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Despite recent advances in natural language processing, many statistical models for processing text perform extremely poorly under domain shift.
Structural scaffolds for citation intent classification in scientific publications
Arman Cohan, Waleed Ammar, Madeleine van Zuylen, and Field Cady. 2019 · 1904
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Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program
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A simple algorithm for identifying abbreviation definitions in biomedical text
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GENIA corpus - a semantically annotated corpus for bio-textmining
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The unified medical language system (UMLS): integrating biomedical terminology
Olivier Bodenreider. 2004 · 2004
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Introduction to the bio-entity recognition task at JNLPBA
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Bidirectional inference with the easiest-first strategy for tagging sequence data
Yoshimasa Tsuruoka and Jun’ichi Tsujii. 2005 · 2005
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Automatically adapting an NLP core engine to the biology domain
Ekaterina Buyko, Joachim Wermter, Michael Poprat, and Udo Hahn. 2006 · 2006
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OntoNotes: The 90% solution
Eduard H. Hovy, Mitchell P. Marcus, Martha Palmer, Lance A. Ramshaw, and Ralph M. Weischedel. 2006 · 2006
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Reranking and self-training for parser adaptation
David McClosky, Eugene Charniak, and Mark Johnson. 2006 · 2006
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Self-training for biomedical parsing
David McClosky and Eugene Charniak. 2008 · 2008
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Adapting a lexicalized-grammar parser to contrasting domains
Laura Rimell and Stephen Clark. 2008 · 2008
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Overview of BioCreative II gene mention recognition
Larry Smith, Lorraine K. Tanabe, Rie Johnson nee Ando, Cheng-Ju Kuo, I-Fang Chung, Chun-Nan Hsu, Y Lin, Roman Klinger, Christoph M. Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu, Barry Haddow, Craig A. Struble, Richard J. Povinelli, Andreas Vlachos, William A. Baumgartner, Lawrence E. Hunter, Bob Carpenter, Richard Tzong-Han Tsai, Hong-Jie Dai, Feng Liu, Yifei Chen, Chengjie Sun, Sophia Katrenko, Pieter Adriaans, Christian Blaschke, Rafael Torres, Mariana Neves, Preslav Nakov, Anna Divoli, Manuel Maña-López, Jacinto Mata, and W. John Wilbur. 2008 · 2008
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LINNAEUS: A species name identification system for biomedical literature
Martin Gerner, Goran Nenadic, and Casey M. Bergman. 2009 · 2009
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Mayo clinical text analysis and knowledge extraction system (cTAKES): architecture, component evaluation and applications
Guergana K. Savova, James J. Masanz, Philip V. Ogren, Jiaping Zheng, Sunghwan Sohn, Karin Kipper Schuler, and Christopher G. Chute. 2010 · 2010
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Concept annotation in the CRAFT corpus
Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner, K. Bretonnel Cohen, Karin M. Verspoor, Judith A. Blake, and Lawrence Hunter. 2011 · 2011
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OntoNotes: A large training corpus for enhanced processing
Ralph Weischedel, Eduard Hovy, Martha Palmer, Mitch Marcus, Robert Belvin adn Sameer Pradhan, Lance Ramshaw, and Nianwen Xue. 2011 · 2011
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A dynamic oracle for arc-eager dependency parsing
Yoav Goldberg and Joakim Nivre. 2012 · 2012
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Overview of the cancer genetics and pathway curation tasks of BioNLP shared task 2013
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun’ichi Tsujii, and Sophia Ananiadou. 2015 · 2013
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BioCreative V CDR task corpus: a resource for chemical disease relation extraction
Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, and Zhiyong Lu. 2016 · 2016
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Enhanced english universal dependencies: An improved representation for natural language understanding tasks
Sebastian Schuster and Christopher D. Manning. 2016 · 2016
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Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, and Zhiyong Lu. 2016 · 2016
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Stack-propagation: Improved representation learning for syntax
Yuan Zhang and David I Weiss. 2016 · 2016
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A neural network multi-task learning approach to biomedical named entity recognition
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Growth rates of modern science: A bibliometric analysis
Lutz Bornmann and Rüdiger Mutz. 2014 · 2014
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NCBI disease corpus: A resource for disease name recognition and concept normalization
Rezarta Islamaj Dogan, Robert Leaman, and Zhiyong Lu. 2014 · 2014
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Literome: PubMed-scale genomic knowledge base in the cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, and David Heckerman. 2014 · 2014
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Anatomical entity mention recognition at literature scale
Sampo Pyysalo and Sophia Ananiadou. 2014 · 2014
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CHEMDNER: The drugs and chemical names extraction challenge
Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzábal, and Alfonso Valencia. 2015 · 2015
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Distant supervision for cancer pathway extraction from text
Hoifung Poon, Kristina Toutanova, and Chris Quirk. 2015 · 2015
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Deep biaffine attention for neural dependency parsing
Timothy Dozat and Christopher D. Manning. 2016 · 2016
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Gamal K. O. Crichton, Sampo Pyysalo, Billy Chiu, and Anna Korhonen. 2017 · 2017
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MetaMap Lite: an evaluation of a new Java implementation of MetaMap
Dina Demner-Fushman, Willie J. Rogers, and Alan R. Aronson. 2017 · 2017
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spaCy 2: Natural language understanding with bloom embeddings, convolutional neural networks and incremental parsing
Matthew Honnibal and Ines Montani. 2017 · 2017
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Effective use of bidirectional language modeling for transfer learning in biomedical named entity recognition
Devendra Singh Sachan, Pengtao Xie, Mrinmaya Sachan, and Eric P. Xing. 2017 · 2017
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Construction of the literature graph in semantic scholar
Waleed Ammar, Dirk Groeneveld, Chandra Bhagavatula, Iz Beltagy, Miles Crawford, Doug Downey, Jason Dunkelberger, Ahmed Elgohary, Sergey Feldman, Vu Ha, Rodney Kinney, Sebastian Kohlmeier, Kyle Lo, Tyler Murray, Hsu-Han Ooi, Matthew E. Peters, Joanna Power, Sam Skjonsberg, Lucy Lu Wang, Chris Wilhelm, Zheng Yuan, Madeleine van Zuylen, and Oren Etzioni. 2018 · 2018
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Extending a parser to distant domains using a few dozen partially annotated examples
Vidur Joshi, Matthew Peters, and Mark Hopkins. 2018 · 2018
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Hierarchical losses and new resources for fine-grained entity typing and linking
Shikhar Murty, Patrick Verga, Luke Vilnis, Irena Radovanovic, and Andrew McCallum. 2018 · 2018
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From POS tagging to dependency parsing for biomedical event extraction
Dat Quoc Nguyen and Karin Verspoor. 2018 · 2018
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Large-scale automated machine reading discovers new cancer-driving mechanisms
Marco Antonio Valenzuela-Escarcega, Ozgun Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir, and Clayton T. Morrison. 2018 · 2018
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Cross-type biomedical named entity recognition with deep multi-task learning
Xuan Wang, Yu Zhang, Xiang Ren, Yuhao Zhang, Marinka Zitnik, Jingbo Shang, Curtis P. Langlotz, and Jiawei Han. 2018 · 2018
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