Prediction of Protein Subcellular Localizations Using Moment Descriptors and Support Vector Machine. - Jianyu Shi; Shao-Wu Zhang 001; Yan Liang 001; Quan Pan 001 (PRIB, 2006)

Using Decision Templates to Predict Subcellular Localization of Protein. - Jianyu Shi; Shao-Wu Zhang 001; Quan Pan 001; Yanning Zhang 001 (PRIB, 2007)

A new system for computer-aided intraoperative simulation and postoperative facial appearance prediction of orthognathic surgery. - Yanning Zhang 001; Pei-Fang Zhai; Jianyu Shi; Jiangbin Zheng 001; Hong Zhou; Jiang-Bo Li (MMSP, 2008)

Fast SCOP Classification of Structural Class and Fold Using Secondary Structure Mining in Distance Matrix. - Jianyu Shi; Yan-Ning Zhang 001 (PRIB, 2009)

Local Phase Quantization Texture Descriptor for Protein Classification. - Sheryl Brahnam; Loris Nanni; Jian-Yu Shi; Alessandra Lumini (BIOCOMP, 2010)

Predicting drug-target interaction for new drugs using enhanced similarity measures and super-target clustering1. - Jianyu Shi; Siu-Ming Yiu; Yiming Li; Henry C. M. Leung; Francis Y. L. Chin (BIBM, 2014)

On the Complexity of Constrained Sequences Alignment Problems. - Yong Zhang 001; Joseph Wun-Tat Chan; Francis Y. L. Chin; Hing-Fung Ting; Deshi Ye; Feng Zhang 021; Jianyu Shi (FAW, 2014)

SRP: A concise non-parametric similarity-rank-based model for predicting drug-target interactions. - Jianyu Shi; Siu-Ming Yiu (BIBM, 2015)

Predicting Drug-Target Interactions Between New Drugs and New Targets via Pairwise K-nearest Neighbor and Automatic Similarity Selection. - Jianyu Shi; Jia-Xin Li; Hui-Meng Lu; Yong Zhang 001 (IScIDE (2), 2015)

The need of accelerators in analyzing biological networks. - Jian-Yu Shi (BIBM, 2016)

LCM-DS: A novel approach of predicting drug-drug interactions for new drugs via Dempster-Shafer theory of evidence. - Jianyu Shi; Ke Gao; Xue-Qun Shang 001; Siu-Ming Yiu (BIBM, 2016)

Predicting existing targets for new drugs base on strategies for missing interactions. - Jianyu Shi; Jia-Xin Li; Hui-Meng Lu (BMC Bioinform., 2016)

Constrained pairwise and center-star sequences alignment problems. - Yong Zhang 001; Joseph Wun-Tat Chan; Francis Y. L. Chin; Hing-Fung Ting; Deshi Ye; Feng Zhang 021; Jianyu Shi (J. Comb. Optim., 2016)

Predicting Comprehensive Drug-Drug Interactions for New Drugs via Triple Matrix Factorization. - Jianyu Shi; Hua Huang; Jia-Xin Li; Peng Lei; Yan-Ning Zhang 001; Siu-Ming Yiu (IWBBIO (1), 2017)

Predicting combinative drug pairs towards realistic screening via integrating heterogeneous features. - Jian-Yu Shi; Jia-Xin Li; Ke Gao; Peng Lei; Siu-Ming Yiu (BMC Bioinform., 2017)

TMFUF: a triple matrix factorization-based unified framework for predicting comprehensive drug-drug interactions of new drugs. - Jian-Yu Shi; Hua Huang; Jia-Xin Li; Peng Lei; Yan-Ning Zhang 001; Kai Dong; Siu-Ming Yiu (BMC Bioinform., 2018)

BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion. - Jianyu Shi; Hua Huang; Yan-Ning Zhang 001; Jiang-Bo Cao; Siu-Ming Yiu (BMC Bioinform., 2018)

Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization. - Hui Yu 011; Kui-Tao Mao; Jian-Yu Shi; Hua Huang; Zhi Chen; Kai Dong; Siu-Ming Yiu (BMC Syst. Biol., 2018)

Predicting combinative drug pairs via multiple classifier system with positive samples only. - Jian-Yu Shi; Jia-Xin Li; Kui-Tao Mao; Jiang-Bo Cao; Peng Lei; Hui-Meng Lu; Siu-Ming Yiu (Comput. Methods Programs Biomed., 2019)

Detecting drug communities and predicting comprehensive drug-drug interactions via balance regularized semi-nonnegative matrix factorization. - Jian-Yu Shi; Kui-Tao Mao; Hui Yu 011; Siu-Ming Yiu (J. Cheminformatics, 2019)

DPDDI: a deep predictor for drug-drug interactions. - Yue-Hua Feng; Shaowu Zhang 001; Jian-Yu Shi (BMC Bioinform., 2020)

SSI-DDI: substructure-substructure interactions for drug-drug interaction prediction. - Arnold K. Nyamabo; Hui Yu 011; Jian-Yu Shi (Briefings Bioinform., 2021)

Interpretable prediction of drug-cell line response by triple matrix factorization. - Xiao-Ying Yan; Shaowu Zhang 001; Siu-Ming Yiu; Jian-Yu Shi (Quant. Biol., 2021)

Enhanced CT Image Generation by GAN for Improving Thyroid Anatomy Detection. - Jianyu Shi; Xiaohong Liu 007; Guoxing Yang; Guangyu Wang (BIBM, 2022)

AIAT: Adaptive Iteration Adversarial Training for Robust Pulmonary Nodule Detection. - Guoxing Yang; Xiaohong Liu 007; Jianyu Shi; Xianchao Zhang 002; Guangyu Wang (BIBM, 2022)

Directed graph attention networks for predicting asymmetric drug-drug interactions. - Yi-Yang Feng; Hui Yu 011; Yue-Hua Feng; Jian-Yu Shi (Briefings Bioinform., 2022)

Drug-drug interaction prediction with learnable size-adaptive molecular substructures. - Arnold K. Nyamabo; Hui Yu 011; Zun Liu; Jian-Yu Shi (Briefings Bioinform., 2022)

STNN-DDI: a Substructure-aware Tensor Neural Network to predict Drug-Drug Interactions. - Hui Yu 011; Shiyu Zhao; Jianyu Shi (Briefings Bioinform., 2022)

MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction. - Bing-Xue Du; Peng-Cheng Zhao; Bei Zhu; Siu-Ming Yiu; Arnold K. Nyamabo; Hui Yu 011; Jian-Yu Shi (Bioinform., 2022)

Predict multi-type drug-drug interactions in cold start scenario. - Zun Liu; Xing-Nan Wang; Hui Yu 011; Jian-Yu Shi; Wenmin Dong (BMC Bioinform., 2022)

RANEDDI: Relation-aware network embedding for drug-drug interaction prediction. - Hui Yu 011; Wenmin Dong; Jianyu Shi (Inf. Sci., 2022)

GELKcat: An Integration Learning of Substrate Graph with Enzyme Embedding for Kcat prediction. - Bing-Xue Du; Haoyang Yu; Bei Zhu; Yahui Long; Min Wu 008; Jian-Yu Shi (BIBM, 2023)

MTGL-ADMET: A Novel Multi-task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow. - Bing-Xue Du; Yi Xu; Siu-Ming Yiu; Hui Yu 011; Jian-Yu Shi (RECOMB, 2023)

Bamboo Agents: Exploring the Potentiality of Digital Craft by Decoding and Recoding Process. - Peizhong Gao; Tanhao Gao; Yanbin Yang; Zhenyuan Liu; Jianyu Shi; Jin Li (TEI, 2023)

CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties. - Jia-Ning Li; Guang Yang 043; Peng-Cheng Zhao; Xue-Xin Wei; Jian-Yu Shi (Bioinform., 2023)

TCM-GPT: Efficient Pre-training of Large Language Models for Domain Adaptation in Traditional Chinese Medicine. - Guoxing Yang; Jianyu Shi; Zan Wang; Xiaohong Liu 007; Guangyu Wang (CoRR, 2023)

DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction. - Hui Yu 011; KangKang Li; Jianyu Shi (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

A social theory-enhanced graph representation learning framework for multitask prediction of drug-drug interactions. - Yue-Hua Feng; Shao-Wu Zhang 001; Yi-Yang Feng; Qing-Qing Zhang; Ming-Hui Shi; Jian-Yu Shi (Briefings Bioinform., 2023)

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction. - Xuan Lin; Lichang Dai; Yafang Zhou; Zu-Guo Yu; Wen Zhang; Jian-Yu Shi; Dong-Sheng Cao 001; Li Zeng; Haowen Chen; Bosheng Song; Philip S. Yu; Xiangxiang Zeng (Briefings Bioinform., 2023)

Attention-based cross domain graph neural network for prediction of drug-drug interactions. - Hui Yu 011; Kangkang Li; Wenmin Dong; Shuanghong Song; Chen Gao; Jianyu Shi (Briefings Bioinform., 2023)

CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning. - Bing-Xue Du; Yahui Long; Xiaoli Li 001; Min Wu 008; Jian-Yu Shi (Bioinform., 2023)

Few-Shot Drug Synergy Prediction With a Prior-Guided Hypernetwork Architecture. - Qing-Qing Zhang; Shaowu Zhang 001; Yue-Hua Feng; Jian-Yu Shi (IEEE Trans. Pattern Anal. Mach. Intell., 2023)

DVL-CC: A Novel Dual-View Learning Framework for Compound Cocrystal Prediction Boosted by View Consistency and Complementarity. - Haoyang Yu; Bei Zhu; Bing-Xue Du; Xue-Xin Wei; Hui Yu 011; Jian-Yu Shi (BCB, 2024)

Exploring User Evaluations of Visualization of Chart Features of Experimental Data. - Fangning Hao; Xiang Ben; Jintang Zhou; Jianyu Shi; Yajing Kan (IEEM, 2024)

Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation. - Guang Yang 043; Jianing Li; Jinlu Hu; Jian-Yu Shi (Briefings Bioinform., 2024)

Prediction of drug-target binding affinity based on multi-scale feature fusion. - Hui Yu 011; Wen-Xin Xu; Tian Tan 022; Zun Liu; Jian-Yu Shi (Comput. Biol. Medicine, 2024)

GGI-DDI: Identification for key molecular substructures by granule learning to interpret predicted drug-drug interactions. - Hui Yu 011; Jing Wang; Shi-Yu Zhao; Omayo Silver; Zun Liu; JingTao Yao 001; Jian-Yu Shi (Expert Syst. Appl., 2024)

Multi-view clustering with semantic fusion and contrastive learning. - Hui Yu 011; Hui-Xiang Bian; Zi-Ling Chong; Zun Liu; Jian-Yu Shi (Neurocomputing, 2024)

Identifying the reaction centers of molecule based on dual-view representation. - Hui Yu 011; Jing Wang; Chao Song; Jian-Yu Shi (Knowl. Based Syst., 2024)

Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities. - Ning-Ning Wang; Bei Zhu; Xin-Liang Li; Shao Liu; Jian-Yu Shi; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2024)

Small Target Insect Detection Based on Improved YOLOv8n. - Jianyu Shi; Yuan Jia; Gang Zhou; Jiajia Wang; Zhenhong Jia (ICASSP, 2025)

Predicting the Imbalanced Impact of Drugs on Microbial Abundance Using Multi-View Learning and Data Augmentation. - Bei Zhu; Haoyang Yu; Bingxue Du; Hui Yu 011; Jianyu Shi (Big Data Min. Anal., 2025)

A decentralized defense model for covert zero-dynamic attacks in industrial control systems. - Xiangzhen Peng; Chengliang Zheng; Jianyu Shi; Xiaohui Cui (Reliab. Eng. Syst. Saf., 2026)