Shanfeng Zhu

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 39

Top Topics

Protein Function Prediction

Biomedical Literature

Genomic Sequences

Top Venues

Briefings Bioinform.

Publications

Junyi Bian, Weiqi Zhai, Xiaodi Huang, Jiaxuan Zheng, Shanfeng Zhu
VANER: Leveraging Large Language Model for Versatile and Adaptive Biomedical Named Entity Recognition. CoRR (2024)
Junyi Bian, Jiaxuan Zheng, Yuyi Zhang, Shanfeng Zhu
Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition. CoRR (2023)
Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. Bioinform. 39 (1) (2023)
Wei Qu, Ronghui You, Hiroshi Mamitsuka, Shanfeng Zhu
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction. Bioinform. 39 (9) (2023)
Weiqi Zhai, Xiaodi Huang, Nan Shen, Shanfeng Zhu
Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities. Briefings Bioinform. 24 (4) (2023)
Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations. Genom. Proteom. Bioinform. 21 (2) (2023)
Zenong Niu, Wenxin Huang, Shanfeng Zhu
Online Identification of Mechanical Systems Using the Simplified Output Error Model. IEEE Trans. Ind. Electron. 70 (7) (2023)
Junyi Bian, Rongze Jiang, Weiqi Zhai, Tianyang Huang, Hong Zhou, Shanfeng Zhu
Biomedical Entity Recognition by Detection and Matching. CoRR (2023)
Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations. Bioinform. 38 (3) (2022)
Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang
META-DDIE: predicting drug-drug interaction events with few-shot learning. Briefings Bioinform. 23 (1) (2022)
Junyi Bian, Xiaodi Huang, Hong Zhou, Shanfeng Zhu
GoSum: Extractive Summarization of Long Documents by Reinforcement Learning and Graph Organized discourse state. CoRR (2022)
Zhirui Liao, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules. BIBM (2021)
Suyang Dai, Yuxia Ding, Zihan Zhang, Wenxuan Zuo, Xiaodi Huang, Shanfeng Zhu
GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Junyi Bian, Li Huang, Xiaodi Huang, Hong Zhou, Shanfeng Zhu
GrantRel: Grant Information Extraction via Joint Entity and Relation Extraction. ACL/IJCNLP (Findings) (2021)
Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings Bioinform. 22 (1) (2021)
Wen Jiang, Wenxin Huang, Xiaogang Lin, Yong Zhao, Shanfeng Zhu
Analysis of Rotor Poles and Armature Winding Configurations Combinations of Wound Field Flux Switching Machines. IEEE Trans. Ind. Electron. 68 (9) (2021)
Xu Wu, Wenxin Huang, Xiaogang Lin, Wen Jiang, Yong Zhao, Shanfeng Zhu
Direct Torque Control for Induction Motors Based on Minimum Voltage Vector Error. IEEE Trans. Ind. Electron. 68 (5) (2021)
Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. Bioinform. 37 (Supplement) (2021)
Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Ronghui You, Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu
BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text. Bioinform. 37 (5) (2021)
Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
HPOFiller: identifying missing protein-phenotype associations by graph convolutional network. Bioinform. 37 (19) (2021)
Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings Bioinform. 21 (3) (2020)
Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank. Bioinform. 36 (14) (2020)
Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
FullMeSH: improving large-scale MeSH indexing with full text. Bioinform. 36 (5) (2020)
Jiawei Zhang, Yanchun Zhang, Shanfeng Zhu, Xiaowei Xu
Constrained Multi-scale Dense Connections for Accurate Biomedical Image Segmentation. BIBM (2020)
Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu
SolidBin: improving metagenome binning with semi-supervised normalized cut. Bioinform. 35 (21) (2019)
Ronghui You, Zihan Zhang, Ziye Wang, Suyang Dai, Hiroshi Mamitsuka, Shanfeng Zhu
AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification. NeurIPS (2019)
Ronghui You, Zihan Zhang, Suyang Dai, Shanfeng Zhu
HAXMLNet: Hierarchical Attention Network for Extreme Multi-Label Text Classification. CoRR (2019)
Zhirui Liao, Ronghui You, Xiaodi Huang, Xiaojun Yao, Tao Huang, Shanfeng Zhu
DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information. BIBM (2019)
Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. Bioinform. 34 (14) (2018)
Suyang Dai, Zihan Zhang, Wenxuan Zuo, Xiaodi Huang, Shanfeng Zhu
GrantExtractor: A Winning System for Extracting Grant Support Information from Biomedical Literature. BIBM (2018)
Junning Gao, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
AiProAnnotator: Low-rank Approximation with network side information for high-performance, large-scale human Protein abnormality Annotator. BIBM (2018)
Ronghui You, Suyang Dai, Zihan Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
AttentionXML: Extreme Multi-Label Text Classification with Multi-Label Attention Based Recurrent Neural Networks. CoRR (2018)
Chunyang Ruan, Ye Wang, Yanchun Zhang, Jiangang Ma, Huijuan Chen, Uwe Aickelin, Shanfeng Zhu, Ting Zhang
THCluster: Herb supplements categorization for precision traditional Chinese medicine. BIBM (2017)
Ronghui You, Shanfeng Zhu
DeepText2Go: Improving large-scale protein function prediction with deep semantic text representation. BIBM (2017)
Junning Gao, Makoto Yamada, Samuel Kaski, Hiroshi Mamitsuka, Shanfeng Zhu
A Robust Convex Formulation for Ensemble Clustering. IJCAI (2016)
Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinform. 32 (12) (2016)
Shengwen Peng, Ronghui You, Hongning Wang, Chengxiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu
DeepMeSH: deep semantic representation for improving large-scale MeSH indexing. Bioinform. 32 (12) (2016)
Shengwen Peng, Ronghui You, Zhikai Xie, Beichen Wang, Yanchun Zhang, Shanfeng Zhu
The Fudan Participation in the 2015 BioASQ Challenge: Large-scale Biomedical Semantic Indexing and Question Answering. CLEF (Working Notes) (2015)
Jing Zhou, Shanfeng Zhu, Xiaodi Huang, Yanchun Zhang
Enhancing Time Series Clustering by Incorporating Multiple Distance Measures with Semi-Supervised Learning. J. Comput. Sci. Technol. 30 (4) (2015)
Ronghui You, Shengwen Peng, Shanfeng Zhu, Yuanjie Zhou
FDUMedSearch at TREC 2015 Clinical Decision Support Track. TREC (2015)
Ke Liu, Shengwen Peng, Junqiu Wu, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu
MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence. Bioinform. 31 (12) (2015)
Xiaodong Zheng, Shanfeng Zhu, Junning Gao, Hiroshi Mamitsuka
Instance-Wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters. IJCAI (2015)
Jing Zhou, Yuxuan Shui, Shengwen Peng, Xuhui Li, Hiroshi Mamitsuka, Shanfeng Zhu
MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents. J. Bioinform. Comput. Biol. 13 (6) (2015)
Xuhui Li, Zhengqi Liu, Mengchi Liu, Xiaoying Wu, Shanfeng Zhu
Towards a Pattern-Based Query Language for Document Databases. DASFAA Workshops (2015)
Xiaodong Li, Haoran Xie, Yangqiu Song, Shanfeng Zhu, Qing Li, Fu Lee Wang
Does Summarization Help Stock Prediction? A News Impact Analysis. IEEE Intell. Syst. 30 (3) (2015)
Xuhui Li, Mengchi Liu, Xiaoying Wu, Shanfeng Zhu
Design Issues of JPQ: a Pattern-based Query Language for Document Databases. CoRR (2015)
Beichen Wang, Xiaodong Chen, Hiroshi Mamitsuka, Shanfeng Zhu
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Xuhui Li, Mengchi Liu, Shanfeng Zhu, Arif Ghafoor
XTQ: A Declarative Functional XML Query Language. CoRR (2014)
Xiaodong Li, Xiaotie Deng, Shanfeng Zhu, Feng Wang, Haoran Xie
An intelligent market making strategy in algorithmic trading. Frontiers Comput. Sci. 8 (4) (2014)
Xiaodong Li, Xiaodi Huang, Xiaotie Deng, Shanfeng Zhu
Enhancing quantitative intra-day stock return prediction by integrating both market news and stock prices information. Neurocomputing 142 (2014)
Ke Liu, Junqiu Wu, Shengwen Peng, Chengxiang Zhai, Shanfeng Zhu
The Fudan-UIUC Participation in the BioASQ Challenge Task 2a: The Antinomyra system. CLEF (Working Notes) (2014)
Hao Ding, Ichigaku Takigawa, Hiroshi Mamitsuka, Shanfeng Zhu
Similarity-based machine learning methods for predicting drug-target interactions: a brief review. Briefings Bioinform. 15 (5) (2014)
Jun Gu, Wei Feng, Jia Zeng, Hiroshi Mamitsuka, Shanfeng Zhu
Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints. IEEE Trans. Cybern. 43 (4) (2013)
Xiaodong Zheng, Hao Ding, Hiroshi Mamitsuka, Shanfeng Zhu
Collaborative matrix factorization with multiple similarities for predicting drug-target interactions. KDD (2013)
Xuhui Li, Shanfeng Zhu, Mengchi Liu, Ming Zhong
Presenting XML Schema Mapping with Conjunctive-Disjunctive Views. WAIM (2013)
Xiaodong Li, Shanfeng Zhu, Haoran Xie, Qing Li
Document Summarization via Self-Present Sentence Relevance Model. DASFAA (2) (2013)
Lianming Zhang, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. Briefings Bioinform. 13 (3) (2012)
Gang Shu, Xiaodi Huang, Shanfeng Zhu
A consensus method for prioritising drug-associated target proteins. Int. J. Data Min. Bioinform. 6 (2) (2012)
Xiaodong Li, Chao Wang, Jiawei Dong, Feng Wang, Xiaotie Deng, Shanfeng Zhu
Improving Stock Market Prediction by Integrating Both Market News and Stock Prices. DEXA (2) (2011)
Shuigeng Zhou, Caiyan Jia, Fei Wang, Qiwen Dong, Shanfeng Zhu, Ruqian Lu
A conversation with Professor Ruqian Lu et al. SIGKDD Explor. 13 (2) (2011)
Xiaodi Huang, Xiaodong Zheng, Wei Yuan, Fei Wang, Shanfeng Zhu
Enhanced clustering of biomedical documents using ensemble non-negative matrix factorization. Inf. Sci. 181 (11) (2011)
Juan Liu, Lian Wang, Shanfeng Zhu
SVR-PAIRWISE method to predict MHC-II binding peptides. Int. J. Bioinform. Res. Appl. 6 (1) (2010)
Xihao Hu, Wenjian Zhou, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu
MetaMHC: a meta approach to predict peptides binding to MHC molecules. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew, Hong Yan
Multiconstrained gene clustering based on generalized projections. BMC Bioinform. 11 (2010)
Qizhi Fang, Han Xiao, Shanfeng Zhu
Rank Aggregation in Web Meta-search Engine - (Extended Abstract). FAW (2010)
Jia Zeng, Shanfeng Zhu, Hong Yan
Towards accurate human promoter recognition: a review of currently used sequence features and classification methods. Briefings Bioinform. 10 (5) (2009)
Shanfeng Zhu, Jia Zeng, Hiroshi Mamitsuka
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinform. 25 (15) (2009)
Shanfeng Zhu, Ichigaku Takigawa, Jia Zeng, Hiroshi Mamitsuka
Field independent probabilistic model for clustering multi-field documents. Inf. Process. Manag. 45 (5) (2009)
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model. BMC Syst. Biol. 1 (S-1) (2007)
Shanfeng Zhu, Ichigaku Takigawa, Shuqin Zhang, Hiroshi Mamitsuka
A Probabilistic Model for Clustering Text Documents with Multiple Fields. ECIR (2007)
Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinform. 22 (13) (2006)
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. ECCB/JBI (2005)
Shanfeng Zhu, Christopher C. Yang, Wai Lam
CatRelate: A New Hierarchical Document Category Integration Algorithm by Learning Category Relationships. ICADL (2004)
Shanfeng Zhu, Qizhi Fang, Weimin Zheng
Social Choice For Data Fusion. Int. J. Inf. Technol. Decis. Mak. 3 (4) (2004)
Francis Y. L. Chin, Xiaotie Deng, Qizhi Fang, Shanfeng Zhu
Approximate and dynamic rank aggregation. Theor. Comput. Sci. 325 (3) (2004)
Shanfeng Zhu, Qizhi Fang, Xiaotie Deng, Weimin Zheng
Metasearch via Voting. IDEAL (2003)
Xiaotie Deng, Qizhi Fang, Shanfeng Zhu
Approximate Rank Aggregation (Preliminary Version). COCOON (2003)
Qizhi Fang, Shanfeng Zhu, Mao-cheng Cai, Xiaotie Deng
On computational complexity of membership test in flow games and linear production games. Int. J. Game Theory 31 (1) (2002)
Qizhi Fang, Shanfeng Zhu
Linear and Integer Programming Techniques for Cooperative Games. Int. J. Found. Comput. Sci. 13 (5) (2002)
Kang Chen, Weimin Zheng, Xiaotie Deng, Haodi Feng, Shanfeng Zhu
Text Distinguishers Used in an Interactive Meta Search Engine. WAIM (2002)
Shanfeng Zhu, Xiaotie Deng, Kang Chen, Weimin Zheng
Using Online Relevance Feedback to Build Effective Personalized Metasearch Engine. WISE (1) (2001)
Xiaotie Deng, Horace Ho-Shing Ip, Ken C. K. Law, Jianping Li, Weimin Zheng, Shanfeng Zhu
Parallel Models and Job Characterization for System Scheduling. International Conference on Computational Science (2) (2001)
Qizhi Fang, Shanfeng Zhu, Mao-cheng Cai, Xiaotie Deng
Membership for Core of LP Games and Other Games. COCOON (2001)
Kang Chen, Weimin Zheng, Hung Chim, Xiaotie Deng, Haodi Feng, Shanfeng Zhu
On-Line Selection Of Distinguishing Elements For Focused Information Retrieval. ICME (2001)