Yang Yang

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 48

Top Topics

Gene Expression

Electron Microscopy

Top Venues

J. Chem. Inf. Model.

Publications

Yuzhang Xie, Qingqing Sang, Qian Da, Guoshuai Niu, Shijie Deng, Haoran Feng, Yunqin Chen, Yuan-Yuan Li, Bing-Ya Liu, Yang Yang, Wentao Dai
Improving diagnosis and outcome prediction of gastric cancer via multimodal learning using whole slide pathological images and gene expression. Artif. Intell. Medicine 152 (2024)
Tian Xia, Zhiwei He, Tong Ren, Yibo Miao, Zhuosheng Zhang, Yang Yang, Rui Wang
Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method. ACL (Findings) (2024)
Hehe Wu, Xiaojian Liu, Yi Fang, Yang Yang, Yan Huang, Xiaoyong Pan, Hong-Bin Shen
Decoding protein binding landscape on circular RNAs with base-resolution transformer models. Comput. Biol. Medicine 171 (2024)
Tian Xia, Zhiwei He, Tong Ren, Yibo Miao, Zhuosheng Zhang, Yang Yang, Rui Wang
Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method. CoRR (2024)
Runhan Shi, Gufeng Yu, Xiaohong Huo, Yang Yang
Prediction of chemical reaction yields with large-scale multi-view pre-training. J. Cheminformatics 16 (1) (2024)
Yang Yang, Yanlun Tu, Houchao Lei, Wei Long
HAMIL: Hierarchical aggregation-based multi-instance learning for microscopy image classification. Pattern Recognit. 136 (2023)
Yuyang Huang, Gufeng Yu, Yang Yang
MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images. PLoS Comput. Biol. 19 (11) (2023)
Zewei Ji, Runhan Shi, Jiarui Lu, Fang Li, Yang Yang
ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities. J. Chem. Inf. Model. 62 (22) (2022)
Jin-Xian Hu, Yang Yang, Ying-Ying Xu, Hong-Bin Shen
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images. Bioinform. 38 (21) (2022)
Yanlun Tu, Houchao Lei, Hong-Bin Shen, Yang Yang
SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images. Briefings Bioinform. 23 (2) (2022)
Lujing Zheng, Zhenhuan Liu, Yang Yang, Hong-Bin Shen
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning. Bioinform. 38 (3) (2022)
Yu-Xuan Chen, Rui Xie, Yang Yang, Lin He, Dagan Feng, Hong-Bin Shen
Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features. J. Chem. Inf. Model. 61 (9) (2021)
Yanlun Tu, Houchao Lei, Wei Long, Yang Yang
HAMIL: Hierarchical Aggregation-Based Multi-Instance Learning for Microscopy Image Classification. CoRR (2021)
Jianwei Hong, Ruitian Gao, Yang Yang
CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks. Bioinform. 37 (20) (2021)
Wei Long, Tiange Li, Yang Yang, Hong-Bin Shen
FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Shu Jiang, Zhuosheng Zhang, Hai Zhao, Jiangtong Li, Yang Yang, Bao-Liang Lu, Ning Xia
When SMILES Smiles, Practicality Judgment and Yield Prediction of Chemical Reaction via Deep Chemical Language Processing. IEEE Access 9 (2021)
Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-Bin Shen
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network. Briefings Bioinform. 22 (6) (2021)
Francesco Arcamone, Yanlun Tu, Yang Yang
Prediction of Protein Subcellular Localization from Microscopic Images via Few-Shot Learning. ISBRA (2021)
Zhimiao Yu, Jiarui Lu, Yuan Jin, Yang Yang
KenDTI: An Ensemble Model for Predicting Drug-Target Interaction by Integrating Multi-Source Information. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Yanlun Tu, Jianxing Feng, Yang Yang
AAG: Self-Supervised Representation Learning by Auxiliary Augmentation with GNT-Xent Loss. CoRR (2020)
Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinform. 36 (2) (2020)
Zhenhuan Liu, Jiafeng Chen, Yang Yang
Tripfly: Predicting Gene-gene Interaction of Drosophila Eye Development Using Triplet Loss. BIBM (2020)
Wangjie Zheng, Yang Yang
An Unsupervised Iterative Model for Single-Particle Cryo-EM Image Denoising Based on Siamese Neural Network. BIBM (2020)
Rui Hu, Jia-Ming Cai, Wangjie Zheng, Yang Yang, Hong-Bin Shen
NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM Image Processing. BIBM (2020)
Rui Xie, Yu-Xuan Chen, Jia-Ming Cai, Yang Yang, Hong-Bin Shen
SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment. J. Chem. Inf. Model. 60 (5) (2020)
Wei Long, Yang Yang, Hong-Bin Shen
ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. Bioinform. 36 (7) (2020)
Yang Yang, Qingwei Fang, Hong-Bin Shen
Predicting gene regulatory interactions based on spatial gene expression data and deep learning. PLoS Comput. Biol. 15 (9) (2019)
Shuo Yin, Biao Zhang, Yang Yang, Yan Huang, Hong-Bin Shen
Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric. J. Chem. Inf. Model. 59 (4) (2019)
Shu Jiang, Zhuosheng Zhang, Hai Zhao, Jiangtong Li, Yang Yang, Bao-Liang Lu, Ning Xia
Judging Chemical Reaction Practicality From Positive Sample only Learning. CoRR (2019)
Xiaofeng Fu, Yang Yang
WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning. Quant. Biol. 7 (4) (2019)
Yang Yang, Mingyu Zhou, Qingwei Fang, Hong-Bin Shen
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model. Bioinform. 35 (16) (2019)
Hanjin Zhang, Yang Yang, Hong-Bin Shen
Line Junction Detection Without Prior-Delineation of Curvilinear Structure in Biomedical Images. IEEE Access 6 (2018)
Yiqun Xiao, Jiaxun Cai, Yang Yang, Hai Zhao, Hong-Bin Shen
Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model. ICDM (2018)
Tiange Li, Yang Yang, Hong-Bin Shen
HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks. BIBM (2018)
Hanjin Zhang, Yang Yang, Hong-Bin Shen
Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method. IEEE Access 6 (2018)
Kaiming Zhang, Yiqun Xiao, Xiaoyong Pan, Yang Yang
Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model. ICIMCS (2018)
Zhen Cao, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinform. 34 (13) (2018)
Yang Yang, Xiaofeng Fu, Wenhao Qu, Yiqun Xiao, Hong-Bin Shen
MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association. Bioinform. 34 (20) (2018)
Xiaofeng Fu, Yiqun Xiao, Yang Yang
Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences. ISBRA (2018)
Guowei Ji, Yang Yang, Hong-Bin Shen
IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment. BIBM (2018)
Hang Zhou, Yang Yang, Hong-Bin Shen
Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features. Bioinform. 33 (6) (2017)
Jin-Xian Hu, Ying-Ying Xu, Yang Yang, Hong-Bin Shen
Deep Learning-Based Classification of Protein Subcellular Localization from Immunohistochemistry Images. ACPR (2017)
Yang Yang, Ning Huang, Luning Hao, Wei Kong
A clustering-based approach for efficient identification of microRNA combinatorial biomarkers. BMC Genom. 18 (S2) (2017)
Hanjin Zhang, Yang Yang, Hong-Bin Shen
Detection of Curvilinear Centerline by Using Hough Voting. ACPR (2017)
Yang Yang, Yiqun Xiao, Tianyu Cao, Wei Kong
MiRFFS: a functional group-based feature selection method for the identification of microRNA biomarkers. Int. J. Data Min. Bioinform. 18 (1) (2017)
Hang Zhou, Yang Yang, Hong-Bin Shen
A New Subcellular Localization Predictor for Human Proteins Considering the Correlation of Annotation Features and Protein Multi-localization. CCPR (2) (2016)
Yang Yang, Zhuangdi Xu, Dandan Song
Missing value imputation for microRNA expression data by using a GO-based similarity measure. BMC Bioinform. 17 (S-1) (2016)
Yang Yang, Tianyu Cao, Wei Kong
Feature selection based on functional group structure for microRNA expression data analysis. BIBM (2016)
Changge Chen, Hai Zhao, Yang Yang
Deceptive Opinion Spam Detection Using Deep Level Linguistic Features. NLPCC (2015)
Yang Yang, Sihui Qi
A new feature selection method for computational prediction of type III secreted effectors. Int. J. Data Min. Bioinform. 10 (4) (2014)
Wei Kong, Jingmao Zhang, Xiaoyang Mou, Yang Yang
Integrating Gene Expression and Protein Interaction Data for Signaling Pathway Prediction of Alzheimer's Disease. Comput. Math. Methods Medicine 2014 (2014)
Wei Kong, Xiaoyang Mou, Xing Zhi, Xing Zhang, Yang Yang
Dynamic Regulatory Network Reconstruction for Alzheimer's Disease Based on Matrix Decomposition Techniques. Comput. Math. Methods Medicine 2014 (2014)
Yang Yang
Identification of Novel Type III Effectors Using Latent Dirichlet Allocation. Comput. Math. Methods Medicine 2012 (2012)
Sihui Qi, Yang Yang, Anjun Song
Feature Reduction Using a Topic Model for the Prediction of Type III Secreted Effectors. ICONIP (1) (2011)
Yang Yang
A comparative study on sequence feature extraction for type III secreted effector prediction. FSKD (2011)
Yang Yang, Bao-Liang Lu
Protein Subcellular Multi-Localization Prediction Using a Min-Max Modular Support Vector Machine. Int. J. Neural Syst. 20 (1) (2010)
Yang Yang, Jiayuan Zhao, Robyn L. Morgan, Wenbo Ma, Tao Jiang
Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinform. 11 (S-1) (2010)
Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang
. BMC Bioinform. 10 (S-1) (2009)
Yang Yang, Bao-Liang Lu, Wen-Yun Yang
Classification of Protein Sequences Based on Word Segmentation Methods. APBC (2008)
Yang Yang, Bao-Liang Lu
Incorporating Domain Knowledge into a Min-Max Modular Support Vector Machine for Protein Subcellular Localization. ICONIP (2) (2007)
Yang Yang, Bao-Liang Lu
Prediction of Protein Subcellular Multi-locations with a Min-Max Modular Support Vector Machine. ISNN (2) (2006)
Wen-Yun Yang, Bao-Liang Lu, Yang Yang
A Comparative Study on Feature Extraction from Protein Sequences for Subcellular Localization Prediction. CIBCB (2006)
Yang Yang, Bao-Liang Lu
Structure Pruning Strategies for Min-Max Modular Network. ISNN (1) (2005)
Yang Yang, Bao-Liang Lu
Extracting Features from Protein Sequences Using Chinese Segmentation Techniques for Subcellular Localization. CIBCB (2005)