; Yaoqi Zhou (J. Comput. Chem., 2012)

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. - James G. Lyons; Abdollah Dehzangi; Rhys Heffernan; Alok Sharma; Kuldip K. Paliwal; Abdul Sattar 001; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2014)

Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. - Huiying Zhao; Yuedong Yang; Mark von Itzstein; Yaoqi Zhou (J. Comput. Chem., 2014)

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. - Lukas Folkman; Yuedong Yang; Zhixiu Li; Bela Stantic; Abdul Sattar 001; Matthew E. Mort; David N. Cooper; Yunlong Liu; Yaoqi Zhou (Bioinform., 2015)

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. - Peter Brown; Wayne Pullan; Yuedong Yang; Yaoqi Zhou (Bioinform., 2016)

Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. - Jianzhao Gao; Yuedong Yang; Yaoqi Zhou (Bioinform., 2016)

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. - Rhys Heffernan; Abdollah Dehzangi; James G. Lyons; Kuldip K. Paliwal; Alok Sharma; Jihua Wang; Abdul Sattar 001; Yaoqi Zhou; Yuedong Yang (Bioinform., 2016)

sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. - Md. Tamjidul Hoque; Yuedong Yang; Avdesh Mishra; Yaoqi Zhou (J. Comput. Chem., 2016)

Sequence-based prediction of protein-peptide binding sites using support vector machine. - Ghazaleh Taherzadeh; Yuedong Yang; Tuo Zhang; Alan Wee-Chung Liew; Yaoqi Zhou (J. Comput. Chem., 2016)

Effective protein conformational sampling based on predicted torsion angles. - Yuedong Yang; Yaoqi Zhou (J. Comput. Chem., 2016)

SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. - Yuedong Yang; Jian Zhan; Yaoqi Zhou (J. Comput. Chem., 2016)

Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. - Ghazaleh Taherzadeh; Yaoqi Zhou; Alan Wee-Chung Liew; Yuedong Yang (J. Chem. Inf. Model., 2016)

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. - Jack Hanson; Yuedong Yang; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2017)

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility. - Rhys Heffernan; Yuedong Yang; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2017)

SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. - Thomas Litfin; Yaoqi Zhou; Yuedong Yang (Bioinform., 2017)

LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. - Tong Wang 014; Yuedong Yang; Yaoqi Zhou; Haipeng Gong (Bioinform., 2017)

A heuristic for the time constrained asymmetric linear sum assignment problem. - Peter Brown; Yuedong Yang; Yaoqi Zhou; Wayne J. Pullan (J. Comb. Optim., 2017)

Sixty-five years of the long march in protein secondary structure prediction: the final stretch? - Yuedong Yang; Jianzhao Gao; Jihua Wang; Rhys Heffernan; Jack Hanson; Kuldip K. Paliwal; Yaoqi Zhou (Briefings Bioinform., 2018)

Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (Bioinform., 2018)

Structure-based prediction of protein- peptide binding regions using Random Forest. - Ghazaleh Taherzadeh; Yaoqi Zhou; Alan Wee-Chung Liew; Yuedong Yang (Bioinform., 2018)

Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures. - Jianzhao Gao; Yuedong Yang; Yaoqi Zhou (BMC Bioinform., 2018)

B-factor profile prediction for RNA flexibility using support vector machines. - Ivantha Guruge; Ghazaleh Taherzadeh; Jian Zhan; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2018)

Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. - Rhys Heffernan; Kuldip K. Paliwal; James G. Lyons; Jaswinder Singh; Yuedong Yang; Yaoqi Zhou (J. Comput. Chem., 2018)

Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. - Ghazaleh Taherzadeh; Yuedong Yang; Hao-Dong Xu; Yu Xue 001; Alan Wee-Chung Liew; Yaoqi Zhou (J. Comput. Chem., 2018)

Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. - Jaswinder Singh; Jack Hanson; Rhys Heffernan; Kuldip K. Paliwal; Yuedong Yang; Yaoqi Zhou (J. Chem. Inf. Model., 2018)

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. - Bailing Zhou; Huiying Zhao; Jia-Feng Yu; Chengang Guo; Xianghua Dou; Feng Song; Guodong Hu; Zanxia Cao; Yuanxu Qu; Yuedong Yang; Yaoqi Zhou; Jihua Wang (Nucleic Acids Res., 2018)

Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (Bioinform., 2019)

Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. - Shuangjia Zheng; Jiahua Rao; Zhongyue Zhang; Jun Xu 017; Yuedong Yang (CoRR, 2019)

DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. - Pin Chen; Yaobin Ke; Yutong Lu; Yunfei Du; Jiahui Li 008; Hui Yan; Huiying Zhao; Yaoqi Zhou; Yuedong Yang (J. Cheminformatics, 2019)

QBMG: quasi-biogenic molecule generator with deep recurrent neural network. - Shuangjia Zheng; Xin Yan 006; Qiong Gu; Yuedong Yang; Yunfei Du; Yutong Lu; Jun Xu 017 (J. Cheminformatics, 2019)

SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. - Thomas Litfin; Yuedong Yang; Yaoqi Zhou (J. Chem. Inf. Model., 2019)

Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. - Shuangjia Zheng; Xin Yan 006; Yuedong Yang; Jun Xu 017 (J. Chem. Inf. Model., 2019)

An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer. - Xuan Lv; Zhiguang Chen 001; Yutong Lu; Yuedong Yang (BIBM, 2020)

Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network. - Yuansong Zeng; Xiang Zhou; Jiahua Rao; Yutong Lu; Yuedong Yang (BIBM, 2020)

HeLPS: Heterogeneous LiDAR-based Positioning System for Autonomous Vehicle. - Yuedong Yang; Chao Xia; Xiaodong Deng; Yanqing Shen; Shitao Chen; Nanning Zheng 001 (IECON, 2020)

Communicative Representation Learning on Attributed Molecular Graphs. - Ying Song; Shuangjia Zheng; Zhangming Niu; Zhang-Hua Fu; Yutong Lu; Yuedong Yang (IJCAI, 2020)

Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting. - Yaobin Ke; Jiahua Rao; Huiying Zhao; Yutong Lu; Nong Xiao 001; Yuedong Yang (Bioinform., 2020)

Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (J. Comput. Biol., 2020)

All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. - Tongchuan Zhang; Guodong Hu; Yuedong Yang; Jihua Wang; Yaoqi Zhou (J. Comput. Biol., 2020)

SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. - Yufeng Cai; Xiongjun Li; Zhe Sun; Yutong Lu; Huiying Zhao; Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2020)

To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. - Sheng Chen; Zhe Sun; Lihua Lin; Zifeng Liu; Xun Liu; Yutian Chong; Yutong Lu; Huiying Zhao; Yuedong Yang (J. Chem. Inf. Model., 2020)

Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. - Xuan Lv; Jianwen Chen; Yutong Lu; Zhiguang Chen 001; Nong Xiao 001; Yuedong Yang (J. Chem. Inf. Model., 2020)

Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. - Shuangjia Zheng; Jiahua Rao; Zhongyue Zhang; Jun Xu 017; Yuedong Yang (J. Chem. Inf. Model., 2020)

Predicting drug-protein interaction using quasi-visual question answering system. - Shuangjia Zheng; Yongjian Li; Sheng Chen; Jun Xu 017; Yuedong Yang (Nat. Mach. Intell., 2020)

Publisher Correction: Predicting drug-protein interaction using quasi-visual question answering system. - Shuangjia Zheng; Yongjian Li; Sheng Chen; Jun Xu 017; Yuedong Yang (Nat. Mach. Intell., 2020)

Communicative Message Passing for Inductive Relation Reasoning. - Sijie Mai; Shuangjia Zheng; Yuedong Yang; Haifeng Hu 001 (AAAI, 2021)

SEGEM: a Fast and Accurate Automated Protein Backbone Structure Modeling Method for Cryo-EM. - Sheng Chen; Sen Zhang; Xiongjun Li; Yubao Liu; Yuedong Yang (BIBM, 2021)

Multi-omics Cancer Prognosis Analysis Based on Graph Convolution Network. - Yi Wang; Zhongyue Zhang; Hua Chai; Yuedong Yang (BIBM, 2021)

DGAT-onco: A differential analysis method to detect oncogenes by integrating functional information of mutations. - Haoyang Zhang; Junkang Wei; Zifeng Liu; Xun Liu; Yutian Chong; Yutong Lu; Huiying Zhao; Yuedong Yang (BIBM, 2021)

DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. - Pan Zhang; Shuangjia Zheng; Jianwen Chen; Yaoqi Zhou; Yuedong Yang (BIBM, 2021)

Anytime Depth Estimation with Limited Sensing and Computation Capabilities on Mobile Devices. - Yuedong Yang; Zihui Xue; Radu Marculescu (CoRL, 2021)

Learning Attributed Graph Representation with Communicative Message Passing Transformer. - Jianwen Chen; Shuangjia Zheng; Ying Song; Jiahua Rao; Yuedong Yang (IJCAI, 2021)

Integration of Patch Features Through Self-supervised Learning and Transformer for Survival Analysis on Whole Slide Images. - Ziwang Huang; Hua Chai; Ruoqi Wang; Haitao Wang 026; Yuedong Yang; Hejun Wu (MICCAI (8), 2021)

scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. - Xiang Zhou; Hua Chai; Yuansong Zeng; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2021)

Structure-aware protein-protein interaction site prediction using deep graph convolutional network. - Qianmu Yuan; Jianwen Chen; Huiying Zhao; Yaoqi Zhou; Yuedong Yang (Bioinform., 2021)

Integrating multi-omics data through deep learning for accurate cancer prognosis prediction. - Hua Chai; Xiang Zhou; Zhongyue Zhang; Jiahua Rao; Huiying Zhao; Yuedong Yang (Comput. Biol. Medicine, 2021)

Predicting bladder cancer prognosis by integrating multi-omics data through a transfer learning-based Cox proportional hazards network. - Hua Chai; Zhongyue Zhang; Yi Wang; Yuedong Yang (CCF Trans. High Perform. Comput., 2021)

BioNavi-NP: Biosynthesis Navigator for Natural Products. - Shuangjia Zheng; Tao Zeng; Chengtao Li; Binghong Chen; Connor W. Coley; Yuedong Yang; Ruibo Wu (CoRR, 2021)

Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. - Jiahua Rao; Shuangjia Zheng; Yuedong Yang (CoRR, 2021)

Learning Attributed Graph Representations with Communicative Message Passing Transformer. - Jianwen Chen; Shuangjia Zheng; Ying Song; Jiahua Rao; Yuedong Yang (CoRR, 2021)

Molecular Attributes Transfer from Non-Parallel Data. - Shuangjia Zheng; Ying Song; Zhang Pan; Chengtao Li; Le Song; Yuedong Yang (CoRR, 2021)

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. - Jianwen Chen; Shuangjia Zheng; Huiying Zhao; Yuedong Yang (J. Cheminformatics, 2021)

Deep scaffold hopping with multimodal transformer neural networks. - Shuangjia Zheng; Zengrong Lei; Haitao Ai; Hongming Chen 001; Daiguo Deng; Yuedong Yang (J. Cheminformatics, 2021)

Meta Learning for Low-Resource Molecular Optimization. - Jiahao Wang; Shuangjia Zheng; Jianwen Chen; Yuedong Yang (J. Chem. Inf. Model., 2021)

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. - Bailing Zhou; Baohua Ji; Kui Liu; Guodong Hu; Fei Wang; Qingshuai Chen; Ru Yu; Pingping Huang; Jing Ren; Chengang Guo; Huiying Zhao; Hongmei Zhang; et al. (Nucleic Acids Res., 2021)

Exploring complex and heterogeneous correlations on hypergraph for the prediction of drug-target interactions. - Ding Ruan; Shuyi Ji; Chenggang Yan 001; Junjie Zhu; Xibin Zhao; Yuedong Yang; Yue Gao 002; Changqing Zou; Qionghai Dai (Patterns, 2021)

Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images. - Ying Song; Shuangjia Zheng; Liang Li; Xiang Zhang; Xiaodong Zhang; Ziwang Huang; Jianwen Chen; Ruixuan Wang; Huiying Zhao; Yutian Chong; Jun Shen 008; Yunfei Zha; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. - Shuangjia Zheng; Jiahua Rao; Ying Song; Jixian Zhang; Xianglu Xiao; Evandro Fei Fang; Yuedong Yang; Zhangming Niu (Briefings Bioinform., 2021)

A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data. - Zixiang Pan; Yuansong Zeng; Yuefan Lin; Weijiang Yu; Haokun Zhang; Yuedong Yang (BIBM, 2022)

Accurately Identifying Coronary Atherosclerotic Heart Disease through Merged Beats of Electrocardiogram. - Xinfeng Wang; Mengling Qi; Chengzhi Dong; Haoyang Zhang; Yuedong Yang; Huiying Zhao (BIBM, 2022)

Genetic and phenotypic relationships between coronary atherosclerotic heart disease and electrocardiographic traits. - Xinfeng Wang; Haoyang Zhang; Xuehao Xiu; Mengling Qi; Yuedong Yang; Huiying Zhao (BIBM, 2022)

SCdenoise: a reference-based scRNA-seq denoising method using semi-supervised learning. - Fengqi Zhong; Yuansong Zeng; Yubao Liu; Yuedong Yang (BIBM, 2022)

Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. - Jiahua Rao; Shuangjia Zheng; Sijie Mai; Yuedong Yang (IJCAI, 2022)

A Multi-constraint Deep Semi-supervised Learning Method for Ovarian Cancer Prognosis Prediction. - Hua Chai; Long-Yi Guo; Minfan He; Zhongyue Zhang; Yuedong Yang (ICSI (2), 2022)

Capturing large genomic contexts for accurately predicting enhancer-promoter interactions. - Ken Chen 006; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

AlphaFold2-aware protein-DNA binding site prediction using graph transformer. - Qianmu Yuan; Sheng Chen; Jiahua Rao; Shuangjia Zheng; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning. - Qianmu Yuan; Sheng Chen; Yu Wang 027; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

A robust and scalable graph neural network for accurate single-cell classification. - Yuansong Zeng; Zhuoyi Wei; Zixiang Pan; Yutong Lu; Yuedong Yang (Briefings Bioinform., 2022)

Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks. - Yuansong Zeng; Zhuoyi Wei; Weijiang Yu; Rui Yin; Yuchen Yuan; Bingling Li; Zhonghui Tang; Yutong Lu; Yuedong Yang (Briefings Bioinform., 2022)

A parameter-free deep embedded clustering method for single-cell RNA-seq data. - Yuansong Zeng; Zhuoyi Wei; Fengqi Zhong; Zixiang Pan; Yutong Lu; Yuedong Yang (Briefings Bioinform., 2022)

Cancer survival prognosis with Deep Bayesian Perturbation Cox Network. - Zhongyue Zhang; Hua Chai; Yi Wang; Zixiang Pan; Yuedong Yang (Comput. Biol. Medicine, 2022)

SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning. - Zihui Xue; Yuedong Yang; Mengtian Yang; Radu Marculescu (CoRR, 2022)

A coarse-refine segmentation network for COVID-19 CT images. - Ziwang Huang; Liang Li; Xiang Zhang; Ying Song; Jianwen Chen; Huiying Zhao; Yutian Chong; Hejun Wu; Yuedong Yang; Jun Shen 008; Yunfei Zha (IET Image Process., 2022)

DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. - Youhai Tan; Lingxue Dai; Weifeng Huang; Yinfeng Guo; Shuangjia Zheng; Jinping Lei; Hongming Chen 001; Yuedong Yang (J. Chem. Inf. Model., 2022)

Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. - Penglei Wang; Shuangjia Zheng; Yize Jiang; Chengtao Li; Junhong Liu; Chang Wen; Atanas Patronov; Dahong Qian; Hongming Chen 001; Yuedong Yang (J. Chem. Inf. Model., 2022)

Imputing DNA Methylation by Transferred Learning Based Neural Network. - Xinfeng Wang; Xiang Zhou; Jiahua Rao; Zhu-Jin Zhang; Yue-Dong Yang (J. Comput. Sci. Technol., 2022)

Dynamic graph dropout for subgraph-based relation prediction. - Sijie Mai; Shuangjia Zheng; Ya Sun; Ying Zeng; Yuedong Yang; Haifeng Hu 001 (Knowl. Based Syst., 2022)

tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. - Jun-Hao Wang; Wen-Xin Chen; Shi-Qiang Mei; Yue-Dong Yang; Jian-Hua Yang; Liang-Hu Qu; Ling-Ling Zheng (Nucleic Acids Res., 2022)

Quantitative evaluation of explainable graph neural networks for molecular property prediction. - Jiahua Rao; Shuangjia Zheng; Yutong Lu; Yuedong Yang (Patterns, 2022)

Integrating supercomputing and artificial intelligence for life science. - Jiahua Rao; Shuangjia Zheng; Yuedong Yang (Patterns, 2022)

To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks. - Zhe Sun; Shuangjia Zheng; Huiying Zhao; Zhangming Niu; Yutong Lu; Yi Pan 001; Yuedong Yang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Accelerated rational PROTAC design via deep learning and molecular simulations. - Shuangjia Zheng; Youhai Tan; Zhenyu Wang; Chengtao Li; Zhiqing Zhang; Xu Sang; Hongming Chen 001; Yuedong Yang (Nat. Mac. Intell., 2022)

SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation. - Deqin Liu; Sheng Chen; Shuangjia Zheng; Sen Zhang; Yuedong Yang (BIBM, 2023)

Accurately Identifying Muscle-Invasive Bladder Cancer from MRI via Weakly Supervised Learning. - Fudan Zheng; Yuedong Yang; Tianxin Lin; Shaoxu Wu; Yong Li; Yutong Lu; Ying Song; Zhiguang Chen 001; Huiying Zhao (BIBM, 2023)

Efficient On-Device Training via Gradient Filtering. - Yuedong Yang; Guihong Li; Radu Marculescu (CVPR, 2023)

ZiCo: Zero-shot NAS via inverse Coefficient of Variation on Gradients. - Guihong Li; Yuedong Yang; Kartikeya Bhardwaj; Radu Marculescu (ICLR, 2023)

TIPS: Topologically Important Path Sampling for Anytime Neural Networks. - Guihong Li; Kartikeya Bhardwaj; Yuedong Yang; Radu Marculescu (ICML, 2023)

Retrieval-based Knowledge Augmented Vision Language Pre-training. - Jiahua Rao; Zifei Shan; Longpo Liu; Yao Zhou; Yuedong Yang (ACM Multimedia, 2023)

Efficient Low-rank Backpropagation for Vision Transformer Adaptation. - Yuedong Yang; Hung-Yueh Chiang; Guihong Li; Diana Marculescu; Radu Marculescu (NeurIPS, 2023)

Node-based Knowledge Graph Contrastive Learning for Medical Relationship Prediction. - Zhiguang Fan; Yuedong Yang; Mingyuan Xu; Hongming Chen 001 (CoRR, 2023)

A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information. - Hegang Chen; Yuyin Lu; Yuedong Yang; Yanghui Rao (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Onboard Sensors-Based Self-Localization for Autonomous Vehicle With Hierarchical Map. - Chao Xia; Yanqing Shen; Yuedong Yang; Xiaodong Deng; Shitao Chen; Jingmin Xin; Nanning Zheng 001 (IEEE Trans. Cybern., 2023)

EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. - Bailing Zhou; Maolin Ding; Jing Feng; Baohua Ji; Pingping Huang; Junye Zhang; Xue Yu; Zanxia Cao; Yuedong Yang; Yaoqi Zhou; Jihua Wang (Briefings Bioinform., 2023)

Identifying spatial domain by adapting transcriptomics with histology through contrastive learning. - Yuansong Zeng; Rui Yin; Mai Luo; Jianing Chen; Zixiang Pan; Yutong Lu; Weijiang Yu; Yuedong Yang (Briefings Bioinform., 2023)

Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model. - Yuansong Zeng; Zhuoyi Wei; Qianmu Yuan; Sheng Chen; Weijiang Yu; Yutong Lu; Jianzhao Gao; Yuedong Yang (Bioinform., 2023)

Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion. - Qianmu Yuan; Junjie Xie; Jiancong Xie; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2023)

Subgraph-Aware Few-Shot Inductive Link Prediction Via Meta-Learning. - Shuangjia Zheng; Sijie Mai; Ya Sun; Haifeng Hu 001; Yuedong Yang (IEEE Trans. Knowl. Data Eng., 2023)

Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. - Yidong Song; Qianmu Yuan; Sheng Chen; Ken Chen 006; Yaoqi Zhou; Yuedong Yang (Briefings Bioinform., 2023)

Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. - Yidong Song; Qianmu Yuan; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2023)

ShockSurv: A machine learning model to accurately predict 28-day mortality for septic shock patients in the intensive care unit. - Fudan Zheng; Luhao Wang; Yuxian Pang; Zhiguang Chen 001; Yutong Lu; Yuedong Yang; Jianfeng Wu (Biomed. Signal Process. Control., 2023)

Inferring the genetic relationship between brain imaging-derived phenotypes and risk of complex diseases by Mendelian randomization and genome-wide colocalization. - Siying Lin; Haoyang Zhang; Mengling Qi; David N. Cooper; Yuedong Yang; Yuanhao Yang; Huiying Zhao (NeuroImage, 2023)

From intuition to AI: evolution of small molecule representations in drug discovery. - Miles McGibbon; Steven R. Shave; Jie Dong; Yumiao Gao; Douglas R. Houston; Jiancong Xie; Yuedong Yang; Philippe Schwaller; Vincent Blay (Briefings Bioinform., 2023)

Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering. - Jiahao Zheng 005; Yuedong Yang; Zhiming Dai (Briefings Bioinform., 2023)

SUGAR: Efficient Subgraph-Level Training via Resource-Aware Graph Partitioning. - Zihui Xue; Yuedong Yang; Radu Marculescu (IEEE Trans. Computers, 2023)

Graph learning of disentangled representation for accurately aligning multiple spatial slices. - Jianing Chen; Yuansong Zeng; Ningyuan Shangguan; Wenhao Zhou; Wenbing Li; Yuedong Yang (BCB, 2024)

Interpretable Drug Response Prediction through Molecule Structure-aware and Knowledge-Guided Visible Neural Network. - Jiancong Xie; Zhe Zhang; Youyou Li; Jiahua Rao; Yuedong Yang (BIBM, 2024)

GP-nano: a geometric graph network for nanobody polyreactivity prediction. - Xiaolong Zhou; Qianmu Yuan; Shuangjia Zheng; Yu Wang 027; Yuedong Yang (BIBM, 2024)

Instance-level Expert Knowledge and Aggregate Discriminative Attention for Radiology Report Generation. - Shenshen Bu; Taiji Li; Yuedong Yang; Zhiming Dai (CVPR, 2024)

Cache and Reuse: Rethinking the Efficiency of On-device Transfer Learning. - Yuedong Yang; Hung-Yueh Chiang; Guihong Li; Diana Marculescu; Radu Marculescu (CVPR Workshops, 2024)

Accurately Deciphering Novel Cell Type in Spatially Resolved Single-Cell Data Through Optimal Transport. - Mai Luo; Yuansong Zeng; Jianing Chen; Ningyuan Shangguan; Wenhao Zhou; Yuedong Yang (ISBRA (2), 2024)

Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge. - Hegang Chen; Yuyin Lu; Zhiming Dai; Yuedong Yang; Qing Li 001; Yanghui Rao (Briefings Bioinform., 2024)

Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. - Ken Chen 006; Yue Zhou 014; Maolin Ding; Yu Wang 027; Zhixiang Ren; Yuedong Yang (Briefings Bioinform., 2024)

Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. - Yuefan Lin; Zixiang Pan; Yuansong Zeng; Yuedong Yang; Zhiming Dai (Briefings Bioinform., 2024)

Applying image features of proximal paracancerous tissues in predicting prognosis of patients with hepatocellular carcinoma. - Siying Lin; Juanjuan Yong; Lei Zhang; Xiaolong Chen; Liang Qiao; Weidong Pan; Yuedong Yang; Huiying Zhao (Comput. Biol. Medicine, 2024)

Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks. - Jiahua Rao; Jiancong Xie; Hanjing Lin; Shuangjia Zheng; Zhen Wang 036; Yuedong Yang (CoRR, 2024)

DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. - Junjie Xie; Sheng Chen; Jinping Lei; Yuedong Yang (J. Chem. Inf. Model., 2024)

Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. - Jiancong Xie; Yi Wang; Jiahua Rao; Shuangjia Zheng; Yuedong Yang (J. Chem. Inf. Model., 2024)

GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. - Hao Zhang; Jinchao Huang 004; Junjie Xie; Weifeng Huang; Yuedong Yang; Mingyuan Xu; Jinping Lei; Hongming Chen 001 (J. Chem. Inf. Model., 2024)

Predicting disease-gene associations through self-supervised mutual infomax graph convolution network. - Jiancong Xie; Jiahua Rao; Junjie Xie; Huiying Zhao; Yuedong Yang (Comput. Biol. Medicine, 2024)

Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. - Jing Wang 208; Sheng Chen; Qianmu Yuan; Jianwen Chen; Danping Li; Lei Wang; Yuedong Yang (J. Comput. Chem., 2024)

Deciphering cell types by integrating scATAC-seq data with genome sequences. - Yuansong Zeng; Mai Luo; Ningyuan Shangguan; Peiyu Shi; Junxi Feng; Jin Xu; Ken Chen 006; Yutong Lu; Weijiang Yu; Yuedong Yang (Nat. Comput. Sci., 2024)

An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome. - Hua Chai; Siyin Lin; Junqi Lin; Minfan He; Yuedong Yang; Yongzhong OuYang; Huiying Zhao (BMC Bioinform., 2024)

EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency. - Zhiguang Fan; Yuedong Yang; Mingyuan Xu; Hongming Chen 001 (J. Cheminformatics, 2024)

Advancing Retrosynthesis with Retrieval-Augmented Graph Generation. - Anjie Qiao; Zhen Wang 036; Jiahua Rao; Yuedong Yang; Zhewei Wei (AAAI, 2025)

Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery. - Jiahua Rao; Hanjing Lin; Leyu Chen; Jiancong Xie; Shuangjia Zheng; Yuedong Yang (CVPR, 2025)

Integrating single-cell multi-omics data through self-supervised clustering. - Yuansong Zeng; Jianing Chen; Zixiang Pan; Weijiang Yu; Yuedong Yang (Appl. Soft Comput., 2025)

A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors. - Anjie Qiao; Yuting Chen; Junjie Xie; Weifeng Huang; Hao Zhang; Qirui Deng; Jiahua Rao; Ji Deng; Fanbo Meng; Zhen Wang 004; Mingyuan Xu; Hongming Chen 001; et al. (Briefings Bioinform., 2025)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)

A 3D pocket-aware and affinity-guided diffusion model for lead optimization. - Anjie Qiao; Junjie Xie; Weifeng Huang; Hao Zhang; Jiahua Rao; Shuangjia Zheng; Yuedong Yang; Zhen Wang 036; Guo-Bo Li; Jinping Lei (CoRR, 2025)