Chih-Hsuan Wei

Publication Activity (10 Years)

Years Active: 2009-2024
Publications (10 Years): 55

Top Topics

Named Entity Recognition

Relation Extraction

Top Venues

Database J. Biol. Databases Curation

Nucleic Acids Res.

Publications

Po-Ting Lai, Elisabeth Coudert, Lucila Aimo, Kristian B. Axelsen, Lionel Breuza, Edouard De Castro, Marc Feuermann, Anne Morgat, Lucille Pourcel, Ivo Pedruzzi, Sylvain Poux, Nicole Redaschi, Catherine Rivoire, Anastasia Sveshnikova, Chih-Hsuan Wei, Robert Leaman, Ling Luo, Zhiyong Lu, Alan J. Bridge
EnzChemRED, a rich enzyme chemistry relation extraction dataset. CoRR (2024)
Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen
Augmenting Biomedical Named Entity Recognition with General-domain Resources. CoRR (2024)
Zhizheng Wang, Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po-Ting Lai, Qingqing Zhu, Chi-Ping Day, Christina Ross, Zhiyong Lu
GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases. CoRR (2024)
Rezarta Islamaj, Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Tiago Almeida, Richard A. A. Jonker, Sofia I R. Conceição, Diana F. Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M. Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee, Yi-Yu Hsu, Mingjie Li, Karin Verspoor, Zhiyong Lu
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database J. Biol. Databases Curation 2024 (2024)
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge. CoRR (2024)
Rezarta Islamaj, Chih-Hsuan Wei, Po-Ting Lai, Ling Luo, Cathleen Coss, Preeti Gokal Kochar, Nicholas Miliaras, Oleg Rodionov, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Zhiyong Lu
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop. Database J. Biol. Databases Curation 2024 (2024)
Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang
Bioformer: an efficient transformer language model for biomedical text mining. CoRR (2023)
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. Bioinform. 39 (5) (2023)
Chih-Hsuan Wei, Ling Luo, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu
GNorm2: an improved gene name recognition and normalization system. Bioinform. 39 (10) (2023)
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets. CoRR (2023)
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
LitCovid in 2022: an information resource for the COVID-19 literature. Nucleic Acids Res. 51 (D1) (2023)
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. J. Biomed. Informatics 146 (2023)
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu
BioRED: a rich biomedical relation extraction dataset. Briefings Bioinform. 23 (5) (2022)
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework. CoRR (2022)
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning. CoRR (2022)
Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
tmVar 3.0: an improved variant concept recognition and normalization tool. CoRR (2022)
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu
A sequence labeling framework for extracting drug-protein relations from biomedical literature. Database J. Biol. Databases Curation 2022 (2022) (2022)
Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu
PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. AMIA (2022)
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. AMIA (2022)
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. CoRR (2022)
Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
tmVar 3.0: an improved variant concept recognition and normalization tool. Bioinform. 38 (18) (2022)
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
LitCovid in 2022: an information resource for the COVID-19 literature. CoRR (2022)
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
Assigning species information to corresponding genes by a sequence labeling framework. Database J. Biol. Databases Curation 2022 (2022) (2022)
Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. Briefings Bioinform. 22 (3) (2021)
Rezarta Islamaj Dogan, Chih-Hsuan Wei, David Cissel, Nicholas Miliaras, Olga Printseva, Oleg Rodionov, Keiko Sekiya, Janice Ward, Zhiyong Lu
NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. J. Biomed. Informatics 118 (2021)
Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9 (2020)
Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). CoRR (2020)
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16 (4) (2020)
Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR (2020)
Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J. Khoury, Zhiyong Lu
Using deep learning to identify translational research in genomic medicine beyond bench to bedside. Database J. Biol. Databases Curation 2019 (2019)
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
Biomedical Mention Disambiguation using a Deep Learning Approach. BCB (2019)
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
PubTator central: automated concept annotation for biomedical full text articles. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
PMC text mining subset in BioC: about three million full-text articles and growing. Bioinform. 35 (18) (2019)
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
Biomedical Mention Disambiguation using a Deep Learning Approach. CoRR (2019)
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019 (2019)
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR (2019)
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. BCB (2019)
Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
ezTag: tagging biomedical concepts via interactive learning. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline A. L. MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput. Biol. 14 (8) (2018)
Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
PMC text mining subset in BioC: 2.3 million full text articles and growing. CoRR (2018)
Chih-Hsuan Wei, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. Bioinform. 34 (1) (2018)
Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation 2018 (2018)
Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu
Assisting document triage for human kinome curation via machine learning. Database J. Biol. Databases Curation 2018 (2018)
Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Sylvain Poux, Cecilia N. Arighi, Michele Magrane, Alex Bateman, Chih-Hsuan Wei, Zhiyong Lu, Emmanuel Boutet, Hema Bye-A-Jee, Maria Livia Famiglietti, Bernd Roechert, The UniProt Consortium
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinform. 33 (21) (2017)
Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP (2017)
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
Large-scale Semantic Indexing with Biomedical Ontologies. ICBO/BioCreative (2016)
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
Beyond accuracy: creating interoperable and scalable text-mining web services. Bioinform. 32 (12) (2016)
Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative (2016)
Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, Zhiyong Lu
BioCreative V CDR task corpus: a resource for chemical disease relation extraction. Database J. Biol. Databases Curation 2016 (2016)
Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu
Mining chemical patents with an ensemble of open systems. Database J. Biol. Databases Curation 2016 (2016)
Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database J. Biol. Databases Curation 2016 (2016)
Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu
Improving chemical disease relation extraction with rich features and weakly labeled data. J. Cheminformatics 8 (1) (2016)
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text. IEEE J. Biomed. Health Informatics 19 (4) (2015)
Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu
tmChem: a high performance approach for chemical named entity recognition and normalization. J. Cheminformatics 7 (S-1) (2015)
Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu
: improving interoperability of text-mining tools with BioC. Database J. Biol. Databases Curation 2014 (2014)
Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu
NCBI at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic Indexing and Question Answering. CLEF (Working Notes) (2014)
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu
Text mining tools for assisting literature curation. BCB (2014)
Jui-Chen Hsiao, Chih-Hsuan Wei, Hung-Yu Kao
Gene Name Disambiguation UsingMulti-Scope Species Detection. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (1) (2014)
Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu
BC4GO: a full-text corpus for the BioCreative IV GO task. Database J. Biol. Databases Curation 2014 (2014)
Ritu Khare, Chih-Hsuan Wei, Zhiyong Lu
Automatic Extraction of Drug Indications from FDA Drug Labels. AMIA (2014)
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. BCB (2014)
John D. Burger, Emily Doughty, Ritu Khare, Chih-Hsuan Wei, Rajashree Mishra, John S. Aberdeen, David Tresner-Kirsch, Ben Wellner, Maricel G. Kann, Zhiyong Lu, Lynette Hirschman
Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing. Database J. Biol. Databases Curation 2014 (2014)
Chih-Hsuan Wei, Bethany R. Harris, Hung-Yu Kao, Zhiyong Lu
tmVar: a text mining approach for extracting sequence variants in biomedical literature. Bioinform. 29 (11) (2013)
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu
PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA (2013)
Chih-Hsuan Wei, Hung-Yu Kao
Unsupervised corpus distillation for represented indicator measurement on focus species detection. Int. J. Data Min. Bioinform. 8 (4) (2013)
Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013)
Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. Database J. Biol. Databases Curation 2012 (2012)
Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database J. Biol. Databases Curation 2012 (2012)
Chih-Hsuan Wei, Hung-Yu Kao
Cross-species gene normalization by species inference. BMC Bioinform. 12 (S-8) (2011)
Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur
The gene normalization task in BioCreative III. BMC Bioinform. 12 (S-8) (2011)
Koun-Tem Sun, Chih-Hsuan Wei, Yi-Yu Hsu, Wen-Chun Liu, Ting-Tsung Chang
On Deriving an Equation of the Mutation Rate of the Hepatitis B Virus. J. Convergence Inf. Technol. 5 (5) (2010)
Chih-Hsuan Wei, Hung-Yu Kao
Represented indicator measurement and corpus distillation on focus species detection. BIBM (2010)
Chih-Hsuan Wei, I-Chin Huang, Yi-Yu Hsu, Hung-Yu Kao
Normalizing Biomedical Name Entities by Similarity-Based Inference Network and De-ambiguity Mining. BIBE (2009)