Robert Leaman

66 papers C 2Misc 9Journal 43Unranked 12
YearRankTypeTitle / Venue / Authors
2026 J jnl
Condition-Gated Reasoning for Context-Dependent Biomedical Question Answering.
CoRR
Jash Rajesh Parekh, Wonbin Kweon, Joey Chan, Rezarta Islamaj, Robert Leaman, Pengcheng Jiang, Chih-Hsuan Wei, Zhizheng Wang, Zhiyong Lu, Jiawei Han
2026 J jnl
Med-V1: Small Language Models for Zero-shot and Scalable Biomedical Evidence Attribution.
CoRR
Qiao Jin, Yin Fang, Lauren He, Yifan Yang, Guangzhi Xiong, Zhizheng Wang, Nicholas Wan, Joey Chan, Donald C. Comeau, Robert Leaman, Charalampos S. Floudas, Aidong Zhang, Michael F. Chiang, Yifan Peng, Zhiyong Lu
2025 J jnl
Enhancing Biomedical Relation Extraction with Directionality.
CoRR
Po-Ting Lai, Chih-Hsuan Wei, Shubo Tian, Robert Leaman, Zhiyong Lu
2025 J jnl
Enhancing biomedical relation extraction with directionality.
Bioinform.
Po-Ting Lai, Chih-Hsuan Wei, Shubo Tian, Robert Leaman, Zhiyong Lu
2025 J jnl
Knowledge-guided Contextual Gene Set Analysis Using Large Language Models.
CoRR
Zhizheng Wang, Chi-Ping Day, Chih-Hsuan Wei, Qiao Jin, Robert Leaman, Yifan Yang, Shubo Tian, Aodong Qiu, Yin Fang, Qingqing Zhu, Xinghua Lu, Zhiyong Lu
2024 J jnl
Demystifying Large Language Models for Medicine: A Primer.
CoRR
Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou, Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald M. Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu
2024 J jnl
Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine.
CoRR
Yifan Yang, Qiao Jin, Robert Leaman, Xiaoyu Liu, Guangzhi Xiong, Maame Sarfo-Gyamfi, Changlin Gong, Santiago Ferrière-Steinert, W. John Wilbur, Xiaojun Li, Jiaxin Yuan, Bang An, Kelvin S. Castro, Francisco Erramuspe Álvarez, Matías Stockle, Aidong Zhang, Furong Huang, Zhiyong Lu
2024 J jnl
EnzChemRED, a rich enzyme chemistry relation extraction dataset.
CoRR
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
2024 J jnl
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge.
CoRR
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
2023 J jnl
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.
Bioinform.
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
2023 J jnl
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII.
Database J. Biol. Databases Curation
Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed 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, Wen-Chao Yeh, Zhiyong Lu
2023 J jnl
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2023 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2023 J jnl
PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search.
CoRR
Qiao Jin, Robert Leaman, Zhiyong Lu
2022 J jnl
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning.
CoRR
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
2022 J jnl
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR
Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2022 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
CoRR
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2022 J jnl
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
Database J. Biol. Databases Curation
Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, 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, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu
2022 J jnl
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
CoRR
Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Dogan, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Zhiyong Lu
2022 J jnl
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles.
Database J. Biol. Databases Curation
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
2021 Misc conf
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors.
AMIA
Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 Misc conf
NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature.
AMIA
Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Dorothy Trinh, Deborah Whitman, Keiko Sekiya, Zhiyong Lu
2020 — conf
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2.
NLP4COVID@EMNLP
Robert Leaman, Zhiyong Lu
2020 J jnl
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2.
CoRR
Robert Leaman, Zhiyong Lu
2020 J jnl
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).
CoRR
Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2020 J jnl
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR
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
2019 — conf
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles.
BCB
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
2019 — conf
Biomedical Mention Disambiguation using a Deep Learning Approach.
BCB
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
2019 J jnl
Biomedical Mention Disambiguation using a Deep Learning Approach.
CoRR
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
2019 J jnl
PubTator central: automated concept annotation for biomedical full text articles.
Nucleic Acids Res.
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
2019 Misc conf
Text Mining and Machine Learning for Precision Medicine.
PSB
Graciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John H. Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu
2018 J jnl
ezTag: tagging biomedical concepts via interactive learning.
Nucleic Acids Res.
Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2016 J jnl
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
Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu
2016 J jnl
Beyond accuracy: creating interoperable and scalable text-mining web services.
Bioinform.
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2016 J jnl
BioCreative V CDR task corpus: a resource for chemical disease relation extraction.
Database J. Biol. Databases Curation
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
2016 J jnl
Crowdsourcing in biomedicine: challenges and opportunities.
Briefings Bioinform.
Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu
2016 — conf
Large-scale Semantic Indexing with Biomedical Ontologies.
ICBO/BioCreative
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2016 J jnl
Mining chemical patents with an ensemble of open systems.
Database J. Biol. Databases Curation
Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu
2016 J jnl
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Database J. Biol. Databases Curation
Ayush Singhal, Robert Leaman, Natalie L. Catlett, Thomas Lemberger, Johanna R. McEntyre, Shawn W. Polson, Ioannis Xenarios, Cecilia N. Arighi, Zhiyong Lu
2016 J jnl
TaggerOne: joint named entity recognition and normalization with semi-Markov Models.
Bioinform.
Robert Leaman, Zhiyong Lu
2015 J jnl
Challenges in clinical natural language processing for automated disorder normalization.
J. Biomed. Informatics
Robert Leaman, Ritu Khare, Zhiyong Lu
2015 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu
2015 J jnl
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text.
IEEE J. Biomed. Health Informatics
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2015 J jnl
The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics
Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia
2015 J jnl
tmChem: a high performance approach for chemical named entity recognition and normalization.
J. Cheminformatics
Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu
2014 — conf
Automated Disease Normalization with Low Rank Approximations.
BioNLP@ACL
Robert Leaman, Zhiyong Lu
2014 — conf
Disease named entity recognition and normalization with DNorm.
BCB
Robert Leaman, Zhiyong Lu
2014 J jnl
NCBI disease corpus: A resource for disease name recognition and concept normalization.
J. Biomed. Informatics
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
2014 Misc conf
Session introduction.
Pacific Symposium on Biocomputing
Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye
2014 — conf
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine.
BCB
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2013 Misc conf
DNorm: A New Method and Online Tool for Disease Name Normalization.
AMIA
Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu
2013 J jnl
DNorm: disease name normalization with pairwise learning to rank.
Bioinform.
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu
2013 Misc conf
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization.
AMIA
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
2013 — conf
NCBI at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with Dnorm.
CLEF (Working Notes)
Robert Leaman, Ritu Khare, Zhiyong Lu
2013 Misc conf
Session introduction.
Pacific Symposium on Biocomputing
Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye
2012 J jnl
A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions.
J. Biomed. Informatics
Jörg Hakenberg, Dmitry Voronov, Nguyen Ha Vo, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral
2011 J jnl
Enhancing phylogeography by improving geographical information from GenBank.
J. Biomed. Informatics
Matthew Scotch, Indra Neil Sarkar, Changjiang Mei, Robert Leaman, Kei-Hoi Cheung, Pierina Ortiz, Ashutosh Singraur, Graciela Gonzalez
2011 — conf
The DIEGO Lab Graph Based Gene Normalization System.
ICMLA (2)
Ryan Sullivan, Robert Leaman, Graciela Gonzalez
2011 J jnl
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform.
Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
2010 C conf
A Distributional Semantics Approach to Simultaneous Recognition of Multiple Classes of Named Entities.
CICLing
Siddhartha Jonnalagadda, Robert Leaman, Trevor Cohen, Graciela Gonzalez
2010 J jnl
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jörg Hakenberg, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez
2010 — conf
Towards Internet-Age Pharmacovigilance: Extracting Adverse Drug Reactions from User Posts in Health-Related Social Networks.
BioNLP@ACL
Robert Leaman, Laura Wojtulewicz, Ryan Sullivan, Annie Skariah, Jian Yang, Graciela Gonzalez
2008 Misc conf
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition.
Pacific Symposium on Biocomputing
Robert Leaman, Graciela Gonzalez
2008 C conf
Inter-species normalization of gene mentions with GNAT.
ECCB
Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez
2007 — conf
Passage Relevancy Through Semantic Relatedness.
TREC
Luis Tari, Phan Huy Tu, Barry Lumpkin, Robert Leaman, Graciela Gonzalez, Chitta Baral
2006 — conf
ASU at TREC 2006 Genomics Track.
TREC
Luis Tari, Graciela Gonzalez, Robert Leaman, Shawn Nikkila, Ryan Wendt, Chitta Baral