Chih-Hsuan Wei

发表

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

Jari Björne, T. Salakoski, Filip Ginter, 2013, PloS one.

SR4GN: A Species Recognition Software Tool for Gene Normalization

Zhiyong Lu, Chih-Hsuan Wei, Hung-Yu Kao, 2012, PloS one.

- like interactive curation system for document triage and literature curation

Zhiyong Lu, Chih-Hsuan Wei, Hung-Yu Kao, 2012 .

PubTator: a web-based text mining tool for assisting biocuration

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, 2013, Nucleic Acids Res..

The gene normalization task in BioCreative III

Zhiyong Lu, Karin M. Verspoor, Hongfang Liu, 2011, BMC Bioinformatics.

PubTator central: automated concept annotation for biomedical full text articles

Robert Leaman, Zhiyong Lu, Chih-Hsuan Wei, 2019, Nucleic Acids Res..

tmChem: a high performance approach for chemical named entity recognition and normalization

Zhiyong Lu, Chih-Hsuan Wei, Robert Leaman, 2015, Journal of Cheminformatics.

Corpus Construction for the BioCreative IV GO Task

Zhiyong Lu, Kimberly Van Auken, Paul W. Sternberg, 2013 .

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

Zhiyong Lu, Alex Bateman, Cecilia N. Arighi, 2016, bioRxiv.

Annotating chemicals , diseases and their interactions in biomedical literature

Zhiyong Lu, Thomas C. Wiegers, Allan Peter Davis, 2015 .

tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine

Zhiyong Lu, Chih-Hsuan Wei, Tim Hefferon, 2018, Bioinform..

tmVar 3.0: an improved variant concept recognition and normalization tool

A. Milosavljevic, Zhiyong Lu, Chih-Hsuan Wei, 2022, Bioinform..

The BioCreative VI Precision Medicine Track corpus Selection , annotation and curation of protein-protein interactions affected by mutations in scientific literature

Zhiyong Lu, Kara Dolinski, Mike Tyers, 2017 .

BioRED: a rich biomedical relation extraction dataset

C. Arighi, Zhiyong Lu, Chih-Hsuan Wei, 2022, Briefings Bioinform..

LitCovid in 2022: an information resource for the COVID-19 literature

Zhiyong Lu, Chih-Hsuan Wei, Alexis Allot, 2022, Nucleic Acids Res..

Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability

Zhiyong Lu, Chih-Hsuan Wei, Alexis Allot, 2020, PLoS biology.

AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning

Zhiyong Lu, Chih-Hsuan Wei, Po-Ting Lai, 2022, ArXiv.

AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning

Zhiyong Lu, Chih-Hsuan Wei, Po-Ting Lai, 2022, ArXiv.

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

Zhiyong Lu, Thomas C. Wiegers, Allan Peter Davis, 2016, Database J. Biol. Databases Curation.

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Akira R. Kinjo, Núria Queralt-Rosinach, Michel Dumontier, 2020, F1000Research.

PMC text mining subset in BioC: about three million full-text articles and growing

Zhiyong Lu, Donald C. Comeau, Chih-Hsuan Wei, 2019, Bioinform..

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Zhiyong Lu, Cecilia N. Arighi, Alex Bateman, 2017, Bioinform..

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC

Yifan Peng, Zhiyong Lu, Alexis Allot, 2018, Nucleic Acids Res..

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP) pdf

Zhiyong Lu, Qingyu Chen, Chih-Hsuan Wei, 2020, Annual review of biomedical data science.

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, 2015, BioMed research international.

Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing

Zhiyong Lu, John D. Burger, John S. Aberdeen, 2014, Database J. Biol. Databases Curation.

tmVar: a text mining approach for extracting sequence variants in biomedical literature

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, 2013, Bioinform..

BC4GO: a full-text corpus for the BioCreative IV GO task

Zhiyong Lu, Kimberly Van Auken, Hans-Michael Müller, 2014, Database J. Biol. Databases Curation.

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Qingyu Chen, Zhiyong Lu, Karin M. Verspoor, 2019, Database J. Biol. Databases Curation.

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

Yifan Peng, Zhiyong Lu, Thomas C. Wiegers, 2016, Database J. Biol. Databases Curation.

Text Mining for Translational Bioinformatics

Zhiyong Lu, Richard Tzong-Han Tsai, Hung-Yu Kao, 2015, BioMed research international.

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources

Zhiyong Lu, Ioannis Xenarios, Aoife McMahon, 2018, PLoS Comput. Biol..

ezTag: tagging biomedical concepts via interactive learning

Zhiyong Lu, Sun Kim, Dongseop Kwon, 2018, Nucleic Acids Res..

Cross-species gene normalization by species inference

Hung-Yu Kao, Chih-Hsuan Wei, Chih-Hsuan Wei, 2011, BMC Bioinformatics.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Jeyakumar Natarajan, Zhiyong Lu, K. Bretonnel Cohen, 2013, Database J. Biol. Databases Curation.

NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature

Donald C. Comeau, Dongseop Kwon, Robert Leaman, 2021, Scientific data.

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale

Zhiyong Lu, Chih-Hsuan Wei, Shankai Yan, 2019, PLoS Comput. Biol..

Using deep learning to identify translational research in genomic medicine beyond bench to bedside

Zhiyong Lu, Muin J. Khoury, Chih-Hsuan Wei, 2019, Database J. Biol. Databases Curation.

NCBI at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic Indexing and Question Answering

Zhiyong Lu, Yuqing Mao, Chih-Hsuan Wei, 2014, CLEF.

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

Zhiyong Lu, Tanya Z. Berardini, Donghui Li, 2012, Database J. Biol. Databases Curation.

Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature

Zhiyong Lu, Chih-Hsuan Wei, Kyubum Lee, 2020, Briefings Bioinform..

AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning

Zhiyong Lu, Chih-Hsuan Wei, Po-Ting Lai, 2022, Bioinform..

Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework

Zhiyong Lu, Chih-Hsuan Wei, R. Dogan, 2022, Database J. Biol. Databases Curation.

NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition

Zhiyong Lu, Chih-Hsuan Wei, Rezarta Islamaj Dogan, 2021, J. Biomed. Informatics.

Bioformer: an efficient transformer language model for biomedical text mining

Chih-Hsuan Wei, Qingyu Chen, Kai Wang, 2023, ArXiv.

BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations

Yifan Peng, Zhiyong Lu, Sun Kim, 2017, BioNLP.

A Sequence Labeling Framework for Extracting Drug-Protein Relations from Biomedical Literature

Zhiyong Lu, Chih-Hsuan Wei, Po-Ting Lai, 2022, bioRxiv.

Beyond accuracy: creating interoperable and scalable text-mining web services

Zhiyong Lu, Chih-Hsuan Wei, Robert Leaman, 2016, Bioinform..

Improving chemical disease relation extraction with rich features and weakly labeled data

Yifan Peng, Zhiyong Lu, Chih-Hsuan Wei, 2016, Journal of Cheminformatics.

NCBI at the BioCreative IV CHEMDNER Task : Recognizing chemical names in PubMed articles with tmChem

Zhiyong Lu, Chih-Hsuan Wei, Robert Leaman, 2013 .

Extracting Drug-Protein Interaction using an Ensemble of Biomedical Pre-trained Language Models through Sequence Labeling and Text Classification Techniques

Zhiyong Lu, Chih-Hsuan Wei, Po-Ting Lai, 2021 .

BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets.

Chih-Hsuan Wei, Ling Luo, Zhiyong Lu, 2023, Journal of Biomedical Informatics.

BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets

Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, 2023, ArXiv.

The gene normalization task in BioCreative III

Karin M. Verspoor, Richard Tzong-Han Tsai, Minlie Huang, 2011, BMC Bioinformatics.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

Zhiyong Lu, W. John Wilbur, Won Kim, 2012, Database J. Biol. Databases Curation.

Automatic Extraction of Drug Indications from FDA Drug Labels

Zhiyong Lu, Ritu Khare, Chih-Hsuan Wei, 2014, AMIA.

A Novel Sequence Labeling Framework for Extracting Drug-Protein Relations from Biomedical Literature

Chih-Hsuan Wei, Ling Luo, Po-Ting Lai, 2022 .

Augmenting Biomedical Named Entity Recognition with General-domain Resources

Chih-Hsuan Wei, Qingyu Chen, Hyunjae Kim, 2024, ArXiv.

Advancing entity recognition in biomedicine via instruction tuning of large language models

Chih-Hsuan Wei, V. Keloth, Yan Hu, 2024, Bioinformatics.

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases

Chih-Hsuan Wei, Shubo Tian, Po-Ting Lai, 2024, ArXiv.