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2020 – today
- 2024
[i12]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 abs/2401.11048 (2024)- [i11]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 abs/2404.14209 (2024) - [i10]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:
Demystifying Large Language Models for Medicine: A Primer. CoRR abs/2410.18856 (2024) - 2023
- [j26]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) - [j25]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) - [j24]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): 1512-1518 (2023) - [j23]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): 100659 (2023) - [i9]Qiao Jin, Robert Leaman, Zhiyong Lu:
PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search. CoRR abs/2307.09683 (2023) - 2022
- [j22]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) - [j21]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) - [i8]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 abs/2204.09781 (2022) - [i7]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 abs/2209.08124 (2022) - [i6]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 abs/2209.13428 (2022) - [i5]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 abs/2211.16944 (2022) - 2021
- [c23]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 - [c22]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 - 2020
- [c21]Robert Leaman, Zhiyong Lu:
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. NLP4COVID@EMNLP 2020 - [i4]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) - [i3]Robert Leaman, Zhiyong Lu:
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. CoRR abs/2010.14588 (2020) - [i2]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
- [j20]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) - [c20]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. BCB 2019: 307-313 - [c19]Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. BCB 2019: 540 - [c18]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: 449-454 - [i1]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. CoRR abs/1909.10416 (2019) - 2018
- [j19]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) - 2016
- [j18]Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu:
Crowdsourcing in biomedicine: challenges and opportunities. Briefings Bioinform. 17(1): 23-32 (2016) - [j17]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) - [j16]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) - [j15]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) - [j14]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) - [j13]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Beyond accuracy: creating interoperable and scalable text-mining web services. Bioinform. 32(12): 1907-1910 (2016) - [j12]Robert Leaman, Zhiyong Lu:
TaggerOne: joint named entity recognition and normalization with semi-Markov Models. Bioinform. 32(18): 2839-2846 (2016) - [c17]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Large-scale Semantic Indexing with Biomedical Ontologies. ICBO/BioCreative 2016 - 2015
- [j11]Robert Leaman, Ritu Khare, Zhiyong Lu:
Challenges in clinical natural language processing for automated disorder normalization. J. Biomed. Informatics 57: 28-37 (2015) - [j10]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): S2 (2015) - [j9]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) - [j8]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) - [c16]Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu:
Session Introduction. Pacific Symposium on Biocomputing 2015: 267-269 - 2014
- [j7]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) - [j6]Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu:
NCBI disease corpus: A resource for disease name recognition and concept normalization. J. Biomed. Informatics 47: 1-10 (2014) - [c15]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. BCB 2014: 138-146 - [c14]Robert Leaman, Zhiyong Lu:
Disease named entity recognition and normalization with DNorm. BCB 2014: 587 - [c13]Robert Leaman, Zhiyong Lu:
Automated Disease Normalization with Low Rank Approximations. BioNLP@ACL 2014: 24-28 - [c12]Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye:
Session introduction. Pacific Symposium on Biocomputing 2014: 312-315 - 2013
- [j5]Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu:
DNorm: disease name normalization with pairwise learning to rank. Bioinform. 29(22): 2909-2917 (2013) - [c11]Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu:
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. AMIA 2013 - [c10]Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu:
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA 2013 - [c9]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 - [c8]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: 368-372 - 2012
- [j4]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): 842-850 (2012) - 2011
- [j3]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:
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): S3 (2011) - [j2]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): S44-S47 (2011) - [c7]Ryan Sullivan, Robert Leaman, Graciela Gonzalez:
The DIEGO Lab Graph Based Gene Normalization System. ICMLA (2) 2011: 78-83 - 2010
- [j1]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): 481-494 (2010) - [c6]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: 117-125 - [c5]Siddhartha Jonnalagadda, Robert Leaman, Trevor Cohen, Graciela Gonzalez:
A Distributional Semantics Approach to Simultaneous Recognition of Multiple Classes of Named Entities. CICLing 2010: 224-235
2000 – 2009
- 2008
- [c4]Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez:
Inter-species normalization of gene mentions with GNAT. ECCB 2008: 126-132 - [c3]Robert Leaman, Graciela Gonzalez:
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition. Pacific Symposium on Biocomputing 2008: 652-663 - 2007
- [c2]Luis Tari, Phan Huy Tu, Barry Lumpkin, Robert Leaman, Graciela Gonzalez, Chitta Baral:
Passage Relevancy Through Semantic Relatedness. TREC 2007 - 2006
- [c1]Luis Tari, Graciela Gonzalez, Robert Leaman, Shawn Nikkila, Ryan Wendt, Chitta Baral:
ASU at TREC 2006 Genomics Track. TREC 2006
Coauthor Index
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