Extracting Features from Protein Sequences Using Chinese Segmentation Techniques for Subcellular Localization. - Yang Yang 030; Bao-Liang Lu (CIBCB, 2005)

Structure Pruning Strategies for Min-Max Modular Network. - Yang Yang 030; Bao-Liang Lu (ISNN (1), 2005)

A Comparative Study on Feature Extraction from Protein Sequences for Subcellular Localization Prediction. - Wen-Yun Yang; Bao-Liang Lu; Yang Yang 030 (CIBCB, 2006)

Prediction of Protein Subcellular Multi-locations with a Min-Max Modular Support Vector Machine. - Yang Yang 030; Bao-Liang Lu (ISNN (2), 2006)

Incorporating Domain Knowledge into a Min-Max Modular Support Vector Machine for Protein Subcellular Localization. - Yang Yang 030; Bao-Liang Lu (ICONIP (2), 2007)

Classification of Protein Sequences Based on Word Segmentation Methods. - Yang Yang 030; Bao-Liang Lu; Wen-Yun Yang (APBC, 2008)

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana. - Dandan Song; Yang Yang 030; Bin Yu; Binglian Zheng; Zhidong Deng; Bao-Liang Lu; Xuemei Chen; Tao Jiang 001 (BMC Bioinform., 2009)

Computational prediction of type III secreted proteins from gram-negative bacteria. - Yang Yang 030; Jiayuan Zhao; Robyn L. Morgan; Wenbo Ma; Tao Jiang 001 (BMC Bioinform., 2010)

Protein Subcellular Multi-Localization Prediction Using a Min-Max Modular Support Vector Machine. - Yang Yang 030; Bao-Liang Lu (Int. J. Neural Syst., 2010)

A comparative study on sequence feature extraction for type III secreted effector prediction. - Yang Yang 030 (FSKD, 2011)

Feature Reduction Using a Topic Model for the Prediction of Type III Secreted Effectors. - Sihui Qi; Yang Yang 030; Anjun Song (ICONIP (1), 2011)

Identification of Novel Type III Effectors Using Latent Dirichlet Allocation. - Yang Yang 030 (Comput. Math. Methods Medicine, 2012)

Dynamic Regulatory Network Reconstruction for Alzheimer's Disease Based on Matrix Decomposition Techniques. - Wei Kong; Xiaoyang Mou; Xing Zhi; Xing Zhang; Yang Yang 030 (Comput. Math. Methods Medicine, 2014)

Integrating Gene Expression and Protein Interaction Data for Signaling Pathway Prediction of Alzheimer's Disease. - Wei Kong; Jingmao Zhang; Xiaoyang Mou; Yang Yang 030 (Comput. Math. Methods Medicine, 2014)

A new feature selection method for computational prediction of type III secreted effectors. - Yang Yang 030; Sihui Qi (Int. J. Data Min. Bioinform., 2014)

Deceptive Opinion Spam Detection Using Deep Level Linguistic Features. - Changge Chen; Hai Zhao 001; Yang Yang 030 (NLPCC, 2015)

Feature selection based on functional group structure for microRNA expression data analysis. - Yang Yang 030; Tianyu Cao; Wei Kong (BIBM, 2016)

A New Subcellular Localization Predictor for Human Proteins Considering the Correlation of Annotation Features and Protein Multi-localization. - Hang Zhou; Yang Yang 030; Hong-Bin Shen (CCPR (2), 2016)

Missing value imputation for microRNA expression data by using a GO-based similarity measure. - Yang Yang 030; Zhuangdi Xu; Dandan Song (BMC Bioinform., 2016)

Deep Learning-Based Classification of Protein Subcellular Localization from Immunohistochemistry Images. - Jin-Xian Hu; Ying-Ying Xu; Yang Yang 030; Hong-Bin Shen (ACPR, 2017)

Detection of Curvilinear Centerline by Using Hough Voting. - Hanjin Zhang; Yang Yang 030; Hong-Bin Shen (ACPR, 2017)

Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features. - Hang Zhou; Yang Yang 030; Hong-Bin Shen (Bioinform., 2017)

A clustering-based approach for efficient identification of microRNA combinatorial biomarkers. - Yang Yang 030; Ning Huang; Luning Hao; Wei Kong (BMC Genom., 2017)

MiRFFS: a functional group-based feature selection method for the identification of microRNA biomarkers. - Yang Yang 030; Yiqun Xiao; Tianyu Cao; Wei Kong (Int. J. Data Min. Bioinform., 2017)

IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment. - Guowei Ji; Yang Yang 030; Hong-Bin Shen (BIBM, 2018)

HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks. - Tiange Li; Yang Yang 030; Hong-Bin Shen (BIBM, 2018)

Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model. - Yiqun Xiao; Jiaxun Cai; Yang Yang 030; Hai Zhao 001; Hong-Bin Shen (ICDM, 2018)

Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model. - Kaiming Zhang; Yiqun Xiao; Xiaoyong Pan; Yang Yang 030 (ICIMCS, 2018)

Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences. - Xiaofeng Fu; Yiqun Xiao; Yang Yang 030 (ISBRA, 2018)

Line Junction Detection Without Prior-Delineation of Curvilinear Structure in Biomedical Images. - Hanjin Zhang; Yang Yang 030; Hong-Bin Shen (IEEE Access, 2018)

Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method. - Hanjin Zhang; Yang Yang 030; Hong-Bin Shen (IEEE Access, 2018)

The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. - Zhen Cao; Xiaoyong Pan; Yang Yang 030; Yan Huang; Hong-Bin Shen (Bioinform., 2018)

MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association. - Yang Yang 030; Xiaofeng Fu; Wenhao Qu; Yiqun Xiao; Hong-Bin Shen (Bioinform., 2018)

AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model. - Yang Yang 030; Mingyu Zhou; Qingwei Fang; Hong-Bin Shen (Bioinform., 2019)

Judging Chemical Reaction Practicality From Positive Sample only Learning. - Shu Jiang; Zhuosheng Zhang 001; Hai Zhao 001; Jiangtong Li; Yang Yang 030; Bao-Liang Lu; Ning Xia (CoRR, 2019)

Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric. - Shuo Yin; Biao Zhang; Yang Yang 030; Yan Huang; Hong-Bin Shen (J. Chem. Inf. Model., 2019)

Predicting gene regulatory interactions based on spatial gene expression data and deep learning. - Yang Yang 030; Qingwei Fang; Hong-Bin Shen (PLoS Comput. Biol., 2019)

WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning. - Xiaofeng Fu; Yang Yang 030 (Quant. Biol., 2019)

NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM Image Processing. - Rui Hu; Jia-Ming Cai; Wangjie Zheng; Yang Yang 030; Hong-Bin Shen (BIBM, 2020)

Tripfly: Predicting Gene-gene Interaction of Drosophila Eye Development Using Triplet Loss. - Zhenhuan Liu; Jiafeng Chen; Yang Yang 030 (BIBM, 2020)

An Unsupervised Iterative Model for Single-Particle Cryo-EM Image Denoising Based on Siamese Neural Network. - Wangjie Zheng; Yang Yang 030 (BIBM, 2020)

ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. - Wei Long; Yang Yang 030; Hong-Bin Shen (Bioinform., 2020)

Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. - Di Wang; Ling Geng; Yu-Jun Zhao; Yang Yang 030; Yan Huang; Yang Zhang 040; Hong-Bin Shen (Bioinform., 2020)

AAG: Self-Supervised Representation Learning by Auxiliary Augmentation with GNT-Xent Loss. - Yanlun Tu; Jianxing Feng; Yang Yang 030 (CoRR, 2020)

SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment. - Rui Xie; Yu-Xuan Chen; Jia-Ming Cai; Yang Yang 030; Hong-Bin Shen (J. Chem. Inf. Model., 2020)

Predicting RNA-RBP Interactions by Using a Pseudo-Siamese Network. - Fu Wang; Liangliang Yuan; Yang Yang 030 (BIBM, 2021)

Prediction of Protein Subcellular Localization from Microscopic Images via Few-Shot Learning. - Francesco Arcamone; Yanlun Tu; Yang Yang 030 (ISBRA, 2021)

When SMILES Smiles, Practicality Judgment and Yield Prediction of Chemical Reaction via Deep Chemical Language Processing. - Shu Jiang; Zhuosheng Zhang 001; Hai Zhao 001; Jiangtong Li; Yang Yang 030; Bao-Liang Lu; Ning Xia (IEEE Access, 2021)

Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network. - Hehe Wu; Xiaoyong Pan; Yang Yang 030; Hong-Bin Shen (Briefings Bioinform., 2021)

CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks. - Jianwei Hong; Ruitian Gao; Yang Yang 030 (Bioinform., 2021)

Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features. - Yu-Xuan Chen; Rui Xie; Yang Yang 030; Lin He; Dagan Feng 001; Hong-Bin Shen (J. Chem. Inf. Model., 2021)

FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks. - Wei Long; Tiange Li; Yang Yang 030; Hong-Bin Shen (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

KenDTI: An Ensemble Model for Predicting Drug-Target Interaction by Integrating Multi-Source Information. - Zhimiao Yu; Jiarui Lu; Yuan Jin; Yang Yang 030 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Learning Time-Series Images of Niacin Skin-Flushing Test for the Diagnosis of Schizophrenia and Affective Disorder. - Yuyang Huang; Shiwen Dong; Dandan Wang; Chunling Wan; Yang Yang 030 (BIBM, 2022)

Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression. - Yuzhang Xie; Guoshuai Niu; Qian Da; Wentao Dai; Yang Yang 030 (BIBM, 2022)

FUSSNet: Fusing Two Sources of Uncertainty for Semi-supervised Medical Image Segmentation. - Jinyi Xiang; Peng Qiu; Yang Yang 030 (MICCAI (8), 2022)

SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images. - Yanlun Tu; Houchao Lei; Hong-Bin Shen; Yang Yang 030 (Briefings Bioinform., 2022)

Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning. - Lujing Zheng; Zhenhuan Liu; Yang Yang 030; Hong-Bin Shen (Bioinform., 2022)

ProtPlat: an efficient pre-training platform for protein classification based on FastText. - Yuan Jin; Yang Yang 030 (BMC Bioinform., 2022)

ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities. - Zewei Ji; Runhan Shi; Jiarui Lu; Fang Li; Yang Yang 030 (J. Chem. Inf. Model., 2022)

GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images. - Jin-Xian Hu; Yang Yang 030; Ying-Ying Xu; Hong-Bin Shen (Bioinform., 2022)

Isoform Function Prediction Based on Heterogeneous Graph Attention Networks. - Kuo Guo; Yifan Li; Hao Chen; Hong-Bin Shen; Yang Yang 030 (BIBM, 2023)

Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models. - Zebei Han; Gufeng Yu; Yang Yang 030 (BIBM, 2023)

UPCoL: Uncertainty-Informed Prototype Consistency Learning for Semi-supervised Medical Image Segmentation. - Wenjing Lu; Jiahao Lei; Peng Qiu; Rui Sheng; Jinhua Zhou; Xinwu Lu; Yang Yang 030 (MICCAI (4), 2023)

HAMIL: Hierarchical aggregation-based multi-instance learning for microscopy image classification. - Yang Yang 030; Yanlun Tu; Houchao Lei; Wei Long (Pattern Recognit., 2023)

MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images. - Yuyang Huang; Gufeng Yu; Yang Yang 030 (PLoS Comput. Biol., 2023)

Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method. - Tian Xia; Zhiwei He 002; Tong Ren; Yibo Miao; Zhuosheng Zhang 001; Yang Yang 030; Rui Wang 015 (ACL (Findings), 2024)

RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs. - Yichong Li; Xiaojian Liu; Fan Cheng; Xiaoyong Pan; Yang Yang 030 (BIBM, 2024)

UP-SAM: Uncertainty-Informed Adaptation of Segment Anything Model for Semi-Supervised Medical Image Segmentation. - Wenjing Lu; Yi Hong; Yang Yang 030 (BIBM, 2024)

An Efficient Prototype-Based Clustering Approach for Edge Pruning in Graph Neural Networks to Battle Over-Smoothing. - Yuyang Huang; Wenjing Lu; Yang Yang 030 (IJCAI, 2024)

Improving diagnosis and outcome prediction of gastric cancer via multimodal learning using whole slide pathological images and gene expression. - Yuzhang Xie; Qingqing Sang; Qian Da; Guoshuai Niu; Shijie Deng; Haoran Feng; Yunqin Chen; Yuan-Yuan Li; Bing-Ya Liu; Yang Yang 030; Wentao Dai (Artif. Intell. Medicine, 2024)

Decoding protein binding landscape on circular RNAs with base-resolution transformer models. - Hehe Wu; Xiaojian Liu; Yi Fang; Yang Yang 030; Yan Huang; Xiaoyong Pan; Hong-Bin Shen (Comput. Biol. Medicine, 2024)

BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction. - Yifei Yang; Runhan Shi; Zuchao Li; Shu Jiang; Bao-Liang Lu; Yang Yang 030; Hai Zhao 001 (CoRR, 2024)

Prediction of chemical reaction yields with large-scale multi-view pre-training. - Runhan Shi; Gufeng Yu; Xiaohong Huo; Yang Yang 030 (J. Cheminformatics, 2024)

DRAG: design RNAs as hierarchical graphs with reinforcement learning. - Yichong Li; Xiaoyong Pan; Hongbin Shen; Yang Yang 030 (Briefings Bioinform., 2025)

Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor. - Gufeng Yu; Xi Wang; Yichong Luo; Guanlin Li; Rui Ding; Runhan Shi; Xiaohong Huo; Yang Yang 030 (J. Chem. Inf. Model., 2025)

Clc-db: an open-source online database of chiral ligands and catalysts. - Gufeng Yu; Kaiwen Yu; Xi Wang; Chenxi Zhang; Yicong Luo; Xiaohong Huo; Yang Yang 030 (J. Cheminformatics, 2025)