Shanfeng Zhu

103 papers A* 4A 3B 1C 1Misc 4Journal 68Unranked 22
YearRankTypeTitle / Venue / Authors
2026 J jnl
Investigation of synonym expansion and self-alignment pretraining for enhancing Human Phenotype Ontology concept recognition.
Artif. Intell. Medicine
Weiqi Zhai, Rongze Jiang, Xiaodi Huang, Junyi Bian, Shanfeng Zhu
2026 J jnl
Vaner2: towards more general biomedical named entity recognition using multi-task large language model encoders.
Health Inf. Sci. Syst.
Yuxuan Liu, Junyi Bian, Weiqi Zhai, Jiaxuan Zheng, Yuyi Zhang, Shanfeng Zhu
2025 J jnl
Constrained multi-scale dense connections for biomedical image segmentation.
Pattern Recognit.
Jiawei Zhang, Yanchun Zhang, Hailong Qiu, Tianchen Wang, Xiaomeng Li, Shanfeng Zhu, Meiping Huang, Jian Zhuang, Yiyu Shi, Xiaowei Xu
2025 J jnl
ContraDTI: Improved drug-target interaction prediction via multi-view contrastive learning.
Artif. Intell. Medicine
Zhirui Liao, Lei Xie, Shanfeng Zhu
2025 B conf
DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins.
RECOMB
Shaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu
2025 J jnl
Enhanced active disturbance rejection speed controller for permanent magnet synchronous motors using virtual friction feedback technique.
Int. J. Circuit Theory Appl.
Dingfeng Dong, Wenxin Huang, Shanfeng Zhu, Feifei Bu
2025 J jnl
GOAnnotator: accurate protein function annotation using automatically retrieved literature.
Bioinform.
Huiying Yan, Hancheng Liu, Shaojun Wang, Shanfeng Zhu
2025 — conf
LYX_DMIIP_FDU At BioASQ 2025: Utilizing BERT Embeddings For Biomedical Text Mining.
CLEF (Working Notes)
Yuxuan Liu, Shanfeng Zhu
2025 J jnl
MultiFusion2HPO: A Multimodal Deep Learning Approach for Enhancing Human Protein-Phenotype Association Prediction.
IEEE Trans. Comput. Biol. Bioinform.
Weiqi Zhai, Yongjun Deng, Xiaodi Huang, Shaojun Wang, Shanfeng Zhu
2025 J jnl
PubLabeler: Enhancing Automatic Classification of Publications in UniProtKB Using Protein Textual Description and PubMedBERT.
IEEE J. Biomed. Health Informatics
Shaojun Wang, Junyi Bian, Xiaodi Huang, Hong Zhou, Shanfeng Zhu
2024 — conf
DMNER: Biomedical Named Entity Recognition by Detection and Matching.
BIBM
Junyi Bian, Rongze Jiang, Weiqi Zhai, Tianyang Huang, Xiaodi Huang, Hong Zhou, Shanfeng Zhu
2024 J jnl
Design and Analysis of Observer-Based Full-Closed Loop Position Control for Servomechanism With Elasticity.
IEEE Trans. Ind. Electron.
Zenong Niu, Wenxin Huang, Shanfeng Zhu, Feifei Bu
2024 J jnl
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation.
Bioinform.
Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2024 J jnl
GoSum: extractive summarization of long documents by reinforcement learning and graph-organized discourse state.
Knowl. Inf. Syst.
Junyi Bian, Xiaodi Huang, Hong Zhou, Tianyang Huang, Shanfeng Zhu
2024 — conf
One-shot Biomedical Named Entity Recognition via Knowledge-Inspired Large Language Model.
BCB
Junyi Bian, Jiaxuan Zheng, Yuyi Zhang, Hong Zhou, Shanfeng Zhu
2024 A conf
VANER: Leveraging Large Language Model for Versatile and Adaptive Biomedical Named Entity Recognition.
ECAI
Junyi Bian, Weiqi Zhai, Xiaodi Huang, Jiaxuan Zheng, Shanfeng Zhu
2024 J jnl
VANER: Leveraging Large Language Model for Versatile and Adaptive Biomedical Named Entity Recognition.
CoRR
Junyi Bian, Weiqi Zhai, Xiaodi Huang, Jiaxuan Zheng, Shanfeng Zhu
2023 J jnl
Biomedical Entity Recognition by Detection and Matching.
CoRR
Junyi Bian, Rongze Jiang, Weiqi Zhai, Tianyang Huang, Hong Zhou, Shanfeng Zhu
2023 J jnl
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction.
Bioinform.
Wei Qu, Ronghui You, Hiroshi Mamitsuka, Shanfeng Zhu
2023 J jnl
Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition.
CoRR
Junyi Bian, Jiaxuan Zheng, Yuyi Zhang, Shanfeng Zhu
2023 J jnl
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations.
Genom. Proteom. Bioinform.
Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu
2023 J jnl
Online Identification of Mechanical Systems Using the Simplified Output Error Model.
IEEE Trans. Ind. Electron.
Zenong Niu, Wenxin Huang, Shanfeng Zhu
2023 J jnl
Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities.
Briefings Bioinform.
Weiqi Zhai, Xiaodi Huang, Nan Shen, Shanfeng Zhu
2023 J jnl
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer.
Bioinform.
Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu
2022 J jnl
DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction.
Bioinform.
Ronghui You, Wei Qu, Hiroshi Mamitsuka, Shanfeng Zhu
2022 J jnl
GoSum: Extractive Summarization of Long Documents by Reinforcement Learning and Graph Organized discourse state.
CoRR
Junyi Bian, Xiaodi Huang, Hong Zhou, Shanfeng Zhu
2022 J jnl
HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations.
Bioinform.
Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2022 J jnl
META-DDIE: predicting drug-drug interaction events with few-shot learning.
Briefings Bioinform.
Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang
2021 J jnl
Analysis of Rotor Poles and Armature Winding Configurations Combinations of Wound Field Flux Switching Machines.
IEEE Trans. Ind. Electron.
Wen Jiang, Wenxin Huang, Xiaogang Lin, Yong Zhao, Shanfeng Zhu
2021 J jnl
BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text.
Bioinform.
Ronghui You, Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2021 J jnl
Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.
Briefings Bioinform.
Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
2021 J jnl
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction.
Bioinform.
Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
2021 J jnl
Direct Torque Control for Induction Motors Based on Minimum Voltage Vector Error.
IEEE Trans. Ind. Electron.
Xu Wu, Wenxin Huang, Xiaogang Lin, Wen Jiang, Yong Zhao, Shanfeng Zhu
2021 — conf
Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules.
BIBM
Zhirui Liao, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2021 J jnl
GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF.
IEEE ACM Trans. Comput. Biol. Bioinform.
Suyang Dai, Yuxia Ding, Zihan Zhang, Wenxuan Zuo, Xiaodi Huang, Shanfeng Zhu
2021 — conf
GrantRel: Grant Information Extraction via Joint Entity and Relation Extraction.
ACL/IJCNLP (Findings)
Junyi Bian, Li Huang, Xiaodi Huang, Hong Zhou, Shanfeng Zhu
2021 J jnl
HPOFiller: identifying missing protein-phenotype associations by graph convolutional network.
Bioinform.
Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2021 J jnl
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information.
Nucleic Acids Res.
Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu
2020 J jnl
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.
Briefings Bioinform.
Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
2020 — conf
Constrained Multi-scale Dense Connections for Accurate Biomedical Image Segmentation.
BIBM
Jiawei Zhang, Yanchun Zhang, Shanfeng Zhu, Xiaowei Xu
2020 J jnl
FullMeSH: improving large-scale MeSH indexing with full text.
Bioinform.
Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2020 J jnl
HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank.
Bioinform.
Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2019 A* conf
AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification.
NeurIPS
Ronghui You, Zihan Zhang, Ziye Wang, Suyang Dai, Hiroshi Mamitsuka, Shanfeng Zhu
2019 — conf
DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information.
BIBM
Zhirui Liao, Ronghui You, Xiaodi Huang, Xiaojun Yao, Tao Huang, Shanfeng Zhu
2019 J jnl
HAXMLNet: Hierarchical Attention Network for Extreme Multi-Label Text Classification.
CoRR
Ronghui You, Zihan Zhang, Suyang Dai, Shanfeng Zhu
2019 J jnl
NetGO: improving large-scale protein function prediction with massive network information.
Nucleic Acids Res.
Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2019 J jnl
SolidBin: improving metagenome binning with semi-supervised normalized cut.
Bioinform.
Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu
2018 — conf
AiProAnnotator: Low-rank Approximation with network side information for high-performance, large-scale human Protein abnormality Annotator.
BIBM
Junning Gao, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
2018 J jnl
AttentionXML: Extreme Multi-Label Text Classification with Multi-Label Attention Based Recurrent Neural Networks.
CoRR
Ronghui You, Suyang Dai, Zihan Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
2018 J jnl
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank.
Bioinform.
Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2018 — conf
GrantExtractor: A Winning System for Extracting Grant Support Information from Biomedical Literature.
BIBM
Suyang Dai, Zihan Zhang, Wenxuan Zuo, Xiaodi Huang, Shanfeng Zhu
2017 — conf
DeepText2Go: Improving large-scale protein function prediction with deep semantic text representation.
BIBM
Ronghui You, Shanfeng Zhu
2017 — conf
THCluster: Herb supplements categorization for precision traditional Chinese medicine.
BIBM
Chunyang Ruan, Ye Wang, Yanchun Zhang, Jiangang Ma, Huijuan Chen, Uwe Aickelin, Shanfeng Zhu, Ting Zhang
2016 A* conf
A Robust Convex Formulation for Ensemble Clustering.
IJCAI
Junning Gao, Makoto Yamada, Samuel Kaski, Hiroshi Mamitsuka, Shanfeng Zhu
2016 J jnl
DeepMeSH: deep semantic representation for improving large-scale MeSH indexing.
Bioinform.
Shengwen Peng, Ronghui You, Hongning Wang, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu
2016 J jnl
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.
Bioinform.
Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
2015 J jnl
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model.
IEEE ACM Trans. Comput. Biol. Bioinform.
Beichen Wang, Xiaodong Chen, Hiroshi Mamitsuka, Shanfeng Zhu
2015 J jnl
Design Issues of JPQ: a Pattern-based Query Language for Document Databases.
CoRR
Xuhui Li, Mengchi Liu, Xiaoying Wu, Shanfeng Zhu
2015 J jnl
Does Summarization Help Stock Prediction? A News Impact Analysis.
IEEE Intell. Syst.
Xiaodong Li, Haoran Xie, Yangqiu Song, Shanfeng Zhu, Qing Li, Fu Lee Wang
2015 J jnl
Enhancing Time Series Clustering by Incorporating Multiple Distance Measures with Semi-Supervised Learning.
J. Comput. Sci. Technol.
Jing Zhou, Shanfeng Zhu, Xiaodi Huang, Yanchun Zhang
2015 — conf
FDUMedSearch at TREC 2015 Clinical Decision Support Track.
TREC
Ronghui You, Shengwen Peng, Shanfeng Zhu, Yuanjie Zhou
2015 A* conf
Instance-Wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters.
IJCAI
Xiaodong Zheng, Shanfeng Zhu, Junning Gao, Hiroshi Mamitsuka
2015 J jnl
MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence.
Bioinform.
Ke Liu, Shengwen Peng, Junqiu Wu, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu
2015 J jnl
MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.
J. Bioinform. Comput. Biol.
Jing Zhou, Yuxuan Shui, Shengwen Peng, Xuhui Li, Hiroshi Mamitsuka, Shanfeng Zhu
2015 — conf
The Fudan Participation in the 2015 BioASQ Challenge: Large-scale Biomedical Semantic Indexing and Question Answering.
CLEF (Working Notes)
Shengwen Peng, Ronghui You, Zhikai Xie, Beichen Wang, Yanchun Zhang, Shanfeng Zhu
2015 — conf
Towards a Pattern-Based Query Language for Document Databases.
DASFAA Workshops
Xuhui Li, Zhengqi Liu, Mengchi Liu, Xiaoying Wu, Shanfeng Zhu
2014 J jnl
An intelligent market making strategy in algorithmic trading.
Frontiers Comput. Sci.
Xiaodong Li, Xiaotie Deng, Shanfeng Zhu, Feng Wang, Haoran Xie
2014 J jnl
Enhancing quantitative intra-day stock return prediction by integrating both market news and stock prices information.
Neurocomputing
Xiaodong Li, Xiaodi Huang, Xiaotie Deng, Shanfeng Zhu
2014 J jnl
Similarity-based machine learning methods for predicting drug-target interactions: a brief review.
Briefings Bioinform.
Hao Ding, Ichigaku Takigawa, Hiroshi Mamitsuka, Shanfeng Zhu
2014 — conf
The Fudan-UIUC Participation in the BioASQ Challenge Task 2a: The Antinomyra system.
CLEF (Working Notes)
Ke Liu, Junqiu Wu, Shengwen Peng, ChengXiang Zhai, Shanfeng Zhu
2014 J jnl
XTQ: A Declarative Functional XML Query Language.
CoRR
Xuhui Li, Mengchi Liu, Shanfeng Zhu, Arif Ghafoor
2013 A* conf
Collaborative matrix factorization with multiple similarities for predicting drug-target interactions.
KDD
Xiaodong Zheng, Hao Ding, Hiroshi Mamitsuka, Shanfeng Zhu
2013 — conf
Document Summarization via Self-Present Sentence Relevance Model.
DASFAA (2)
Xiaodong Li, Shanfeng Zhu, Haoran Xie, Qing Li
2013 J jnl
Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints.
IEEE Trans. Cybern.
Jun Gu, Wei Feng, Jia Zeng, Hiroshi Mamitsuka, Shanfeng Zhu
2013 — conf
Presenting XML Schema Mapping with Conjunctive-Disjunctive Views.
WAIM
Xuhui Li, Shanfeng Zhu, Mengchi Liu, Ming Zhong
2012 J jnl
A consensus method for prioritising drug-associated target proteins.
Int. J. Data Min. Bioinform.
Gang Shu, Xiaodi Huang, Shanfeng Zhu
2012 J jnl
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools.
Briefings Bioinform.
Lianming Zhang, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu
2011 J jnl
A conversation with Professor Ruqian Lu et al.
SIGKDD Explor.
Shuigeng Zhou, Caiyan Jia, Fei Wang, Qiwen Dong, Shanfeng Zhu, Ruqian Lu
2011 J jnl
Enhanced clustering of biomedical documents using ensemble non-negative matrix factorization.
Inf. Sci.
Xiaodi Huang, Xiaodong Zheng, Wei Yuan, Fei Wang, Shanfeng Zhu
2011 — conf
Improving Stock Market Prediction by Integrating Both Market News and Stock Prices.
DEXA (2)
Xiaodong Li, Chao Wang, Jiawei Dong, Feng Wang, Xiaotie Deng, Shanfeng Zhu
2010 J jnl
MetaMHC: a meta approach to predict peptides binding to MHC molecules.
Nucleic Acids Res.
Xihao Hu, Wenjian Zhou, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu
2010 J jnl
Multiconstrained gene clustering based on generalized projections.
BMC Bioinform.
Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew, Hong Yan
2010 J jnl
SVR-PAIRWISE method to predict MHC-II binding peptides.
Int. J. Bioinform. Res. Appl.
Juan Liu, Lian Wang, Shanfeng Zhu
2010 Misc conf
Top-
FAW
Qizhi Fang, Han Xiao, Shanfeng Zhu
2009 J jnl
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity.
Bioinform.
Shanfeng Zhu, Jia Zeng, Hiroshi Mamitsuka
2009 J jnl
Field independent probabilistic model for clustering multi-field documents.
Inf. Process. Manag.
Shanfeng Zhu, Ichigaku Takigawa, Jia Zeng, Hiroshi Mamitsuka
2009 J jnl
Towards accurate human promoter recognition: a review of currently used sequence features and classification methods.
Briefings Bioinform.
Jia Zeng, Shanfeng Zhu, Hong Yan
2007 A conf
A Probabilistic Model for Clustering Text Documents with Multiple Fields.
ECIR
Shanfeng Zhu, Ichigaku Takigawa, Shuqin Zhang, Hiroshi Mamitsuka
2007 J jnl
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model.
BMC Syst. Biol.
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
2006 J jnl
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules.
Bioinform.
Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka
2005 — conf
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature.
ECCB/JBI
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
2004 J jnl
Approximate and dynamic rank aggregation.
Theor. Comput. Sci.
Francis Y. L. Chin, Xiaotie Deng, Qizhi Fang, Shanfeng Zhu
2004 — conf
CatRelate: A New Hierarchical Document Category Integration Algorithm by Learning Category Relationships.
ICADL
Shanfeng Zhu, Christopher C. Yang, Wai Lam
2004 J jnl
Social Choice For Data Fusion.
Int. J. Inf. Technol. Decis. Mak.
Shanfeng Zhu, Qizhi Fang, Weimin Zheng
2003 Misc conf
Approximate Rank Aggregation (Preliminary Version).
COCOON
Xiaotie Deng, Qizhi Fang, Shanfeng Zhu
2003 C conf
Metasearch via Voting.
IDEAL
Shanfeng Zhu, Qizhi Fang, Xiaotie Deng, Weimin Zheng
2002 J jnl
Linear and Integer Programming Techniques for Cooperative Games.
Int. J. Found. Comput. Sci.
Qizhi Fang, Shanfeng Zhu
2002 J jnl
On computational complexity of membership test in flow games and linear production games.
Int. J. Game Theory
Qizhi Fang, Shanfeng Zhu, Mao-cheng Cai, Xiaotie Deng
2002 — conf
Text Distinguishers Used in an Interactive Meta Search Engine.
WAIM
Kang Chen, Weimin Zheng, Xiaotie Deng, Haodi Feng, Shanfeng Zhu
2001 Misc conf
Membership for Core of LP Games and Other Games.
COCOON
Qizhi Fang, Shanfeng Zhu, Mao-cheng Cai, Xiaotie Deng
2001 A conf
On-Line Selection Of Distinguishing Elements For Focused Information Retrieval.
ICME
Kang Chen, Weimin Zheng, Hung Chim, Xiaotie Deng, Haodi Feng, Shanfeng Zhu
2001 Misc conf
Parallel Models and Job Characterization for System Scheduling.
International Conference on Computational Science (2)
Xiaotie Deng, Horace Ho-Shing Ip, Ken C. K. Law, Jianping Li, Weimin Zheng, Shanfeng Zhu
2001 — conf
Using Online Relevance Feedback to Build Effective Personalized Metasearch Engine.
WISE (1)
Shanfeng Zhu, Xiaotie Deng, Kang Chen, Weimin Zheng