Yang Yang

80 papers A* 2B 1C 2Journal 47Unranked 28
YearRankTypeTitle / Venue / Authors
2026 J jnl
Align then clip: Refining graph for face clustering.
Neural Networks
Yanlun Tu, Guoliang Cao, Jialiang Shen, Yuyang Huang, Min Wang, Wentao Liu, Chen Qian, Yang Yang
2025 J jnl
Clc-db: an open-source online database of chiral ligands and catalysts.
J. Cheminformatics
Gufeng Yu, Kaiwen Yu, Xi Wang, Chenxi Zhang, Yicong Luo, Xiaohong Huo, Yang Yang
2025 J jnl
DRAG: design RNAs as hierarchical graphs with reinforcement learning.
Briefings Bioinform.
Yichong Li, Xiaoyong Pan, Hongbin Shen, Yang Yang
2025 J jnl
Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor.
J. Chem. Inf. Model.
Gufeng Yu, Xi Wang, Yichong Luo, Guanlin Li, Rui Ding, Runhan Shi, Xiaohong Huo, Yang Yang
2024 A* conf
An Efficient Prototype-Based Clustering Approach for Edge Pruning in Graph Neural Networks to Battle Over-Smoothing.
IJCAI
Yuyang Huang, Wenjing Lu, Yang Yang
2024 J jnl
BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction.
CoRR
Yifei Yang, Runhan Shi, Zuchao Li, Shu Jiang, Bao-Liang Lu, Yang Yang, Hai Zhao
2024 J jnl
Decoding protein binding landscape on circular RNAs with base-resolution transformer models.
Comput. Biol. Medicine
Hehe Wu, Xiaojian Liu, Yi Fang, Yang Yang, Yan Huang, Xiaoyong Pan, Hong-Bin Shen
2024 J jnl
Improving diagnosis and outcome prediction of gastric cancer via multimodal learning using whole slide pathological images and gene expression.
Artif. Intell. Medicine
Yuzhang Xie, Qingqing Sang, Qian Da, Guoshuai Niu, Shijie Deng, Haoran Feng, Yunqin Chen, Yuan-Yuan Li, Bing-Ya Liu, Yang Yang, Wentao Dai
2024 — conf
Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method.
ACL (Findings)
Tian Xia, Zhiwei He, Tong Ren, Yibo Miao, Zhuosheng Zhang, Yang Yang, Rui Wang
2024 J jnl
Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method.
CoRR
Tian Xia, Zhiwei He, Tong Ren, Yibo Miao, Zhuosheng Zhang, Yang Yang, Rui Wang
2024 J jnl
Prediction of chemical reaction yields with large-scale multi-view pre-training.
J. Cheminformatics
Runhan Shi, Gufeng Yu, Xiaohong Huo, Yang Yang
2024 — conf
RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs.
BIBM
Yichong Li, Xiaojian Liu, Fan Cheng, Xiaoyong Pan, Yang Yang
2024 — conf
UP-SAM: Uncertainty-Informed Adaptation of Segment Anything Model for Semi-Supervised Medical Image Segmentation.
BIBM
Wenjing Lu, Yi Hong, Yang Yang
2023 — conf
Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models.
BIBM
Zebei Han, Gufeng Yu, Yang Yang
2023 J jnl
HAMIL: Hierarchical aggregation-based multi-instance learning for microscopy image classification.
Pattern Recognit.
Yang Yang, Yanlun Tu, Houchao Lei, Wei Long
2023 — conf
Isoform Function Prediction Based on Heterogeneous Graph Attention Networks.
BIBM
Kuo Guo, Yifan Li, Hao Chen, Hong-Bin Shen, Yang Yang
2023 J jnl
MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images.
PLoS Comput. Biol.
Yuyang Huang, Gufeng Yu, Yang Yang
2023 — conf
UPCoL: Uncertainty-Informed Prototype Consistency Learning for Semi-supervised Medical Image Segmentation.
MICCAI (4)
Wenjing Lu, Jiahao Lei, Peng Qiu, Rui Sheng, Jinhua Zhou, Xinwu Lu, Yang Yang
2022 J jnl
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning.
Bioinform.
Lujing Zheng, Zhenhuan Liu, Yang Yang, Hong-Bin Shen
2022 — conf
FUSSNet: Fusing Two Sources of Uncertainty for Semi-supervised Medical Image Segmentation.
MICCAI (8)
Jinyi Xiang, Peng Qiu, Yang Yang
2022 J jnl
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images.
Bioinform.
Jin-Xian Hu, Yang Yang, Ying-Ying Xu, Hong-Bin Shen
2022 — conf
Learning Time-Series Images of Niacin Skin-Flushing Test for the Diagnosis of Schizophrenia and Affective Disorder.
BIBM
Yuyang Huang, Shiwen Dong, Dandan Wang, Chunling Wan, Yang Yang
2022 J jnl
ProtPlat: an efficient pre-training platform for protein classification based on FastText.
BMC Bioinform.
Yuan Jin, Yang Yang
2022 J jnl
ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities.
J. Chem. Inf. Model.
Zewei Ji, Runhan Shi, Jiarui Lu, Fang Li, Yang Yang
2022 J jnl
SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images.
Briefings Bioinform.
Yanlun Tu, Houchao Lei, Hong-Bin Shen, Yang Yang
2022 — conf
Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression.
BIBM
Yuzhang Xie, Guoshuai Niu, Qian Da, Wentao Dai, Yang Yang
2021 J jnl
CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks.
Bioinform.
Jianwei Hong, Ruitian Gao, Yang Yang
2021 J jnl
Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features.
J. Chem. Inf. Model.
Yu-Xuan Chen, Rui Xie, Yang Yang, Lin He, Dagan Feng, Hong-Bin Shen
2021 J jnl
FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Wei Long, Tiange Li, Yang Yang, Hong-Bin Shen
2021 J jnl
HAMIL: Hierarchical Aggregation-Based Multi-Instance Learning for Microscopy Image Classification.
CoRR
Yanlun Tu, Houchao Lei, Wei Long, Yang Yang
2021 J jnl
KenDTI: An Ensemble Model for Predicting Drug-Target Interaction by Integrating Multi-Source Information.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhimiao Yu, Jiarui Lu, Yuan Jin, Yang Yang
2021 — conf
Predicting RNA-RBP Interactions by Using a Pseudo-Siamese Network.
BIBM
Fu Wang, Liangliang Yuan, Yang Yang
2021 — conf
Prediction of Protein Subcellular Localization from Microscopic Images via Few-Shot Learning.
ISBRA
Francesco Arcamone, Yanlun Tu, Yang Yang
2021 J jnl
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.
Briefings Bioinform.
Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-Bin Shen
2021 J jnl
When SMILES Smiles, Practicality Judgment and Yield Prediction of Chemical Reaction via Deep Chemical Language Processing.
IEEE Access
Shu Jiang, Zhuosheng Zhang, Hai Zhao, Jiangtong Li, Yang Yang, Bao-Liang Lu, Ning Xia
2020 J jnl
AAG: Self-Supervised Representation Learning by Auxiliary Augmentation with GNT-Xent Loss.
CoRR
Yanlun Tu, Jianxing Feng, Yang Yang
2020 — conf
An Unsupervised Iterative Model for Single-Particle Cryo-EM Image Denoising Based on Siamese Neural Network.
BIBM
Wangjie Zheng, Yang Yang
2020 J jnl
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.
Bioinform.
Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen
2020 J jnl
ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images.
Bioinform.
Wei Long, Yang Yang, Hong-Bin Shen
2020 — conf
NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM Image Processing.
BIBM
Rui Hu, Jia-Ming Cai, Wangjie Zheng, Yang Yang, Hong-Bin Shen
2020 J jnl
SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment.
J. Chem. Inf. Model.
Rui Xie, Yu-Xuan Chen, Jia-Ming Cai, Yang Yang, Hong-Bin Shen
2020 — conf
Tripfly: Predicting Gene-gene Interaction of Drosophila Eye Development Using Triplet Loss.
BIBM
Zhenhuan Liu, Jiafeng Chen, Yang Yang
2019 J jnl
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model.
Bioinform.
Yang Yang, Mingyu Zhou, Qingwei Fang, Hong-Bin Shen
2019 J jnl
Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric.
J. Chem. Inf. Model.
Shuo Yin, Biao Zhang, Yang Yang, Yan Huang, Hong-Bin Shen
2019 J jnl
Judging Chemical Reaction Practicality From Positive Sample only Learning.
CoRR
Shu Jiang, Zhuosheng Zhang, Hai Zhao, Jiangtong Li, Yang Yang, Bao-Liang Lu, Ning Xia
2019 J jnl
Predicting gene regulatory interactions based on spatial gene expression data and deep learning.
PLoS Comput. Biol.
Yang Yang, Qingwei Fang, Hong-Bin Shen
2019 J jnl
WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning.
Quant. Biol.
Xiaofeng Fu, Yang Yang
2018 J jnl
Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method.
IEEE Access
Hanjin Zhang, Yang Yang, Hong-Bin Shen
2018 — conf
HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks.
BIBM
Tiange Li, Yang Yang, Hong-Bin Shen
2018 — conf
IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment.
BIBM
Guowei Ji, Yang Yang, Hong-Bin Shen
2018 J jnl
Line Junction Detection Without Prior-Delineation of Curvilinear Structure in Biomedical Images.
IEEE Access
Hanjin Zhang, Yang Yang, Hong-Bin Shen
2018 J jnl
MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association.
Bioinform.
Yang Yang, Xiaofeng Fu, Wenhao Qu, Yiqun Xiao, Hong-Bin Shen
2018 A* conf
Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model.
ICDM
Yiqun Xiao, Jiaxun Cai, Yang Yang, Hai Zhao, Hong-Bin Shen
2018 — conf
Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model.
ICIMCS
Kaiming Zhang, Yiqun Xiao, Xiaoyong Pan, Yang Yang
2018 — conf
Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences.
ISBRA
Xiaofeng Fu, Yiqun Xiao, Yang Yang
2018 J jnl
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier.
Bioinform.
Zhen Cao, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
2017 J jnl
A clustering-based approach for efficient identification of microRNA combinatorial biomarkers.
BMC Genom.
Yang Yang, Ning Huang, Luning Hao, Wei Kong
2017 — conf
Deep Learning-Based Classification of Protein Subcellular Localization from Immunohistochemistry Images.
ACPR
Jin-Xian Hu, Ying-Ying Xu, Yang Yang, Hong-Bin Shen
2017 — conf
Detection of Curvilinear Centerline by Using Hough Voting.
ACPR
Hanjin Zhang, Yang Yang, Hong-Bin Shen
2017 J jnl
Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features.
Bioinform.
Hang Zhou, Yang Yang, Hong-Bin Shen
2017 J jnl
MiRFFS: a functional group-based feature selection method for the identification of microRNA biomarkers.
Int. J. Data Min. Bioinform.
Yang Yang, Yiqun Xiao, Tianyu Cao, Wei Kong
2016 — conf
A New Subcellular Localization Predictor for Human Proteins Considering the Correlation of Annotation Features and Protein Multi-localization.
CCPR (2)
Hang Zhou, Yang Yang, Hong-Bin Shen
2016 — conf
Feature selection based on functional group structure for microRNA expression data analysis.
BIBM
Yang Yang, Tianyu Cao, Wei Kong
2016 J jnl
Missing value imputation for microRNA expression data by using a GO-based similarity measure.
BMC Bioinform.
Yang Yang, Zhuangdi Xu, Dandan Song
2015 — conf
Deceptive Opinion Spam Detection Using Deep Level Linguistic Features.
NLPCC
Changge Chen, Hai Zhao, Yang Yang
2014 J jnl
A new feature selection method for computational prediction of type III secreted effectors.
Int. J. Data Min. Bioinform.
Yang Yang, Sihui Qi
2014 J jnl
Dynamic Regulatory Network Reconstruction for Alzheimer's Disease Based on Matrix Decomposition Techniques.
Comput. Math. Methods Medicine
Wei Kong, Xiaoyang Mou, Xing Zhi, Xing Zhang, Yang Yang
2014 J jnl
Integrating Gene Expression and Protein Interaction Data for Signaling Pathway Prediction of Alzheimer's Disease.
Comput. Math. Methods Medicine
Wei Kong, Jingmao Zhang, Xiaoyang Mou, Yang Yang
2012 J jnl
Identification of Novel Type III Effectors Using Latent Dirichlet Allocation.
Comput. Math. Methods Medicine
Yang Yang
2011 — conf
A comparative study on sequence feature extraction for type III secreted effector prediction.
FSKD
Yang Yang
2011 — conf
Feature Reduction Using a Topic Model for the Prediction of Type III Secreted Effectors.
ICONIP (1)
Sihui Qi, Yang Yang, Anjun Song
2010 J jnl
Computational prediction of type III secreted proteins from gram-negative bacteria.
BMC Bioinform.
Yang Yang, Jiayuan Zhao, Robyn L. Morgan, Wenbo Ma, Tao Jiang
2010 J jnl
Protein Subcellular Multi-Localization Prediction Using a Min-Max Modular Support Vector Machine.
Int. J. Neural Syst.
Yang Yang, Bao-Liang Lu
2009 J jnl
Computational prediction of novel non-coding RNAs in
BMC Bioinform.
Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang
2008 B conf
Classification of Protein Sequences Based on Word Segmentation Methods.
APBC
Yang Yang, Bao-Liang Lu, Wen-Yun Yang
2007 — conf
Incorporating Domain Knowledge into a Min-Max Modular Support Vector Machine for Protein Subcellular Localization.
ICONIP (2)
Yang Yang, Bao-Liang Lu
2006 C conf
A Comparative Study on Feature Extraction from Protein Sequences for Subcellular Localization Prediction.
CIBCB
Wen-Yun Yang, Bao-Liang Lu, Yang Yang
2006 — conf
Prediction of Protein Subcellular Multi-locations with a Min-Max Modular Support Vector Machine.
ISNN (2)
Yang Yang, Bao-Liang Lu
2005 C conf
Extracting Features from Protein Sequences Using Chinese Segmentation Techniques for Subcellular Localization.
CIBCB
Yang Yang, Bao-Liang Lu
2005 — conf
Structure Pruning Strategies for Min-Max Modular Network.
ISNN (1)
Yang Yang, Bao-Liang Lu