Robert Leaman

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 33

Top Topics

Medical Literature

Named Entity Recognition

Manually Annotated

Relation Extraction

Top Venues

Database J. Biol. Databases Curation

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)
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)
Qiao Jin, Robert Leaman, Zhiyong Lu
PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search. CoRR (2023)
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
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database J. Biol. Databases Curation 2023 (2023)
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. Patterns 4 (1) (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)
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)
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
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. CoRR (2022)
Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. 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)
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)
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
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles. Database J. Biol. Databases Curation 2022 (2022) (2022)
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
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 2022 (2022) (2022)
Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Dorothy Trinh, Deborah Whitman, Keiko Sekiya, Zhiyong Lu
NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature. AMIA (2021)
Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. AMIA (2021)
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)
Robert Leaman, Zhiyong Lu
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. CoRR (2020)
Robert Leaman, Zhiyong Lu
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. NLP4COVID@EMNLP (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)
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)
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
Biomedical Mention Disambiguation using a Deep Learning Approach. 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)
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
Text Mining and Machine Learning for Precision Medicine. PSB (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)
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)
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)
Ayush Singhal, Robert Leaman, Natalie L. Catlett, Thomas Lemberger, Johanna R. McEntyre, Shawn W. Polson, Ioannis Xenarios, Cecilia N. Arighi, Zhiyong Lu
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database J. Biol. Databases Curation 2016 (2016)
Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu
Crowdsourcing in biomedicine: challenges and opportunities. Briefings Bioinform. 17 (1) (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)
Robert Leaman, Zhiyong Lu
TaggerOne: joint named entity recognition and normalization with semi-Markov Models. Bioinform. 32 (18) (2016)
Robert Leaman, Ritu Khare, Zhiyong Lu
Challenges in clinical natural language processing for automated disorder normalization. J. Biomed. Informatics 57 (2015)
Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu
Session Introduction. Pacific Symposium on Biocomputing (2015)
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)
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
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7 (S-1) (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)
Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye
Session introduction. Pacific Symposium on Biocomputing (2014)
Robert Leaman, Zhiyong Lu
Disease named entity recognition and normalization with DNorm. BCB (2014)
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
NCBI disease corpus: A resource for disease name recognition and concept normalization. J. Biomed. Informatics 47 (2014)
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. BCB (2014)
Robert Leaman, Zhiyong Lu
Automated Disease Normalization with Low Rank Approximations. BioNLP@ACL (2014)
Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye
Session introduction. Pacific Symposium on Biocomputing (2013)
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. AMIA (2013)
Robert Leaman, Ritu Khare, Zhiyong Lu
NCBI at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with Dnorm. CLEF (Working Notes) (2013)
Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA (2013)
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu
DNorm: disease name normalization with pairwise learning to rank. Bioinform. 29 (22) (2013)
Jörg Hakenberg, Dmitry Voronov, Nguyen Ha Vo, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral
A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. J. Biomed. Informatics 45 (5) (2012)
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 Mateus Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12 (S-8) (2011)
Matthew Scotch, Indra Neil Sarkar, Changjiang Mei, Robert Leaman, Kei-Hoi Cheung, Pierina Ortiz, Ashutosh Singraur, Graciela Gonzalez
Enhancing phylogeography by improving geographical information from GenBank. J. Biomed. Informatics 44 (Supplement-1) (2011)
Ryan Sullivan, Robert Leaman, Graciela Gonzalez
The DIEGO Lab Graph Based Gene Normalization System. ICMLA (2) (2011)
Jörg Hakenberg, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (3) (2010)
Siddhartha Jonnalagadda, Robert Leaman, Trevor Cohen, Graciela Gonzalez
A Distributional Semantics Approach to Simultaneous Recognition of Multiple Classes of Named Entities. CICLing (2010)
Robert Leaman, Laura Wojtulewicz, Ryan Sullivan, Annie Skariah, Jian Yang, Graciela Gonzalez
Towards Internet-Age Pharmacovigilance: Extracting Adverse Drug Reactions from User Posts in Health-Related Social Networks. BioNLP@ACL (2010)
Robert Leaman, Graciela Gonzalez
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition. Pacific Symposium on Biocomputing (2008)
Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez
Inter-species normalization of gene mentions with GNAT. ECCB (2008)
Luis Tari, Phan Huy Tu, Barry Lumpkin, Robert Leaman, Graciela Gonzalez, Chitta Baral
Passage Relevancy Through Semantic Relatedness. TREC (2007)
Luis Tari, Graciela Gonzalez, Robert Leaman, Shawn Nikkila, Ryan Wendt, Chitta Baral
ASU at TREC 2006 Genomics Track. TREC (2006)