Yuedong Yang - RankMe

164 papers A* 16C 1Misc 1Journal 121Unranked 25

Year	Rank	Type	Title / Venue / Authors
2026	A*	`conf`	Advancing Protein Design via Multi-Agent Reinforcement Learning with Pareto-Based Collaborative Optimization. AAAI Mingming Zhu, Jiahua Rao, Xiaoyu Chen, Qianmu Yuan, Yuedong Yang
2026	J	`jnl`	BindCLIP: A Unified Contrastive-Generative Representation Learning Framework for Virtual Screening. CoRR Anjie Qiao, Zhen Wang, Yaliang Li, Jiahua Rao, Yuedong Yang
2026	A*	`conf`	De Novo Molecular Generation from Mass Spectra via Many-Body Enhanced Diffusion. AAAI Xichen Sun, Wentao Wei, Jiahua Rao, Jiancong Xie, Yuedong Yang
2026	J	`jnl`	De Novo Molecular Generation from Mass Spectra via Many-Body Enhanced Diffusion. CoRR Xichen Sun, Wentao Wei, Jiahua Rao, Jiancong Xie, Yuedong Yang
2026	J	`jnl`	Fuel Gauge: Estimating Chain-of-Thought Length Ahead of Time in Large Multimodal Models. CoRR Yuedong Yang, Xiwen Wei, Mustafa Munir, Radu Marculescu
2026	A*	`conf`	Informative Subgraph Extraction with Deep Reinforcement Learning for Drug-Drug Interaction Prediction. AAAI Jiancong Xie, Wentao Wei, Chi Zhang, Jiahua Rao, Yuedong Yang
2026	J	`jnl`	Training-free Latent Inter-Frame Pruning with Attention Recovery. CoRR Dennis Menn, Yuedong Yang, Bokun Wang, Xiwen Wei, Mustafa Munir, Feng Liang, Radu Marculescu, Chenfeng Xu, Diana Marculescu
2025	J	`jnl`	A 3D pocket-aware and affinity-guided diffusion model for lead optimization. CoRR Anjie Qiao, Junjie Xie, Weifeng Huang, Hao Zhang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang, Zhen Wang, Guo-Bo Li, Jinping Lei
2025	J	`jnl`	A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors. Briefings Bioinform. Anjie Qiao, Yuting Chen, Junjie Xie, Weifeng Huang, Hao Zhang, Qirui Deng, Jiahua Rao, Ji Deng, Fanbo Meng, Zhen Wang, Mingyuan Xu, Hongming Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang, Guo-Bo Li, Jinping Lei
2025	J	`jnl`	A Novel Framework for Multi-Modal Protein Representation Learning. CoRR Runjie Zheng, Zhen Wang, Anjie Qiao, Jiancong Xie, Jiahua Rao, Yuedong Yang
2025	A*	`conf`	Advancing Retrosynthesis with Retrieval-Augmented Graph Generation. AAAI Anjie Qiao, Zhen Wang, Jiahua Rao, Yuedong Yang, Zhewei Wei
2025	—	`conf`	Cellular-Resolution Reconstruction of Spatial Transcriptomics from Histology Images via Foundation Models and KANs. BIBM Ruipeng Huang, Leiming Fang, Wenbing Li, Yuansong Zeng, Yuedong Yang
2025	—	`conf`	Drug Sensitivity Inference Through Foundation Model-Driven Contrastive Integration of Bulk and Single-Cell Omics. BIBM Ningyuan Shangguan, Yuansong Zeng, Wenbing Li, Yuedong Yang
2025	J	`jnl`	Foundation Model: A New Era for Plant Single-cell Genomics. Genom. Proteom. Bioinform. Yuansong Zeng, Yuedong Yang
2025	—	`conf`	Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Molecular Graph Learning. KDD (2) Jiahua Rao, Hanjing Lin, Jiancong Xie, Zhen Wang, Shuangjia Zheng, Yuedong Yang
2025	J	`jnl`	Integrating single-cell multi-omics data through self-supervised clustering. Appl. Soft Comput. Yuansong Zeng, Jianing Chen, Zixiang Pan, Weijiang Yu, Yuedong Yang
2025	—	`conf`	Interpretably Predicting Chemical Perturbation via Biologically Informed Visible Neural Network. BIBM Wenhao Zhou, Jiancong Xie, Yuedong Yang
2025	A*	`conf`	Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery. CVPR Jiahua Rao, Hanjing Lin, Leyu Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang
2025	J	`jnl`	OIG-Bench: A Multi-Agent Annotated Benchmark for Multimodal One-Image Guides Understanding. CoRR Jiancong Xie, Wenjin Wang, Zhuomeng Zhang, Zihan Liu, Qi Liu, Ke Feng, Zixun Sun, Yuedong Yang
2025	A*	`conf`	Quadruple Attention in Many-body Systems for Accurate Molecular Property Predictions. ICML Jiahua Rao, Dahao Xu, Wentao Wei, Yicong Chen, Mingjun Yang, Yuedong Yang
2025	J	`jnl`	Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. CoRR Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo
2024	—	`conf`	Accurately Deciphering Novel Cell Type in Spatially Resolved Single-Cell Data Through Optimal Transport. ISBRA (2) Mai Luo, Yuansong Zeng, Jianing Chen, Ningyuan Shangguan, Wenhao Zhou, Yuedong Yang
2024	J	`jnl`	An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome. BMC Bioinform. Hua Chai, Siyin Lin, Junqi Lin, Minfan He, Yuedong Yang, Yongzhong Ouyang, Huiying Zhao
2024	J	`jnl`	Applying image features of proximal paracancerous tissues in predicting prognosis of patients with hepatocellular carcinoma. Comput. Biol. Medicine Siying Lin, Juanjuan Yong, Lei Zhang, Xiaolong Chen, Liang Qiao, Weidong Pan, Yuedong Yang, Huiying Zhao
2024	—	`conf`	Cache and Reuse: Rethinking the Efficiency of On-device Transfer Learning. CVPR Workshops Yuedong Yang, Hung-Yueh Chiang, Guihong Li, Diana Marculescu, Radu Marculescu
2024	J	`jnl`	Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge. Briefings Bioinform. Hegang Chen, Yuyin Lu, Zhiming Dai, Yuedong Yang, Qing Li, Yanghui Rao
2024	J	`jnl`	Deciphering cell types by integrating scATAC-seq data with genome sequences. Nat. Comput. Sci. Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang
2024	J	`jnl`	Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. Briefings Bioinform. Yuefan Lin, Zixiang Pan, Yuansong Zeng, Yuedong Yang, Zhiming Dai
2024	J	`jnl`	DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. J. Chem. Inf. Model. Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang
2024	J	`jnl`	EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency. J. Cheminformatics Zhiguang Fan, Yuedong Yang, Mingyuan Xu, Hongming Chen
2024	J	`jnl`	From intuition to AI: evolution of small molecule representations in drug discovery. Briefings Bioinform. Miles McGibbon, Steven R. Shave, Jie Dong, Yumiao Gao, Douglas R. Houston, Jiancong Xie, Yuedong Yang, Philippe Schwaller, Vincent Blay
2024	—	`conf`	GP-nano: a geometric graph network for nanobody polyreactivity prediction. BIBM Xiaolong Zhou, Qianmu Yuan, Shuangjia Zheng, Yu Wang, Yuedong Yang
2024	J	`jnl`	GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. J. Chem. Inf. Model. Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen
2024	—	`conf`	Graph learning of disentangled representation for accurately aligning multiple spatial slices. BCB Jianing Chen, Yuansong Zeng, Ningyuan Shangguan, Wenhao Zhou, Wenbing Li, Yuedong Yang
2024	J	`jnl`	Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks. CoRR Jiahua Rao, Jiancong Xie, Hanjing Lin, Shuangjia Zheng, Zhen Wang, Yuedong Yang
2024	A*	`conf`	Instance-level Expert Knowledge and Aggregate Discriminative Attention for Radiology Report Generation. CVPR Shenshen Bu, Taiji Li, Yuedong Yang, Zhiming Dai
2024	—	`conf`	Interpretable Drug Response Prediction through Molecule Structure-aware and Knowledge-Guided Visible Neural Network. BIBM Jiancong Xie, Zhe Zhang, Youyou Li, Jiahua Rao, Yuedong Yang
2024	J	`jnl`	Predicting disease-gene associations through self-supervised mutual infomax graph convolution network. Comput. Biol. Medicine Jiancong Xie, Jiahua Rao, Junjie Xie, Huiying Zhao, Yuedong Yang
2024	J	`jnl`	Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. J. Comput. Chem. Jing Wang, Sheng Chen, Qianmu Yuan, Jianwen Chen, Danping Li, Lei Wang, Yuedong Yang
2024	J	`jnl`	Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. J. Chem. Inf. Model. Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
2024	J	`jnl`	Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Briefings Bioinform. Ken Chen, Yue Zhou, Maolin Ding, Yu Wang, Zhixiang Ren, Yuedong Yang
2024	J	`jnl`	Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering. Briefings Bioinform. Jiahao Zheng, Yuedong Yang, Zhiming Dai
2023	J	`jnl`	A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information. IEEE ACM Trans. Comput. Biol. Bioinform. Hegang Chen, Yuyin Lu, Yuedong Yang, Yanghui Rao
2023	—	`conf`	Accurately Identifying Muscle-Invasive Bladder Cancer from MRI via Weakly Supervised Learning. BIBM Fudan Zheng, Yuedong Yang, Tianxin Lin, Shaoxu Wu, Yong Li, Yutong Lu, Ying Song, Zhiguang Chen, Huiying Zhao
2023	J	`jnl`	Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. Briefings Bioinform. Yidong Song, Qianmu Yuan, Huiying Zhao, Yuedong Yang
2023	J	`jnl`	EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. Briefings Bioinform. Bailing Zhou, Maolin Ding, Jing Feng, Baohua Ji, Pingping Huang, Junye Zhang, Xue Yu, Zanxia Cao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
2023	A*	`conf`	Efficient Low-rank Backpropagation for Vision Transformer Adaptation. NeurIPS Yuedong Yang, Hung-Yueh Chiang, Guihong Li, Diana Marculescu, Radu Marculescu
2023	J	`jnl`	Efficient Low-rank Backpropagation for Vision Transformer Adaptation. CoRR Yuedong Yang, Hung-Yueh Chiang, Guihong Li, Diana Marculescu, Radu Marculescu
2023	A*	`conf`	Efficient On-Device Training via Gradient Filtering. CVPR Yuedong Yang, Guihong Li, Radu Marculescu
2023	J	`jnl`	Efficient On-device Training via Gradient Filtering. CoRR Yuedong Yang, Guihong Li, Radu Marculescu
2023	J	`jnl`	Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion. Briefings Bioinform. Qianmu Yuan, Junjie Xie, Jiancong Xie, Huiying Zhao, Yuedong Yang
2023	J	`jnl`	Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. Briefings Bioinform. Yidong Song, Qianmu Yuan, Sheng Chen, Ken Chen, Yaoqi Zhou, Yuedong Yang
2023	J	`jnl`	Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model. Bioinform. Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao, Yuedong Yang
2023	J	`jnl`	Identifying spatial domain by adapting transcriptomics with histology through contrastive learning. Briefings Bioinform. Yuansong Zeng, Rui Yin, Mai Luo, Jianing Chen, Zixiang Pan, Yutong Lu, Weijiang Yu, Yuedong Yang
2023	J	`jnl`	Inferring the genetic relationship between brain imaging-derived phenotypes and risk of complex diseases by Mendelian randomization and genome-wide colocalization. NeuroImage Siying Lin, Haoyang Zhang, Mengling Qi, David N. Cooper, Yuedong Yang, Yuanhao Yang, Huiying Zhao
2023	J	`jnl`	Node-based Knowledge Graph Contrastive Learning for Medical Relationship Prediction. CoRR Zhiguang Fan, Yuedong Yang, Mingyuan Xu, Hongming Chen
2023	J	`jnl`	Onboard Sensors-Based Self-Localization for Autonomous Vehicle With Hierarchical Map. IEEE Trans. Cybern. Chao Xia, Yanqing Shen, Yuedong Yang, Xiaodong Deng, Shitao Chen, Jingmin Xin, Nanning Zheng
2023	A*	`conf`	Retrieval-based Knowledge Augmented Vision Language Pre-training. ACM Multimedia Jiahua Rao, Zifei Shan, Longpo Liu, Yao Zhou, Yuedong Yang
2023	J	`jnl`	Retrieval-based Knowledge Augmented Vision Language Pre-training. CoRR Jiahua Rao, Zifei Shan, Longpo Liu, Yao Zhou, Yuedong Yang
2023	—	`conf`	SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation. BIBM Deqin Liu, Sheng Chen, Shuangjia Zheng, Sen Zhang, Yuedong Yang
2023	J	`jnl`	SUGAR: Efficient Subgraph-Level Training via Resource-Aware Graph Partitioning. IEEE Trans. Computers Zihui Xue, Yuedong Yang, Radu Marculescu
2023	J	`jnl`	ShockSurv: A machine learning model to accurately predict 28-day mortality for septic shock patients in the intensive care unit. Biomed. Signal Process. Control. Fudan Zheng, Luhao Wang, Yuxian Pang, Zhiguang Chen, Yutong Lu, Yuedong Yang, Jianfeng Wu
2023	J	`jnl`	Subgraph-Aware Few-Shot Inductive Link Prediction Via Meta-Learning. IEEE Trans. Knowl. Data Eng. Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang
2023	A*	`conf`	TIPS: Topologically Important Path Sampling for Anytime Neural Networks. ICML Guihong Li, Kartikeya Bhardwaj, Yuedong Yang, Radu Marculescu
2023	J	`jnl`	TIPS: Topologically Important Path Sampling for Anytime Neural Networks. CoRR Guihong Li, Kartikeya Bhardwaj, Yuedong Yang, Radu Marculescu
2023	J	`jnl`	ZiCo: Zero-shot NAS via Inverse Coefficient of Variation on Gradients. CoRR Guihong Li, Yuedong Yang, Kartikeya Bhardwaj, Radu Marculescu
2023	A*	`conf`	ZiCo: Zero-shot NAS via inverse Coefficient of Variation on Gradients. ICLR Guihong Li, Yuedong Yang, Kartikeya Bhardwaj, Radu Marculescu
2022	—	`conf`	A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data. BIBM Zixiang Pan, Yuansong Zeng, Yuefan Lin, Weijiang Yu, Haokun Zhang, Yuedong Yang
2022	—	`conf`	A Multi-constraint Deep Semi-supervised Learning Method for Ovarian Cancer Prognosis Prediction. ICSI (2) Hua Chai, Long-Yi Guo, Minfan He, Zhongyue Zhang, Yuedong Yang
2022	J	`jnl`	A coarse-refine segmentation network for COVID-19 CT images. IET Image Process. Ziwang Huang, Liang Li, Xiang Zhang, Ying Song, Jianwen Chen, Huiying Zhao, Yutian Chong, Hejun Wu, Yuedong Yang, Jun Shen, Yunfei Zha
2022	J	`jnl`	A parameter-free deep embedded clustering method for single-cell RNA-seq data. Briefings Bioinform. Yuansong Zeng, Zhuoyi Wei, Fengqi Zhong, Zixiang Pan, Yutong Lu, Yuedong Yang
2022	J	`jnl`	A robust and scalable graph neural network for accurate single-cell classification. Briefings Bioinform. Yuansong Zeng, Zhuoyi Wei, Zixiang Pan, Yutong Lu, Yuedong Yang
2022	J	`jnl`	Accelerated rational PROTAC design via deep learning and molecular simulations. Nat. Mac. Intell. Shuangjia Zheng, Youhai Tan, Zhenyu Wang, Chengtao Li, Zhiqing Zhang, Xu Sang, Hongming Chen, Yuedong Yang
2022	—	`conf`	Accurately Identifying Coronary Atherosclerotic Heart Disease through Merged Beats of Electrocardiogram. BIBM Xinfeng Wang, Mengling Qi, Chengzhi Dong, Haoyang Zhang, Yuedong Yang, Huiying Zhao
2022	J	`jnl`	Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning. Briefings Bioinform. Qianmu Yuan, Sheng Chen, Yu Wang, Huiying Zhao, Yuedong Yang
2022	J	`jnl`	AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Briefings Bioinform. Qianmu Yuan, Sheng Chen, Jiahua Rao, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
2022	J	`jnl`	Cancer survival prognosis with Deep Bayesian Perturbation Cox Network. Comput. Biol. Medicine Zhongyue Zhang, Hua Chai, Yi Wang, Zixiang Pan, Yuedong Yang
2022	J	`jnl`	Capturing large genomic contexts for accurately predicting enhancer-promoter interactions. Briefings Bioinform. Ken Chen, Huiying Zhao, Yuedong Yang
2022	A*	`conf`	Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. IJCAI Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
2022	J	`jnl`	Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. CoRR Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
2022	J	`jnl`	DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. J. Chem. Inf. Model. Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang
2022	J	`jnl`	Dynamic graph dropout for subgraph-based relation prediction. Knowl. Based Syst. Sijie Mai, Shuangjia Zheng, Ya Sun, Ying Zeng, Yuedong Yang, Haifeng Hu
2022	—	`conf`	Genetic and phenotypic relationships between coronary atherosclerotic heart disease and electrocardiographic traits. BIBM Xinfeng Wang, Haoyang Zhang, Xuehao Xiu, Mengling Qi, Yuedong Yang, Huiying Zhao
2022	J	`jnl`	Integrating supercomputing and artificial intelligence for life science. Patterns Jiahua Rao, Shuangjia Zheng, Yuedong Yang
2022	J	`jnl`	Quantitative evaluation of explainable graph neural networks for molecular property prediction. Patterns Jiahua Rao, Shuangjia Zheng, Yutong Lu, Yuedong Yang
2022	—	`conf`	SCdenoise: a reference-based scRNA-seq denoising method using semi-supervised learning. BIBM Fengqi Zhong, Yuansong Zeng, Yubao Liu, Yuedong Yang
2022	J	`jnl`	SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning. CoRR Zihui Xue, Yuedong Yang, Mengtian Yang, Radu Marculescu
2022	J	`jnl`	Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks. Briefings Bioinform. Yuansong Zeng, Zhuoyi Wei, Weijiang Yu, Rui Yin, Yuchen Yuan, Bingling Li, Zhonghui Tang, Yutong Lu, Yuedong Yang
2022	J	`jnl`	Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. J. Chem. Inf. Model. Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang
2022	J	`jnl`	To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan, Yuedong Yang
2021	Misc	`conf`	Anytime Depth Estimation with Limited Sensing and Computation Capabilities on Mobile Devices. CoRL Yuedong Yang, Zihui Xue, Radu Marculescu
2021	J	`jnl`	BioNavi-NP: Biosynthesis Navigator for Natural Products. CoRR Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu
2021	A*	`conf`	Communicative Message Passing for Inductive Relation Reasoning. AAAI Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu
2021	—	`conf`	DGAT-onco: A differential analysis method to detect oncogenes by integrating functional information of mutations. BIBM Haoyang Zhang, Junkang Wei, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao, Yuedong Yang
2021	J	`jnl`	Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images. IEEE ACM Trans. Comput. Biol. Bioinform. Ying Song, Shuangjia Zheng, Liang Li, Xiang Zhang, Xiaodong Zhang, Ziwang Huang, Jianwen Chen, Ruixuan Wang, Huiying Zhao, Yutian Chong, Jun Shen, Yunfei Zha, Yuedong Yang
2021	J	`jnl`	Deep scaffold hopping with multimodal transformer neural networks. J. Cheminformatics Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang
2021	—	`conf`	DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang
2021	J	`jnl`	EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
2021	J	`jnl`	Exploring complex and heterogeneous correlations on hypergraph for the prediction of drug-target interactions. Patterns Ding Ruan, Shuyi Ji, Chenggang Yan, Junjie Zhu, Xibin Zhao, Yuedong Yang, Yue Gao, Changqing Zou, Qionghai Dai
2021	J	`jnl`	Integrating multi-omics data through deep learning for accurate cancer prognosis prediction. Comput. Biol. Medicine Hua Chai, Xiang Zhou, Zhongyue Zhang, Jiahua Rao, Huiying Zhao, Yuedong Yang
2021	—	`conf`	Integration of Patch Features Through Self-supervised Learning and Transformer for Survival Analysis on Whole Slide Images. MICCAI (8) Ziwang Huang, Hua Chai, Ruoqi Wang, Haitao Wang, Yuedong Yang, Hejun Wu
2021	A*	`conf`	Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang
2021	J	`jnl`	Learning Attributed Graph Representations with Communicative Message Passing Transformer. CoRR Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang
2021	J	`jnl`	Meta Learning for Low-Resource Molecular Optimization. J. Chem. Inf. Model. Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang
2021	J	`jnl`	Molecular Attributes Transfer from Non-Parallel Data. CoRR Shuangjia Zheng, Ying Song, Zhang Pan, Chengtao Li, Le Song, Yuedong Yang
2021	—	`conf`	Multi-omics Cancer Prognosis Analysis Based on Graph Convolution Network. BIBM Yi Wang, Zhongyue Zhang, Hua Chai, Yuedong Yang
2021	J	`jnl`	PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. Briefings Bioinform. Shuangjia Zheng, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, Zhangming Niu
2021	J	`jnl`	Predicting bladder cancer prognosis by integrating multi-omics data through a transfer learning-based Cox proportional hazards network. CCF Trans. High Perform. Comput. Hua Chai, Zhongyue Zhang, Yi Wang, Yuedong Yang
2021	J	`jnl`	Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. CoRR Jiahua Rao, Shuangjia Zheng, Yuedong Yang
2021	—	`conf`	SEGEM: a Fast and Accurate Automated Protein Backbone Structure Modeling Method for Cryo-EM. BIBM Sheng Chen, Sen Zhang, Xiongjun Li, Yubao Liu, Yuedong Yang
2021	J	`jnl`	Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J. Cheminformatics Jianwen Chen, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
2021	J	`jnl`	Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinform. Qianmu Yuan, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
2021	J	`jnl`	Subgraph-aware Few-Shot Inductive Link Prediction via Meta-Learning. CoRR Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang
2021	J	`jnl`	scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. Briefings Bioinform. Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang
2020	J	`jnl`	Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting. Bioinform. Yaobin Ke, Jiahua Rao, Huiying Zhao, Yutong Lu, Nong Xiao, Yuedong Yang
2020	—	`conf`	Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network. BIBM Yuansong Zeng, Xiang Zhou, Jiahua Rao, Yutong Lu, Yuedong Yang
2020	J	`jnl`	Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. J. Chem. Inf. Model. Xuan lv, Jianwen Chen, Yutong Lu, Zhiguang Chen, Nong Xiao, Yuedong Yang
2020	J	`jnl`	All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. J. Comput. Biol. Tongchuan Zhang, Guodong Hu, Yuedong Yang, Jihua Wang, Yaoqi Zhou
2020	—	`conf`	An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer. BIBM Xuan lv, Zhiguang Chen, Yutong Lu, Yuedong Yang
2020	J	`jnl`	Communicative Message Passing for Inductive Relation Reasoning. CoRR Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu
2020	A*	`conf`	Communicative Representation Learning on Attributed Molecular Graphs. IJCAI Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang
2020	J	`jnl`	Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. J. Comput. Biol. Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2020	C	`conf`	HeLPS: Heterogeneous LiDAR-based Positioning System for Autonomous Vehicle. IECON Yuedong Yang, Chao Xia, Xiaodong Deng, Yanqing Shen, Shitao Chen, Nanning Zheng
2020	J	`jnl`	Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. J. Chem. Inf. Model. Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
2020	J	`jnl`	Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang
2020	J	`jnl`	Publisher Correction: Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang
2020	J	`jnl`	SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. J. Comput. Chem. Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang
2020	J	`jnl`	To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. J. Chem. Inf. Model. Sheng Chen, Zhe Sun, Lihua Lin, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao, Yuedong Yang
2019	J	`jnl`	DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. J. Cheminformatics Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
2019	J	`jnl`	Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. J. Chem. Inf. Model. Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu
2019	J	`jnl`	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. Bioinform. Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2019	J	`jnl`	Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. CoRR Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
2019	J	`jnl`	QBMG: quasi-biogenic molecule generator with deep recurrent neural network. J. Cheminformatics Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu, Jun Xu
2019	J	`jnl`	SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. J. Chem. Inf. Model. Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2018	J	`jnl`	Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. Bioinform. Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2018	J	`jnl`	Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. J. Chem. Inf. Model. Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip K. Paliwal, Yuedong Yang, Yaoqi Zhou
2018	J	`jnl`	EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 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
2018	J	`jnl`	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. BMC Bioinform. Jianzhao Gao, Yuedong Yang, Yaoqi Zhou
2018	J	`jnl`	Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. J. Comput. Chem. Ghazaleh Taherzadeh, Yuedong Yang, Hao-Dong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
2018	J	`jnl`	Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. J. Comput. Chem. Rhys Heffernan, Kuldip K. Paliwal, James G. Lyons, Jaswinder Singh, Yuedong Yang, Yaoqi Zhou
2018	J	`jnl`	Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Briefings Bioinform. Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou
2018	J	`jnl`	Structure-based prediction of protein- peptide binding regions using Random Forest. Bioinform. Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
2017	J	`jnl`	A heuristic for the time constrained asymmetric linear sum assignment problem. J. Comb. Optim. Peter Brown, Yuedong Yang, Yaoqi Zhou, Wayne J. Pullan
2017	J	`jnl`	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. Bioinform. Rhys Heffernan, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou
2017	J	`jnl`	Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinform. Jack Hanson, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou
2017	J	`jnl`	LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. Bioinform. Tong Wang, Yuedong Yang, Yaoqi Zhou, Haipeng Gong
2017	J	`jnl`	SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinform. Thomas Litfin, Yaoqi Zhou, Yuedong Yang
2016	J	`jnl`	Effective protein conformational sampling based on predicted torsion angles. J. Comput. Chem. Yuedong Yang, Yaoqi Zhou
2016	J	`jnl`	Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinform. Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou
2016	J	`jnl`	Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinform. Rhys Heffernan, Abdollah Dehzangi, James G. Lyons, Kuldip K. Paliwal, Alok Sharma, Jihua Wang, Abdul Sattar, Yaoqi Zhou, Yuedong Yang
2016	J	`jnl`	Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. Bioinform. Jianzhao Gao, Yuedong Yang, Yaoqi Zhou
2016	J	`jnl`	SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. J. Comput. Chem. Yuedong Yang, Jian Zhan, Yaoqi Zhou
2016	J	`jnl`	Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. J. Chem. Inf. Model. Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
2016	J	`jnl`	Sequence-based prediction of protein-peptide binding sites using support vector machine. J. Comput. Chem. Ghazaleh Taherzadeh, Yuedong Yang, Tuo Zhang, Alan Wee-Chung Liew, Yaoqi Zhou
2016	J	`jnl`	sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. J. Comput. Chem. Md. Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou
2015	J	`jnl`	DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinform. Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou
2014	J	`jnl`	Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. J. Comput. Chem. Huiying Zhao, Yuedong Yang, Mark von Itzstein, Yaoqi Zhou
2014	J	`jnl`	Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J. Comput. Chem. James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip K. Paliwal, Abdul Sattar, Yaoqi Zhou, Yuedong Yang
2012	J	`jnl`	SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J. Comput. Chem. Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, Yaoqi Zhou
2011	J	`jnl`	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. Bioinform. Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou
2010	J	`jnl`	Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinform. Huiying Zhao, Yuedong Yang, Yaoqi Zhou
2008	—	`conf`	DTW-Curve for Classification of Logically Similar Motions. GRAPP Yuedong Yang, Qinping Zhao, Aimin Hao, Weihe Wu
2008	—	`conf`	View-invariant action recognition using interest points. Multimedia Information Retrieval Yuedong Yang, Aimin Hao, Qinping Zhao
2006	J	`jnl`	Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. J. Comput. Chem. Yuedong Yang, Haiyan Liu