Shanfeng Zhu

Orcid: 0000-0002-6067-5312

According to our database1, Shanfeng Zhu authored at least 85 papers between 2001 and 2023.

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Bibliography

2023
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction.
Bioinform., September, 2023

Online Identification of Mechanical Systems Using the Simplified Output Error Model.
IEEE Trans. Ind. Electron., July, 2023

Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities.
Briefings Bioinform., July, 2023

NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations.
Genom. Proteom. Bioinform., April, 2023

Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer.
Bioinform., January, 2023

Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition.
CoRR, 2023

Biomedical Entity Recognition by Detection and Matching.
CoRR, 2023

2022
GoSum: Extractive Summarization of Long Documents by Reinforcement Learning and Graph Organized discourse state.
CoRR, 2022

HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations.
Bioinform., 2022

META-DDIE: predicting drug-drug interaction events with few-shot learning.
Briefings Bioinform., 2022

2021
Direct Torque Control for Induction Motors Based on Minimum Voltage Vector Error.
IEEE Trans. Ind. Electron., 2021

Analysis of Rotor Poles and Armature Winding Configurations Combinations of Wound Field Flux Switching Machines.
IEEE Trans. Ind. Electron., 2021

GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information.
Nucleic Acids Res., 2021

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction.
Bioinform., 2021

BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text.
Bioinform., 2021

HPOFiller: identifying missing protein-phenotype associations by graph convolutional network.
Bioinform., 2021

Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.
Briefings Bioinform., 2021

Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

GrantRel: Grant Information Extraction via Joint Entity and Relation Extraction.
Proceedings of the Findings of the Association for Computational Linguistics: ACL/IJCNLP 2021, 2021

2020
HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank.
Bioinform., 2020

FullMeSH: improving large-scale MeSH indexing with full text.
Bioinform., 2020

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.
Briefings Bioinform., 2020

Constrained Multi-scale Dense Connections for Accurate Biomedical Image Segmentation.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019
NetGO: improving large-scale protein function prediction with massive network information.
Nucleic Acids Res., 2019

HAXMLNet: Hierarchical Attention Network for Extreme Multi-Label Text Classification.
CoRR, 2019

SolidBin: improving metagenome binning with semi-supervised normalized cut.
Bioinform., 2019

AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification.
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018
AttentionXML: Extreme Multi-Label Text Classification with Multi-Label Attention Based Recurrent Neural Networks.
CoRR, 2018

GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank.
Bioinform., 2018

AiProAnnotator: Low-rank Approximation with network side information for high-performance, large-scale human Protein abnormality Annotator.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

GrantExtractor: A Winning System for Extracting Grant Support Information from Biomedical Literature.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017
DeepText2Go: Improving large-scale protein function prediction with deep semantic text representation.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

THCluster: Herb supplements categorization for precision traditional Chinese medicine.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.
Bioinform., 2016

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing.
Bioinform., 2016

A Robust Convex Formulation for Ensemble Clustering.
Proceedings of the Twenty-Fifth International Joint Conference on Artificial Intelligence, 2016

2015
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Enhancing Time Series Clustering by Incorporating Multiple Distance Measures with Semi-Supervised Learning.
J. Comput. Sci. Technol., 2015

MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.
J. Bioinform. Comput. Biol., 2015

Does Summarization Help Stock Prediction? A News Impact Analysis.
IEEE Intell. Syst., 2015

Design Issues of JPQ: a Pattern-based Query Language for Document Databases.
CoRR, 2015

MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence.
Bioinform., 2015

FDUMedSearch at TREC 2015 Clinical Decision Support Track.
Proceedings of The Twenty-Fourth Text REtrieval Conference, 2015

Instance-Wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters.
Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence, 2015

Towards a Pattern-Based Query Language for Document Databases.
Proceedings of the Database Systems for Advanced Applications, 2015

The Fudan Participation in the 2015 BioASQ Challenge: Large-scale Biomedical Semantic Indexing and Question Answering.
Proceedings of the Working Notes of CLEF 2015, 2015

2014
Enhancing quantitative intra-day stock return prediction by integrating both market news and stock prices information.
Neurocomputing, 2014

An intelligent market making strategy in algorithmic trading.
Frontiers Comput. Sci., 2014

XTQ: A Declarative Functional XML Query Language.
CoRR, 2014

Similarity-based machine learning methods for predicting drug-target interactions: a brief review.
Briefings Bioinform., 2014

The Fudan-UIUC Participation in the BioASQ Challenge Task 2a: The Antinomyra system.
Proceedings of the Working Notes for CLEF 2014 Conference, 2014

2013
Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints.
IEEE Trans. Cybern., 2013

Presenting XML Schema Mapping with Conjunctive-Disjunctive Views.
Proceedings of the Web-Age Information Management - 14th International Conference, 2013

Collaborative matrix factorization with multiple similarities for predicting drug-target interactions.
Proceedings of the 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2013

Document Summarization via Self-Present Sentence Relevance Model.
Proceedings of the Database Systems for Advanced Applications, 2013

2012
A consensus method for prioritising drug-associated target proteins.
Int. J. Data Min. Bioinform., 2012

Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools.
Briefings Bioinform., 2012

2011
A conversation with Professor Ruqian Lu et al.
SIGKDD Explor., 2011

Enhanced clustering of biomedical documents using ensemble non-negative matrix factorization.
Inf. Sci., 2011

Improving Stock Market Prediction by Integrating Both Market News and Stock Prices.
Proceedings of the Database and Expert Systems Applications, 2011

2010
MetaMHC: a meta approach to predict peptides binding to MHC molecules.
Nucleic Acids Res., 2010

SVR-PAIRWISE method to predict MHC-II binding peptides.
Int. J. Bioinform. Res. Appl., 2010

Multiconstrained gene clustering based on generalized projections.
BMC Bioinform., 2010

Top-<i>d</i> Rank Aggregation in Web Meta-search Engine - (Extended Abstract).
Proceedings of the Frontiers in Algorithmics, 4th International Workshop, 2010

2009
Field independent probabilistic model for clustering multi-field documents.
Inf. Process. Manag., 2009

Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity.
Bioinform., 2009

Towards accurate human promoter recognition: a review of currently used sequence features and classification methods.
Briefings Bioinform., 2009

2007
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model.
BMC Syst. Biol., 2007

A Probabilistic Model for Clustering Text Documents with Multiple Fields.
Proceedings of the Advances in Information Retrieval, 2007

2006
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules.
Bioinform., 2006

2005
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004
Approximate and dynamic rank aggregation.
Theor. Comput. Sci., 2004

Social Choice For Data Fusion.
Int. J. Inf. Technol. Decis. Mak., 2004

CatRelate: A New Hierarchical Document Category Integration Algorithm by Learning Category Relationships.
Proceedings of the Digital Libraries: International Collaboration and Cross-Fertilization, 2004

2003
Metasearch via Voting.
Proceedings of the Intelligent Data Engineering and Automated Learning, 2003

Approximate Rank Aggregation (Preliminary Version).
Proceedings of the Computing and Combinatorics, 9th Annual International Conference, 2003

2002
On computational complexity of membership test in flow games and linear production games.
Int. J. Game Theory, 2002

Linear and Integer Programming Techniques for Cooperative Games.
Int. J. Found. Comput. Sci., 2002

Text Distinguishers Used in an Interactive Meta Search Engine.
Proceedings of the Advances in Web-Age Information Management, 2002

2001
Using Online Relevance Feedback to Build Effective Personalized Metasearch Engine.
Proceedings of the 2nd International Conference on Web Information Systems Engineering, 2001

On-Line Selection Of Distinguishing Elements For Focused Information Retrieval.
Proceedings of the 2001 IEEE International Conference on Multimedia and Expo, 2001

Parallel Models and Job Characterization for System Scheduling.
Proceedings of the Computational Science - ICCS 2001, 2001

Membership for Core of LP Games and Other Games.
Proceedings of the Computing and Combinatorics, 7th Annual International Conference, 2001


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