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2020 – today
- 2022
- [j35]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) - [i8]Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu:
tmVar 3.0: an improved variant concept recognition and normalization tool. CoRR abs/2204.03637 (2022) - [i7]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. CoRR abs/2204.04263 (2022) - [i6]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 abs/2205.03853 (2022) - 2021
- [j34]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) - [j33]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: 103779 (2021) - 2020
- [j32]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) - [i5]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 abs/2008.03397 (2020) - [i4]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 abs/2010.16413 (2020)
2010 – 2019
- 2019
- [j31]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: bay147 (2019) - [j30]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: baz010 (2019) - [j29]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): 3533-3535 (2019) - [j28]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): W587-W593 (2019) - [c12]Chih-Hsuan Wei, Kyubum Lee
, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. BCB 2019: 307-313 - [c11]Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. BCB 2019: 540 - [i3]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. CoRR abs/1909.10416 (2019) - [i2]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 abs/1912.10846 (2019) - 2018
- [j27]Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu:
Assisting document triage for human kinome curation via machine learning. Database J. Biol. Databases Curation 2018: bay091 (2018) - [j26]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: bay104 (2018) - [j25]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): 80-87 (2018) - [j24]Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
:
ezTag: tagging biomedical concepts via interactive learning. Nucleic Acids Res. 46(Webserver-Issue): W523-W529 (2018) - [j23]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): W530-W536 (2018) - [j22]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) - [i1]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 abs/1804.05957 (2018) - 2017
- [j21]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): 3454-3460 (2017) - [c10]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: 171-175 - 2016
- [j20]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) - [j19]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) - [j18]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) - [j17]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Beyond accuracy: creating interoperable and scalable text-mining web services. Bioinform. 32(12): 1907-1910 (2016) - [j16]Yifan Peng
, Chih-Hsuan Wei, Zhiyong Lu:
Improving chemical disease relation extraction with rich features and weakly labeled data. J. Cheminformatics 8(1): 53:1-53:12 (2016) - [c9]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 - [c8]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Large-scale Semantic Indexing with Biomedical Ontologies. ICBO/BioCreative 2016 - 2015
- [j15]Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu:
tmChem: a high performance approach for chemical named entity recognition and normalization. J. Cheminformatics 7(S-1): S3 (2015) - [j14]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): 1385-1391 (2015) - 2014
- [j13]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) - [j12]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) - [j11]Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu:
tmBioC: improving interoperability of text-mining tools with BioC. Database J. Biol. Databases Curation 2014 (2014) - [j10]Jui-Chen Hsiao, Chih-Hsuan Wei, Hung-Yu Kao:
Gene Name Disambiguation UsingMulti-Scope Species Detection. IEEE ACM Trans. Comput. Biol. Bioinform. 11(1): 55-62 (2014) - [c7]Ritu Khare, Chih-Hsuan Wei, Zhiyong Lu:
Automatic Extraction of Drug Indications from FDA Drug Labels. AMIA 2014 - [c6]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. BCB 2014: 138-146 - [c5]Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
Text mining tools for assisting literature curation. BCB 2014: 590-591 - [c4]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: 1319-1327 - 2013
- [j9]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) - [j8]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): 1433-1439 (2013) - [j7]Chih-Hsuan Wei, Hung-Yu Kao:
Unsupervised corpus distillation for represented indicator measurement on focus species detection. Int. J. Data Min. Bioinform. 8(4): 413-426 (2013) - [j6]Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 41(Webserver-Issue): 518-522 (2013) - [c3]Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu:
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA 2013 - 2012
- [j5]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) - [j4]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) - 2011
- [j3]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): S2 (2011) - [j2]Chih-Hsuan Wei, Hung-Yu Kao
:
Cross-species gene normalization by species inference. BMC Bioinform. 12(S-8): S5 (2011) - 2010
- [j1]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): 131-137 (2010) - [c2]Chih-Hsuan Wei, Hung-Yu Kao
:
Represented indicator measurement and corpus distillation on focus species detection. BIBM 2010: 657-662
2000 – 2009
- 2009
- [c1]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: 461-466
Coauthor Index

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last updated on 2022-07-29 20:59 CEST by the dblp team
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