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2020 – today
- 2025
[j53]Jiawei Zhang
, Yanchun Zhang, Hailong Qiu, Tianchen Wang, Xiaomeng Li, Shanfeng Zhu, Meiping Huang, Jian Zhuang, Yiyu Shi, Xiaowei Xu:
Constrained multi-scale dense connections for biomedical image segmentation. Pattern Recognit. 158: 111031 (2025)- 2024
- [j52]Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu:
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation. Bioinform. 40(Supplement_2): ii53-ii61 (2024) - [j51]Junyi Bian, Xiaodi Huang, Hong Zhou, Tianyang Huang, Shanfeng Zhu:
GoSum: extractive summarization of long documents by reinforcement learning and graph-organized discourse state. Knowl. Inf. Syst. 66(12): 7557-7580 (2024) - [j50]Zenong Niu, Wenxin Huang, Shanfeng Zhu, Feifei Bu:
Design and Analysis of Observer-Based Full-Closed Loop Position Control for Servomechanism With Elasticity. IEEE Trans. Ind. Electron. 71(11): 13742-13753 (2024) - [c32]Junyi Bian, Jiaxuan Zheng, Yuyi Zhang, Hong Zhou, Shanfeng Zhu:
One-shot Biomedical Named Entity Recognition via Knowledge-Inspired Large Language Model. BCB 2024: 26:1-26:10 - [c31]Junyi Bian, Weiqi Zhai, Xiaodi Huang, Jiaxuan Zheng, Shanfeng Zhu:
VANER: Leveraging Large Language Model for Versatile and Adaptive Biomedical Named Entity Recognition. ECAI 2024: 1583-1590 - [i8]Junyi Bian, Weiqi Zhai, Xiaodi Huang, Jiaxuan Zheng, Shanfeng Zhu:
VANER: Leveraging Large Language Model for Versatile and Adaptive Biomedical Named Entity Recognition. CoRR abs/2404.17835 (2024) - 2023
- [j49]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) - [j48]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) - [j47]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) - [j46]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): 349-358 (2023) - [j45]Zenong Niu, Wenxin Huang, Shanfeng Zhu:
Online Identification of Mechanical Systems Using the Simplified Output Error Model. IEEE Trans. Ind. Electron. 70(7): 6653-6662 (2023) - [i7]Junyi Bian, Rongze Jiang, Weiqi Zhai, Tianyang Huang, Hong Zhou, Shanfeng Zhu:
Biomedical Entity Recognition by Detection and Matching. CoRR abs/2306.15736 (2023) - [i6]Junyi Bian, Jiaxuan Zheng, Yuyi Zhang, Shanfeng Zhu:
Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition. CoRR abs/2309.12278 (2023) - 2022
- [j44]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) - [j43]Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu:
HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations. Bioinform. 38(3): 799-808 (2022) - [j42]Ronghui You, Wei Qu, Hiroshi Mamitsuka, Shanfeng Zhu:
DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction. Bioinform. 38(Supplement_1): i220-i228 (2022) - [i5]Junyi Bian, Xiaodi Huang, Hong Zhou, Shanfeng Zhu:
GoSum: Extractive Summarization of Long Documents by Reinforcement Learning and Graph Organized discourse state. CoRR abs/2211.10247 (2022) - 2021
- [j41]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): 611 (2021) - [j40]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): 684-692 (2021) - [j39]Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu:
HPOFiller: identifying missing protein-phenotype associations by graph convolutional network. Bioinform. 37(19): 3328-3336 (2021) - [j38]Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu:
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. Bioinform. 37(Supplement): 262-271 (2021) - [j37]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): 469-475 (2021) - [j36]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): 205-215 (2021) - [j35]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): 3794-3804 (2021) - [j34]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): 7838-7849 (2021) - [c30]Junyi Bian, Li Huang, Xiaodi Huang, Hong Zhou, Shanfeng Zhu:
GrantRel: Grant Information Extraction via Joint Entity and Relation Extraction. ACL/IJCNLP (Findings) 2021: 2674-2685 - [c29]Zhirui Liao, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu:
Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules. BIBM 2021: 340-347 - 2020
- [j33]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): 777-790 (2020) - [j32]Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu:
FullMeSH: improving large-scale MeSH indexing with full text. Bioinform. 36(5): 1533-1541 (2020) - [j31]Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu:
HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank. Bioinform. 36(14): 4180-4188 (2020) - [c28]Jiawei Zhang, Yanchun Zhang, Shanfeng Zhu, Xiaowei Xu:
Constrained Multi-scale Dense Connections for Accurate Biomedical Image Segmentation. BIBM 2020: 877-884
2010 – 2019
- 2019
- [j30]Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu:
SolidBin: improving metagenome binning with semi-supervised normalized cut. Bioinform. 35(21): 4229-4238 (2019) - [j29]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): W379-W387 (2019) - [c27]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: 311-317 - [c26]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: 5812-5822 - [i4]Ronghui You, Zihan Zhang, Suyang Dai, Shanfeng Zhu:
HAXMLNet: Hierarchical Attention Network for Extreme Multi-Label Text Classification. CoRR abs/1904.12578 (2019) - 2018
- [j28]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): 2465-2473 (2018) - [c25]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: 13-20 - [c24]Suyang Dai, Zihan Zhang, Wenxuan Zuo, Xiaodi Huang, Shanfeng Zhu:
GrantExtractor: A Winning System for Extracting Grant Support Information from Biomedical Literature. BIBM 2018: 333-340 - [i3]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 abs/1811.01727 (2018) - 2017
- [c23]Ronghui You, Shanfeng Zhu:
DeepText2Go: Improving large-scale protein function prediction with deep semantic text representation. BIBM 2017: 42-49 - [c22]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: 417-424 - 2016
- [j27]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): 18-27 (2016) - [j26]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): 70-79 (2016) - [c21]Junning Gao, Makoto Yamada, Samuel Kaski, Hiroshi Mamitsuka, Shanfeng Zhu:
A Robust Convex Formulation for Ensemble Clustering. IJCAI 2016: 1476-1482 - 2015
- [j25]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): 339-347 (2015) - [j24]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): 26-34 (2015) - [j23]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): 1542002:1-1542002:17 (2015) - [j22]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): 859-873 (2015) - [j21]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): 1286-1294 (2015) - [c20]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 - [c19]Xuhui Li, Zhengqi Liu, Mengchi Liu, Xiaoying Wu, Shanfeng Zhu:
Towards a Pattern-Based Query Language for Document Databases. DASFAA Workshops 2015: 320-325 - [c18]Xiaodong Zheng, Shanfeng Zhu, Junning Gao, Hiroshi Mamitsuka:
Instance-Wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters. IJCAI 2015: 4091-4097 - [c17]Ronghui You, Shengwen Peng, Shanfeng Zhu, Yuanjie Zhou:
FDUMedSearch at TREC 2015 Clinical Decision Support Track. TREC 2015 - [i2]Xuhui Li, Mengchi Liu, Xiaoying Wu, Shanfeng Zhu:
Design Issues of JPQ: a Pattern-based Query Language for Document Databases. CoRR abs/1504.03770 (2015) - 2014
- [j20]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): 734-747 (2014) - [j19]Xiaodong Li, Xiaotie Deng, Shanfeng Zhu, Feng Wang, Haoran Xie:
An intelligent market making strategy in algorithmic trading. Frontiers Comput. Sci. 8(4): 596-608 (2014) - [j18]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: 228-238 (2014) - [c16]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: 1311-1318 - [i1]Xuhui Li, Mengchi Liu, Shanfeng Zhu, Arif Ghafoor:
XTQ: A Declarative Functional XML Query Language. CoRR abs/1406.1224 (2014) - 2013
- [j17]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): 1265-1276 (2013) - [c15]Xiaodong Li, Shanfeng Zhu, Haoran Xie, Qing Li:
Document Summarization via Self-Present Sentence Relevance Model. DASFAA (2) 2013: 309-323 - [c14]Xiaodong Zheng, Hao Ding, Hiroshi Mamitsuka, Shanfeng Zhu:
Collaborative matrix factorization with multiple similarities for predicting drug-target interactions. KDD 2013: 1025-1033 - [c13]Xuhui Li, Shanfeng Zhu, Mengchi Liu, Ming Zhong:
Presenting XML Schema Mapping with Conjunctive-Disjunctive Views. WAIM 2013: 105-110 - 2012
- [j16]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): 350-364 (2012) - [j15]Gang Shu, Xiaodi Huang, Shanfeng Zhu:
A consensus method for prioritising drug-associated target proteins. Int. J. Data Min. Bioinform. 6(2): 178-195 (2012) - 2011
- [j14]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): 2293-2302 (2011) - [j13]Shuigeng Zhou, Caiyan Jia, Fei Wang, Qiwen Dong, Shanfeng Zhu, Ruqian Lu:
A conversation with Professor Ruqian Lu et al. SIGKDD Explor. 13(2): 79-81 (2011) - [c12]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: 279-293 - 2010
- [j12]Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew, Hong Yan:
Multiconstrained gene clustering based on generalized projections. BMC Bioinform. 11: 164 (2010) - [j11]Juan Liu, Lian Wang, Shanfeng Zhu:
SVR-PAIRWISE method to predict MHC-II binding peptides. Int. J. Bioinform. Res. Appl. 6(1): 58-68 (2010) - [j10]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): 474-479 (2010) - [c11]Qizhi Fang, Han Xiao, Shanfeng Zhu:
Top-d Rank Aggregation in Web Meta-search Engine - (Extended Abstract). FAW 2010: 35-44
2000 – 2009
- 2009
- [j9]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): 498-508 (2009) - [j8]Shanfeng Zhu, Jia Zeng, Hiroshi Mamitsuka:
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinform. 25(15): 1944-1951 (2009) - [j7]Shanfeng Zhu, Ichigaku Takigawa, Jia Zeng, Hiroshi Mamitsuka:
Field independent probabilistic model for clustering multi-field documents. Inf. Process. Manag. 45(5): 555-570 (2009) - 2007
- [j6]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): P16 (2007) - [c10]Shanfeng Zhu, Ichigaku Takigawa, Shuqin Zhang, Hiroshi Mamitsuka:
A Probabilistic Model for Clustering Text Documents with Multiple Fields. ECIR 2007: 331-342 - 2006
- [j5]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): 1648-1655 (2006) - 2005
- [c9]Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka:
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. ECCB/JBI 2005: 251 - 2004
- [j4]Shanfeng Zhu, Qizhi Fang, Weimin Zheng:
Social Choice For Data Fusion. Int. J. Inf. Technol. Decis. Mak. 3(4): 619-631 (2004) - [j3]Francis Y. L. Chin, Xiaotie Deng, Qizhi Fang, Shanfeng Zhu:
Approximate and dynamic rank aggregation. Theor. Comput. Sci. 325(3): 409-424 (2004) - [c8]Shanfeng Zhu, Christopher C. Yang, Wai Lam:
CatRelate: A New Hierarchical Document Category Integration Algorithm by Learning Category Relationships. ICADL 2004: 280-289 - 2003
- [c7]Xiaotie Deng, Qizhi Fang, Shanfeng Zhu:
Approximate Rank Aggregation (Preliminary Version). COCOON 2003: 262-271 - [c6]Shanfeng Zhu, Qizhi Fang, Xiaotie Deng, Weimin Zheng:
Metasearch via Voting. IDEAL 2003: 734-741 - 2002
- [j2]Qizhi Fang, Shanfeng Zhu:
Linear and Integer Programming Techniques for Cooperative Games. Int. J. Found. Comput. Sci. 13(5): 653-666 (2002) - [j1]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): 39-45 (2002) - [c5]Kang Chen, Weimin Zheng, Xiaotie Deng, Haodi Feng, Shanfeng Zhu:
Text Distinguishers Used in an Interactive Meta Search Engine. WAIM 2002: 181-188 - 2001
- [c4]Qizhi Fang, Shanfeng Zhu, Mao-cheng Cai, Xiaotie Deng:
Membership for Core of LP Games and Other Games. COCOON 2001: 247-256 - [c3]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: 648-658 - [c2]Kang Chen, Weimin Zheng, Hung Chim, Xiaotie Deng, Haodi Feng, Shanfeng Zhu:
On-Line Selection Of Distinguishing Elements For Focused Information Retrieval. ICME 2001 - [c1]Shanfeng Zhu, Xiaotie Deng, Kang Chen, Weimin Zheng:
Using Online Relevance Feedback to Build Effective Personalized Metasearch Engine. WISE (1) 2001: 262-270
Coauthor Index
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