default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDYuedong Yang
Yue-Dong Yang
Person information
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
showing all ?? records
2020 – today
- 2024
[j97]Ken Chen
, Yue Zhou, Maolin Ding, Yu Wang, Zhixiang Ren, Yuedong Yang:
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Briefings Bioinform. 25(3) (2024)- [j96]Hegang Chen, Yuyin Lu, Zhiming Dai, Yuedong Yang, Qing Li, Yanghui Rao:
Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge. Briefings Bioinform. 25(4) (2024) - [j95]Yuefan Lin, Zixiang Pan, Yuansong Zeng, Yuedong Yang, Zhiming Dai:
Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. Briefings Bioinform. 25(5) (2024) - [j94]Hua Chai, Siyin Lin, Junqi Lin, Minfan He, Yuedong Yang, Yongzhong OuYang, Huiying Zhao:
An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome. BMC Bioinform. 25(1): 88 (2024) - [j93]Jiancong Xie, Jiahua Rao, Junjie Xie, Huiying Zhao, Yuedong Yang:
Predicting disease-gene associations through self-supervised mutual infomax graph convolution network. Comput. Biol. Medicine 170: 108048 (2024) - [j92]Siying Lin, Juanjuan Yong, Lei Zhang, Xiaolong Chen, Liang Qiao, Weidong Pan, Yuedong Yang, Huiying Zhao:
Applying image features of proximal paracancerous tissues in predicting prognosis of patients with hepatocellular carcinoma. Comput. Biol. Medicine 173: 108365 (2024) - [j91]Jing Wang, Sheng Chen, Qianmu Yuan, Jianwen Chen, Danping Li, Lei Wang, Yuedong Yang:
Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. J. Comput. Chem. 45(8): 436-445 (2024) - [j90]Zhiguang Fan, Yuedong Yang, Mingyuan Xu, Hongming Chen:
EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency. J. Cheminformatics 16(1): 107 (2024) - [j89]Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen:
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. J. Chem. Inf. Model. 64(3): 666-676 (2024) - [j88]Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. J. Chem. Inf. Model. 64(6): 1945-1954 (2024) - [j87]Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang:
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. J. Chem. Inf. Model. 64(7): 2554-2564 (2024) - [j86]Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang:
Deciphering cell types by integrating scATAC-seq data with genome sequences. Nat. Comput. Sci. 4(4): 285-298 (2024) - [c30]Yuedong Yang, Hung-Yueh Chiang, Guihong Li, Diana Marculescu, Radu Marculescu:
Cache and Reuse: Rethinking the Efficiency of On-device Transfer Learning. CVPR Workshops 2024: 8040-8049 - [c29]Shenshen Bu, Taiji Li, Yuedong Yang, Zhiming Dai:
Instance-level Expert Knowledge and Aggregate Discriminative Attention for Radiology Report Generation. CVPR 2024: 14194-14204 - [c28]Mai Luo, Yuansong Zeng, Jianing Chen, Ningyuan Shangguan, Wenhao Zhou, Yuedong Yang:
Accurately Deciphering Novel Cell Type in Spatially Resolved Single-Cell Data Through Optimal Transport. ISBRA (2) 2024: 107-118 - [i16]Jiahua Rao, Jiancong Xie, Hanjing Lin, Shuangjia Zheng, Zhen Wang, Yuedong Yang:
Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks. CoRR abs/2402.04710 (2024) - 2023
- [j85]Bailing Zhou, Maolin Ding, Jing Feng, Baohua Ji, Pingping Huang, Junye Zhang, Xue Yu, Zanxia Cao, Yuedong Yang, Yaoqi Zhou, Jihua Wang:
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. Briefings Bioinform. 24(1) (2023) - [j84]Yuansong Zeng, Rui Yin, Mai Luo, Jianing Chen, Zixiang Pan, Yutong Lu, Weijiang Yu, Yuedong Yang:
Identifying spatial domain by adapting transcriptomics with histology through contrastive learning. Briefings Bioinform. 24(2) (2023) - [j83]Qianmu Yuan, Junjie Xie, Jiancong Xie, Huiying Zhao, Yuedong Yang:
Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion. Briefings Bioinform. 24(3) (2023) - [j82]Yidong Song, Qianmu Yuan, Sheng Chen, Ken Chen, Yaoqi Zhou, Yuedong Yang:
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. Briefings Bioinform. 24(4) (2023) - [j81]Yidong Song, Qianmu Yuan, Huiying Zhao, Yuedong Yang:
Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. Briefings Bioinform. 24(6) (2023) - [j80]Miles McGibbon, Steven R. Shave, Jie Dong, Yumiao Gao, Douglas R. Houston, Jiancong Xie, Yuedong Yang, Philippe Schwaller, Vincent Blay:
From intuition to AI: evolution of small molecule representations in drug discovery. Briefings Bioinform. 25(1) (2023) - [j79]Jiahao Zheng, Yuedong Yang, Zhiming Dai:
Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering. Briefings Bioinform. 25(1) (2023) - [j78]Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao, Yuedong Yang:
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model. Bioinform. 39(4) (2023) - [j77]Fudan Zheng, Luhao Wang, Yuxian Pang, Zhiguang Chen, Yutong Lu, Yuedong Yang, Jianfeng Wu:
ShockSurv: A machine learning model to accurately predict 28-day mortality for septic shock patients in the intensive care unit. Biomed. Signal Process. Control. 86(Part A): 105146 (2023) - [j76]Siying Lin, Haoyang Zhang, Mengling Qi, David N. Cooper, Yuedong Yang, Yuanhao Yang, Huiying Zhao:
Inferring the genetic relationship between brain imaging-derived phenotypes and risk of complex diseases by Mendelian randomization and genome-wide colocalization. NeuroImage 279: 120325 (2023) - [j75]Zihui Xue, Yuedong Yang, Radu Marculescu:
SUGAR: Efficient Subgraph-Level Training via Resource-Aware Graph Partitioning. IEEE Trans. Computers 72(11): 3167-3177 (2023) - [j74]Hegang Chen, Yuyin Lu, Yuedong Yang, Yanghui Rao:
A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information. IEEE ACM Trans. Comput. Biol. Bioinform. 20(3): 1917-1925 (2023) - [j73]Chao Xia, Yanqing Shen, Yuedong Yang, Xiaodong Deng, Shitao Chen, Jingmin Xin, Nanning Zheng:
Onboard Sensors-Based Self-Localization for Autonomous Vehicle With Hierarchical Map. IEEE Trans. Cybern. 53(7): 4218-4231 (2023) - [j72]Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang:
Subgraph-Aware Few-Shot Inductive Link Prediction Via Meta-Learning. IEEE Trans. Knowl. Data Eng. 35(6): 6512-6517 (2023) - [c27]Deqin Liu, Sheng Chen, Shuangjia Zheng, Sen Zhang, Yuedong Yang:
SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation. BIBM 2023: 120-123 - [c26]Fudan Zheng, Yuedong Yang, Tianxin Lin, Shaoxu Wu, Yong Li, Yutong Lu, Ying Song, Zhiguang Chen, Huiying Zhao:
Accurately Identifying Muscle-Invasive Bladder Cancer from MRI via Weakly Supervised Learning. BIBM 2023: 1770-1777 - [c25]Yuedong Yang, Guihong Li, Radu Marculescu:
Efficient On-Device Training via Gradient Filtering. CVPR 2023: 3811-3820 - [c24]Guihong Li, Yuedong Yang, Kartikeya Bhardwaj, Radu Marculescu:
ZiCo: Zero-shot NAS via inverse Coefficient of Variation on Gradients. ICLR 2023 - [c23]Guihong Li, Kartikeya Bhardwaj, Yuedong Yang, Radu Marculescu:
TIPS: Topologically Important Path Sampling for Anytime Neural Networks. ICML 2023: 19343-19359 - [c22]Jiahua Rao, Zifei Shan, Longpo Liu, Yao Zhou, Yuedong Yang:
Retrieval-based Knowledge Augmented Vision Language Pre-training. ACM Multimedia 2023: 5399-5409 - [c21]Yuedong Yang, Hung-Yueh Chiang, Guihong Li, Diana Marculescu, Radu Marculescu:
Efficient Low-rank Backpropagation for Vision Transformer Adaptation. NeurIPS 2023 - [i15]Yuedong Yang, Guihong Li, Radu Marculescu:
Efficient On-device Training via Gradient Filtering. CoRR abs/2301.00330 (2023) - [i14]Guihong Li, Yuedong Yang, Kartikeya Bhardwaj, Radu Marculescu:
ZiCo: Zero-shot NAS via Inverse Coefficient of Variation on Gradients. CoRR abs/2301.11300 (2023) - [i13]Jiahua Rao, Zifei Shan, Longpo Liu, Yao Zhou, Yuedong Yang:
Retrieval-based Knowledge Augmented Vision Language Pre-training. CoRR abs/2304.13923 (2023) - [i12]Guihong Li, Kartikeya Bhardwaj, Yuedong Yang, Radu Marculescu:
TIPS: Topologically Important Path Sampling for Anytime Neural Networks. CoRR abs/2305.08021 (2023) - [i11]Yuedong Yang, Hung-Yueh Chiang, Guihong Li, Diana Marculescu, Radu Marculescu:
Efficient Low-rank Backpropagation for Vision Transformer Adaptation. CoRR abs/2309.15275 (2023) - [i10]Zhiguang Fan, Yuedong Yang, Mingyuan Xu, Hongming Chen:
Node-based Knowledge Graph Contrastive Learning for Medical Relationship Prediction. CoRR abs/2310.10138 (2023) - 2022
- [j71]Ken Chen, Huiying Zhao, Yuedong Yang:
Capturing large genomic contexts for accurately predicting enhancer-promoter interactions. Briefings Bioinform. 23(2) (2022) - [j70]Qianmu Yuan, Sheng Chen, Jiahua Rao, Shuangjia Zheng, Huiying Zhao, Yuedong Yang:
AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Briefings Bioinform. 23(2) (2022) - [j69]Yuansong Zeng, Zhuoyi Wei, Zixiang Pan, Yutong Lu, Yuedong Yang:
A robust and scalable graph neural network for accurate single-cell classification. Briefings Bioinform. 23(2) (2022) - [j68]Yuansong Zeng, Zhuoyi Wei, Weijiang Yu, Rui Yin, Yuchen Yuan, Bingling Li, Zhonghui Tang, Yutong Lu, Yuedong Yang:
Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks. Briefings Bioinform. 23(5) (2022) - [j67]Yuansong Zeng, Zhuoyi Wei, Fengqi Zhong, Zixiang Pan, Yutong Lu, Yuedong Yang:
A parameter-free deep embedded clustering method for single-cell RNA-seq data. Briefings Bioinform. 23(5) (2022) - [j66]Qianmu Yuan, Sheng Chen, Yu Wang, Huiying Zhao, Yuedong Yang:
Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning. Briefings Bioinform. 23(6) (2022) - [j65]Zhongyue Zhang, Hua Chai, Yi Wang, Zixiang Pan, Yuedong Yang:
Cancer survival prognosis with Deep Bayesian Perturbation Cox Network. Comput. Biol. Medicine 141: 105012 (2022) - [j64]Ziwang Huang, Liang Li, Xiang Zhang, Ying Song, Jianwen Chen, Huiying Zhao, Yutian Chong, Hejun Wu, Yuedong Yang, Jun Shen, Yunfei Zha:
A coarse-refine segmentation network for COVID-19 CT images. IET Image Process. 16(2): 333-343 (2022) - [j63]Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang:
Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. J. Chem. Inf. Model. 62(5): 1308-1317 (2022) - [j62]Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang:
DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. J. Chem. Inf. Model. 62(23): 5907-5917 (2022) - [j61]Xinfeng Wang, Xiang Zhou, Jiahua Rao, Zhu-Jin Zhang, Yue-Dong Yang:
Imputing DNA Methylation by Transferred Learning Based Neural Network. J. Comput. Sci. Technol. 37(2): 320-329 (2022) - [j60]Sijie Mai, Shuangjia Zheng, Ya Sun, Ying Zeng, Yuedong Yang, Haifeng Hu:
Dynamic graph dropout for subgraph-based relation prediction. Knowl. Based Syst. 250: 109172 (2022) - [j59]Jun-Hao Wang, Wen-Xin Chen, Shi-Qiang Mei, Yue-Dong Yang, Jian-Hua Yang, Liang-Hu Qu, Ling-Ling Zheng:
tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. Nucleic Acids Res. 50(D1): 421-431 (2022) - [j58]Shuangjia Zheng, Youhai Tan, Zhenyu Wang, Chengtao Li, Zhiqing Zhang, Xu Sang, Hongming Chen, Yuedong Yang:
Accelerated rational PROTAC design via deep learning and molecular simulations. Nat. Mac. Intell. 4(9): 739-748 (2022) - [j57]Jiahua Rao, Shuangjia Zheng, Yutong Lu, Yuedong Yang:
Quantitative evaluation of explainable graph neural networks for molecular property prediction. Patterns 3(12): 100628 (2022) - [j56]Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Integrating supercomputing and artificial intelligence for life science. Patterns 3(12): 100653 (2022) - [j55]Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan, Yuedong Yang:
To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3735-3743 (2022) - [c20]Fengqi Zhong, Yuansong Zeng, Yubao Liu, Yuedong Yang:
SCdenoise: a reference-based scRNA-seq denoising method using semi-supervised learning. BIBM 2022: 182-185 - [c19]Zixiang Pan, Yuansong Zeng, Yuefan Lin, Weijiang Yu, Haokun Zhang, Yuedong Yang:
A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data. BIBM 2022: 226-232 - [c18]Xinfeng Wang, Haoyang Zhang, Xuehao Xiu, Mengling Qi, Yuedong Yang, Huiying Zhao:
Genetic and phenotypic relationships between coronary atherosclerotic heart disease and electrocardiographic traits. BIBM 2022: 241-246 - [c17]Xinfeng Wang, Mengling Qi, Chengzhi Dong, Haoyang Zhang, Yuedong Yang, Huiying Zhao:
Accurately Identifying Coronary Atherosclerotic Heart Disease through Merged Beats of Electrocardiogram. BIBM 2022: 1249-1254 - [c16]Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang:
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. IJCAI 2022: 3919-3925 - [c15]Hua Chai, Long-Yi Guo, Minfan He, Zhongyue Zhang, Yuedong Yang:
A Multi-constraint Deep Semi-supervised Learning Method for Ovarian Cancer Prognosis Prediction. ICSI (2) 2022: 219-229 - [i9]Zihui Xue, Yuedong Yang, Mengtian Yang, Radu Marculescu:
SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning. CoRR abs/2202.00075 (2022) - [i8]Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang:
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. CoRR abs/2205.05957 (2022) - 2021
- [j54]Shuangjia Zheng, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, Zhangming Niu:
PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. Briefings Bioinform. 22(4) (2021) - [j53]Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang:
scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. Briefings Bioinform. 22(6) (2021) - [j52]Qianmu Yuan, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang:
Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinform. 38(1): 125-132 (2021) - [j51]Hua Chai, Xiang Zhou, Zhongyue Zhang, Jiahua Rao, Huiying Zhao, Yuedong Yang:
Integrating multi-omics data through deep learning for accurate cancer prognosis prediction. Comput. Biol. Medicine 134: 104481 (2021) - [j50]Hua Chai, Zhongyue Zhang, Yi Wang, Yuedong Yang:
Predicting bladder cancer prognosis by integrating multi-omics data through a transfer learning-based Cox proportional hazards network. CCF Trans. High Perform. Comput. 3(3): 311-319 (2021) - [j49]Jianwen Chen, Shuangjia Zheng, Huiying Zhao, Yuedong Yang:
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J. Cheminformatics 13(1): 7 (2021) - [j48]Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang:
Deep scaffold hopping with multimodal transformer neural networks. J. Cheminformatics 13(1): 87 (2021) - [j47]Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang:
Meta Learning for Low-Resource Molecular Optimization. J. Chem. Inf. Model. 61(4): 1627-1636 (2021) - [j46]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:
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 49(Database-Issue): D86-D91 (2021) - [j45]Ding Ruan, Shuyi Ji, Chenggang Yan, Junjie Zhu, Xibin Zhao, Yuedong Yang, Yue Gao, Changqing Zou, Qionghai Dai:
Exploring complex and heterogeneous correlations on hypergraph for the prediction of drug-target interactions. Patterns 2(12): 100390 (2021) - [j44]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:
Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2775-2780 (2021) - [c14]Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu:
Communicative Message Passing for Inductive Relation Reasoning. AAAI 2021: 4294-4302 - [c13]Sheng Chen, Sen Zhang, Xiongjun Li, Yubao Liu, Yuedong Yang:
SEGEM: a Fast and Accurate Automated Protein Backbone Structure Modeling Method for Cryo-EM. BIBM 2021: 24-31 - [c12]Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang:
DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM 2021: 118-124 - [c11]Haoyang Zhang, Junkang Wei, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao, Yuedong Yang:
DGAT-onco: A differential analysis method to detect oncogenes by integrating functional information of mutations. BIBM 2021: 793-796 - [c10]Yi Wang, Zhongyue Zhang, Hua Chai, Yuedong Yang:
Multi-omics Cancer Prognosis Analysis Based on Graph Convolution Network. BIBM 2021: 1564-1568 - [c9]Yuedong Yang, Zihui Xue, Radu Marculescu:
Anytime Depth Estimation with Limited Sensing and Computation Capabilities on Mobile Devices. CoRL 2021: 609-618 - [c8]Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang:
Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI 2021: 2242-2248 - [c7]Ziwang Huang, Hua Chai, Ruoqi Wang, Haitao Wang, Yuedong Yang, Hejun Wu:
Integration of Patch Features Through Self-supervised Learning and Transformer for Survival Analysis on Whole Slide Images. MICCAI (8) 2021: 561-570 - [i7]Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu:
BioNavi-NP: Biosynthesis Navigator for Natural Products. CoRR abs/2105.13121 (2021) - [i6]Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. CoRR abs/2107.04119 (2021) - [i5]Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang:
Learning Attributed Graph Representations with Communicative Message Passing Transformer. CoRR abs/2107.08773 (2021) - [i4]Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang:
Subgraph-aware Few-Shot Inductive Link Prediction via Meta-Learning. CoRR abs/2108.00954 (2021) - [i3]Shuangjia Zheng, Ying Song, Zhang Pan, Chengtao Li, Le Song, Yuedong Yang:
Molecular Attributes Transfer from Non-Parallel Data. CoRR abs/2111.15146 (2021) - 2020
- [j43]Yaobin Ke, Jiahua Rao, Huiying Zhao, Yutong Lu, Nong Xiao, Yuedong Yang:
Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting. Bioinform. 36(17): 4576-4582 (2020) - [j42]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. J. Comput. Biol. 27(5): 796-814 (2020) - [j41]Tongchuan Zhang, Guodong Hu, Yuedong Yang, Jihua Wang, Yaoqi Zhou:
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. J. Comput. Biol. 27(6): 856-867 (2020) - [j40]Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. J. Comput. Chem. 41(8): 745-750 (2020) - [j39]Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang:
Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. J. Chem. Inf. Model. 60(1): 47-55 (2020) - [j38]Sheng Chen, Zhe Sun, Lihua Lin, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao, Yuedong Yang:
To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. J. Chem. Inf. Model. 60(1): 391-399 (2020) - [j37]Xuan Lv, Jianwen Chen, Yutong Lu, Zhiguang Chen, Nong Xiao, Yuedong Yang:
Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. J. Chem. Inf. Model. 60(4): 2388-2395 (2020) - [j36]Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang:
Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. 2(2): 134-140 (2020) - [j35]Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang:
Publisher Correction: Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. 2(9): 551 (2020) - [c6]Xuan Lv, Zhiguang Chen, Yutong Lu, Yuedong Yang:
An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer. BIBM 2020: 337-342 - [c5]Yuansong Zeng, Xiang Zhou, Jiahua Rao, Yutong Lu, Yuedong Yang:
Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network. BIBM 2020: 519-522 - [c4]Yuedong Yang, Chao Xia, Xiaodong Deng, Yanqing Shen, Shitao Chen, Nanning Zheng:
HeLPS: Heterogeneous LiDAR-based Positioning System for Autonomous Vehicle. IECON 2020: 618-625 - [c3]Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang:
Communicative Representation Learning on Attributed Molecular Graphs. IJCAI 2020: 2831-2838 - [i2]Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu:
Communicative Message Passing for Inductive Relation Reasoning. CoRR abs/2012.08911 (2020)
2010 – 2019
- 2019
- [j34]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
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. 35(14): 2403-2410 (2019) - [j33]Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu, Jun Xu:
QBMG: quasi-biogenic molecule generator with deep recurrent neural network. J. Cheminformatics 11(1): 5:1-5:12 (2019) - [j32]Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang:
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. J. Cheminformatics 11(1): 52:1-52:11 (2019) - [j31]Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu:
Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. J. Chem. Inf. Model. 59(2): 914-923 (2019) - [j30]Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. J. Chem. Inf. Model. 59(2): 924-930 (2019) - [i1]Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang:
Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. CoRR abs/1907.01356 (2019) - 2018
- [j29]Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou:
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Briefings Bioinform. 19(3): 482-494 (2018) - [j28]Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang:
Structure-based prediction of protein- peptide binding regions using Random Forest. Bioinform. 34(3): 477-484 (2018) - [j27]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. Bioinform. 34(23): 4039-4045 (2018) - [j26]Jianzhao Gao, Yuedong Yang, Yaoqi Zhou:
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. 19(1): 29:1-29:8 (2018) - [j25]Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang:
B-factor profile prediction for RNA flexibility using support vector machines. J. Comput. Chem. 39(8): 407-411 (2018) - [j24]Ghazaleh Taherzadeh, Yuedong Yang, Hao-Dong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou:
Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. J. Comput. Chem. 39(22): 1757-1763 (2018) - [j23]Rhys Heffernan, Kuldip K. Paliwal, James G. Lyons, Jaswinder Singh, Yuedong Yang, Yaoqi Zhou:
Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. J. Comput. Chem. 39(26): 2210-2216 (2018) - [j22]Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip K. Paliwal, Yuedong Yang, Yaoqi Zhou:
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. J. Chem. Inf. Model. 58(9): 2033-2042 (2018) - [j21]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:
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 46(Database-Issue): D100-D105 (2018) - 2017
- [j20]Tong Wang, Yuedong Yang, Yaoqi Zhou, Haipeng Gong:
LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. Bioinform. 33(5): 677-684 (2017) - [j19]Jack Hanson, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou:
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinform. 33(5): 685-692 (2017) - [j18]Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinform. 33(8): 1238-1240 (2017) - [j17]Rhys Heffernan, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou:
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. 33(18): 2842-2849 (2017) - [j16]Peter Brown, Yuedong Yang, Yaoqi Zhou, Wayne J. Pullan:
A heuristic for the time constrained asymmetric linear sum assignment problem. J. Comb. Optim. 33(2): 551-566 (2017) - 2016
- [j15]Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou:
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinform. 32(3): 370-377 (2016) - [j14]Rhys Heffernan, Abdollah Dehzangi, James G. Lyons, Kuldip K. Paliwal, Alok Sharma, Jihua Wang, Abdul Sattar, Yaoqi Zhou, Yuedong Yang:
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinform. 32(6): 843-849 (2016) - [j13]Jianzhao Gao, Yuedong Yang, Yaoqi Zhou:
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. Bioinform. 32(24): 3768-3773 (2016) - [j12]Yuedong Yang, Yaoqi Zhou:
Effective protein conformational sampling based on predicted torsion angles. J. Comput. Chem. 37(11): 976-980 (2016) - [j11]Md. Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou:
sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. J. Comput. Chem. 37(12): 1119-1124 (2016) - [j10]Ghazaleh Taherzadeh, Yuedong Yang, Tuo Zhang, Alan Wee-Chung Liew, Yaoqi Zhou:
Sequence-based prediction of protein-peptide binding sites using support vector machine. J. Comput. Chem. 37(13): 1223-1229 (2016) - [j9]Yuedong Yang, Jian Zhan, Yaoqi Zhou:
SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. J. Comput. Chem. 37(18): 1734-1739 (2016) - [j8]Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang:
Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. J. Chem. Inf. Model. 56(10): 2123 (2016) - 2015
- [j7]Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou:
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. 31(10): 1599-1606 (2015) - 2014
- [j6]James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip K. Paliwal, Abdul Sattar, Yaoqi Zhou, Yuedong Yang:
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J. Comput. Chem. 35(28): 2040-2046 (2014) - [j5]Huiying Zhao, Yuedong Yang, Mark von Itzstein, Yaoqi Zhou:
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. J. Comput. Chem. 35(30): 2177-2183 (2014) - 2012
- [j4]Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, Yaoqi Zhou:
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. 33(3): 259-267 (2012) - 2011
- [j3]Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou:
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. 27(15): 2076-2082 (2011) - 2010
- [j2]Huiying Zhao, Yuedong Yang, Yaoqi Zhou:
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinform. 26(15): 1857-1863 (2010)
2000 – 2009
- 2008
- [c2]Yuedong Yang, Qinping Zhao, Aimin Hao, Weihe Wu:
DTW-Curve for Classification of Logically Similar Motions. GRAPP 2008: 281-289 - [c1]Yuedong Yang, Aimin Hao, Qinping Zhao:
View-invariant action recognition using interest points. Multimedia Information Retrieval 2008: 305-312 - 2006
- [j1]Yuedong Yang, Haiyan Liu:
Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. J. Comput. Chem. 27(13): 1593-1602 (2006)
Coauthor Index
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from 
.
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-11-15 19:32 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
