Epistasis detection using a permutation-based Gradient Boosting Machine. - Kai Che; Xiaoyan Liu; Maozu Guo 001; Junwei Zhang; Lei Wang 085; Yin Zhang 009 (BIBM, 2016)

CIDExtractor: A chemical-induced disease relation extraction system for biomedical literature. - Zhiheng Li 004; Zhihao Yang; Hongfei Lin; Jian Wang 021; Yingyi Gui; Yin Zhang 009; Lei Wang 085 (BIBM, 2016)

Reconstructing gene regulatory network based on candidate auto selection method. - Linlin Xing; Maozu Guo 001; Xiaoyan Liu; Chunyu Wang 002; Lei Wang 085; Yin Zhang 009 (BIBM, 2016)

ML-CNN: A novel deep learning based disease named entity recognition architecture. - Zhehuan Zhao; Zhihao Yang; Ling Luo 001; Yin Zhang 009; Lei Wang 085; Hongfei Lin; Jian Wang 021 (BIBM, 2016)

Disease-specific protein complex detection in the human protein interaction network with a supervised learning method. - Ziwei Zhou; Yingyi Gui; Zhihao Yang; Xiaoxia Liu; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BIBM, 2016)

A hybrid protein-protein interaction triple extraction method for biomedical literature. - Zhehuan Zhao; Zhihao Yang; Cong Sun 004; Lei Wang 085; Hongfei Lin (BIBM, 2017)

Constructing an integrated gene similarity network for the identification of disease genes. - Zhen Tian; Maozu Guo 001; Chunyu Wang 002; Linlin Xing; Lei Wang 085; Yin Zhang 009 (J. Biomed. Semant., 2017)

A multi-task learning based approach to biomedical entity relation extraction. - Qingqing Li; Zhihao Yang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (BIBM, 2018)

HMNPPID: A Database of Protein-protein Interactions Associated with Human Malignant Neoplasms. - Qingqing Li; Zhihao Yang; Zhehuan Zhao; Ling Luo 001; Zhiheng Li 004; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Yijia Zhang 001 (BIBM, 2018)

PC-SENE: A node embedding based method for protein complex detection. - Xiaoxia Liu; Zhihao Yang; Shengtian Sang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Bo Xu 009; Yijia Zhang 001; Liang Yang 003; Kan Xu; Jian Wang 021 (BIBM, 2018)

Protein-Protein Interaction Article Classification: A Knowledge-enriched Self-Attention Convolutional Neural Network Approach. - Ling Luo 001; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (BIBM, 2018)

A Knowledge Graph based Bidirectional Recurrent Neural Network Method for Literature-based Discovery. - Shengtian Sang; Zhihao Yang; Xiaoxia Liu; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (BIBM, 2018)

Hierarchical Recurrent Convolutional Neural Network for Chemical-protein Relation Extraction from Biomedical Literature. - Cong Sun 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (BIBM, 2018)

An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition. - Ling Luo 001; Zhihao Yang; Pei Yang; Yin Zhang 009; Lei Wang 085; Hongfei Lin; Jian Wang 021 (Bioinform., 2018)

Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks. - Xiaoxia Liu; Zhihao Yang; Shengtian Sang; Ziwei Zhou; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Bo Xu 008 (BMC Bioinform., 2018)

SemaTyP: a knowledge graph based literature mining method for drug discovery. - Shengtian Sang; Zhihao Yang; Lei Wang 085; Xiaoxia Liu; Hongfei Lin; Jian Wang 021 (BMC Bioinform., 2018)

A neural network approach to chemical and gene/protein entity recognition in patents. - Ling Luo 001; Zhihao Yang; Pei Yang; Yin Zhang 009; Lei Wang 085; Jian Wang 021; Hongfei Lin (J. Cheminformatics, 2018)

GrEDeL: A Knowledge Graph Embedding Based Method for Drug Discovery From Biomedical Literatures. - Shengtian Sang; Zhihao Yang; Xiaoxia Liu; Lei Wang 085; Hongfei Lin; Jian Wang 021; Michel Dumontier (IEEE Access, 2019)

A Deep Learning Approach With Deep Contextualized Word Representations for Chemical-Protein Interaction Extraction From Biomedical Literature. - Cong Sun 004; Zhihao Yang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (IEEE Access, 2019)

KeSACNN: a protein-protein interaction article classification approach based on deep neural network. - Ling Luo 001; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (Int. J. Data Min. Bioinform., 2019)

Chemical-protein interaction extraction from biomedical literature: a hierarchical recurrent convolutional neural network method. - Cong Sun 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (Int. J. Data Min. Bioinform., 2019)

Extracting biomedical relations via a multi-head attention based graph convolutional network. - Erniu Wang; Fan Wang 005; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BIBM, 2020)

Star-BiLSTM-LAN for Document-level Mutation-Disease Relation Extraction from Biomedical Literature. - Yuan Xu; Zhihao Yang; Yawen Song; Zhiheng Li 004; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BIBM, 2020)

Chemical-protein interaction extraction via Gaussian probability distribution and external biomedical knowledge. - Cong Sun 004; Zhihao Yang; Leilei Su; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (Bioinform., 2020)

A neural network-based joint learning approach for biomedical entity and relation extraction from biomedical literature. - Ling Luo 001; Zhihao Yang; Mingyu Cao; Lei Wang 085; Yin Zhang 009; Hongfei Lin (J. Biomed. Informatics, 2020)

Attention guided capsule networks for chemical-protein interaction extraction. - Cong Sun 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (J. Biomed. Informatics, 2020)

KGHC: a knowledge graph for hepatocellular carcinoma. - Nan Li; Zhihao Yang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BMC Medical Informatics Decis. Mak., 2020)

SGAT: a Self-supervised Graph Attention Network for Biomedical Relation Extraction. - Qiming Liu; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jinzhong Ning (BIBM, 2021)

Deep learning with language models improves named entity recognition for PharmaCoNER. - Cong Sun 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BMC Bioinform., 2021)

Biomedical named entity recognition using BERT in the machine reading comprehension framework. - Cong Sun 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (J. Biomed. Informatics, 2021)

Lexicon Knowledge Boosted Interaction Graph Network for Adverse Drug Reaction Recognition From Social Media. - Zhiheng Li 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (IEEE J. Biomed. Health Informatics, 2021)

BioNER-CFEM: Biomedical Named Entity Recognition Based on Character Feature Enhancement with Multimodal Method. - Jinzhong Ning; Jiru Li; Zhihao Yang; Yuanyuan Sun 002; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BIBM, 2022)

Adaptive Multi-view Graph Convolutional Network for Gene Ontology Annotations of Proteins. - Yingwen Zhao; Zhihao Yang; Yongkai Hong; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BIBM, 2022)

MRC4BioER: Joint extraction of biomedical entities and relations in the machine reading comprehension framework. - Cong Sun 004; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (J. Biomed. Informatics, 2022)

Joint Biomedical Entity and Relation Extraction Based on Triple Region Vertices. - Yuqi Liu; Zhihao Yang; Jinzhong Ning; Zhijun Wang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Wei Liu; Hongfei Lin; Jian Wang 021 (BIBM, 2023)

Joint Biomedical Entity and Relation Extraction with Unified Interaction Maps. - Haixin Tan; Zhihao Yang; Zeyuan Ding; Zhijun Wang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Wei Liu; Hongfei Lin; Jian Wang 021 (BIBM, 2023)

Improving Protein Function Prediction by Adaptively Fusing Information From Protein Sequences and Biomedical Literature. - Yingwen Zhao; Zhihao Yang; Yongkai Hong; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (IEEE J. Biomed. Health Informatics, 2023)

Biomedical Event Extraction as Semantic Segmentation. - Liangyu Gao; Zhihao Yang; Jinzhong Ning; Kai Ma; Lei Wang 085; Wei Liu; Yin Zhang 009; Ling Luo 001; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; et al. (BIBM, 2024)

Document-level Biomedical Relation Extraction Based on Relation-guided Entity-level Graphs. - Liangyu Gao; Zhihao Yang; Haixin Tan; Lei Wang 085; Wei Liu; Yin Zhang 009; Ling Luo 001; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; Yuanyuan Sun 002; et al. (BIBM, 2024)

Document Embeddings Enhance Biomedical Retrieval-Augmented Generation. - Yongle Kong; Zhihao Yang; Ling Luo 001; Zeyuan Ding; Lei Wang 085; Wei Liu; Yin Zhang 009; Bo Xu 009; Jian Wang 021; Yuanyuan Sun 002; Zhehuan Zhao; Hongfei Lin (BIBM, 2024)

Biomedical Document-level Relation Extraction with Coreference and Anaphor Graphs. - Jiru Li; Yuanyuan Sun 002; Zhihao Yang; Ling Luo 001; Lei Wang 085; Wei Liu; Yin Zhang 009; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; Hongfei Lin (BIBM, 2024)

Efficient Knowledge Graph Embedding Framework to Alleviate Data Sparsity for Polypharmacy Side Effects Prediction. - Senbo Tu; Zhihao Yang; Lei Wang 085; Wei Liu; Yin Zhang 009; Ling Luo 001; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; Hongfei Lin (BIBM, 2024)

Predicting Protein Functions Based on Heterogeneous Graph Attention Technique. - Yingwen Zhao; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (IEEE J. Biomed. Health Informatics, 2024)