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Authors: Zhiyong Lu
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Journal Article
MedHopQA: a disease-centred multi-hop reasoning benchmark and evaluation framework for LLM-based biomedical question answering
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Rezarta Islamaj, Robert Leaman, Joey Chan, Nicholas Wan, Qiao Jin, Natalie Xie, John Wilbur, Shubo Tian, Lana Yeganova, Po-Ting Lai, Chih-Hsuan Wei, Yifan Yang, Yao Ge, Qingqing Zhu, Zhizheng Wang, Zhiyong Lu
Database, Volume 2026, 2026, baag057, https://doi.org/10.1093/database/baag057
Published: 15 September 2026
Journal Article
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop
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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
Database, Volume 2024, 2024, baae071, https://doi.org/10.1093/database/baae071
Published: 09 August 2024
Journal Article
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII
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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 … Zhiyong Lu
Database, Volume 2024, 2024, baae069, https://doi.org/10.1093/database/baae069
Published: 08 August 2024
Journal Article
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII
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Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura … Zhiyong Lu
Database, Volume 2023, 2023, baad005, https://doi.org/10.1093/database/baad005
Published: 07 March 2023
Journal Article
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles
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Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu
Database, Volume 2022, 2022, baac102, https://doi.org/10.1093/database/baac102
Published: 01 December 2022
Journal Article
Assigning species information to corresponding genes by a sequence labeling framework
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Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
Database, Volume 2022, 2022, baac090, https://doi.org/10.1093/database/baac090
Published: 13 October 2022
Journal Article
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
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Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak … Zhiyong Lu
Database, Volume 2022, 2022, baac069, https://doi.org/10.1093/database/baac069
Published: 31 August 2022
Journal Article
A roadmap for the functional annotation of protein families: a community perspective
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Valérie de Crécy-lagard, Rocio Amorin de Hegedus, Cecilia Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J Bridge, Stephen K Burley, Stacey Cleveland, Lucy J Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang … Jin Xu
Database, Volume 2022, 2022, baac062, https://doi.org/10.1093/database/baac062
Published: 12 August 2022
Journal Article
A sequence labeling framework for extracting drug–protein relations from biomedical literature
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Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu
Database, Volume 2022, 2022, baac058, https://doi.org/10.1093/database/baac058
Published: 20 July 2022
Journal Article
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database
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Rezarta Islamaj, W John Wilbur, Natalie Xie, Noreen R Gonzales, Narmada Thanki, Roxanne Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu
Database, Volume 2019, 2019, baz064, https://doi.org/10.1093/database/baz064
Published: 02 July 2019
Journal Article
Using deep learning to identify translational research in genomic medicine beyond bench to bedside
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Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J Khoury, Zhiyong Lu
Database, Volume 2019, 2019, baz010, https://doi.org/10.1093/database/baz010
Published: 08 February 2019
Journal Article
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
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Rezarta Islamaj Doğan, 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 Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang … Zhiyong Lu
Database, Volume 2019, 2019, bay147, https://doi.org/10.1093/database/bay147
Published: 28 January 2019
Journal Article
Overview of the BioCreative VI text-mining services for Kinome Curation Track
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Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
Database, Volume 2018, 2018, bay104, https://doi.org/10.1093/database/bay104
Published: 17 October 2018
Journal Article
Assisting document triage for human kinome curation via machine learning
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Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu
Database, Volume 2018, 2018, bay091, https://doi.org/10.1093/database/bay091
Published: 18 September 2018
Journal Article
PubMed Labs: an experimental system for improving biomedical literature search
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Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu
Database, Volume 2018, 2018, bay094, https://doi.org/10.1093/database/bay094
Published: 18 September 2018
Journal Article
Extracting chemical–protein relations with ensembles of SVM and deep learning models
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Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu
Database, Volume 2018, 2018, bay073, https://doi.org/10.1093/database/bay073
Published: 17 July 2018
Journal Article
A Field Sensor: computing the composition and intent of PubMed queries
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Lana Yeganova, Won Kim, Donald C Comeau, W John Wilbur, Zhiyong Lu
Database, Volume 2018, 2018, bay052, https://doi.org/10.1093/database/bay052
Published: 12 July 2018
Journal Article
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu
Database, Volume 2016, 2016, baw161, https://doi.org/10.1093/database/baw161
Published: 26 December 2016
Journal Article
Overview of the interactive task in BioCreative V
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Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen … Cecilia N. Arighi
Database, Volume 2016, 2016, baw119, https://doi.org/10.1093/database/baw119
Published: 01 September 2016
Journal Article
Mining chemical patents with an ensemble of open systems
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Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu
Database, Volume 2016, 2016, baw065, https://doi.org/10.1093/database/baw065
Published: 12 May 2016