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Pretrained language models have shown success in many natural language processing tasks.
Pre-training with whole word masking for chinese bert
Yiming Cui, Wanxiang Che, Ting Liu, Bing Qin, Ziqing Yang, Shijin Wang, and Guoping Hu. 2019 · 1906
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Kepler: A unified model for knowledge embedding and pre-trained language representation
Xiaozhi Wang, Tianyu Gao, Zhaocheng Zhu, Zhiyuan Liu, Juanzi Li, and Jian Tang. 2019 · 1911
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Gene ontology: tool for the unification of biology
Michael Ashburner, Catherine A Ball, Judith A Blake, David Botstein, Heather Butler, J Michael Cherry, Allan P Davis, Kara Dolinski, Selina S Dwight, Janan T Eppig, et al. 2000 · 2000
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Medical subject headings (mesh)
Carolyn E Lipscomb. 2000 · 2000
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Snomed clinical terms: overview of the development process and project status
Michael Q Stearns, Colin Price, Kent A Spackman, and Amy Y Wang. 2001 · 2001
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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
Nigel Collier and Jin-Dong Kim. 2004 · 2004
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Medtype: Improving medical entity linking with semantic type prediction
Shikhar Vashishth, Rishabh Joshi, Ritam Dutt, Denis Newman-Griffis, and Carolyn Rose. 2020 · 2005
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Domain-specific language model pretraining for biomedical natural language processing
Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, and Hoifung Poon. 2020 · 2007
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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, Yu-Shi Lin, Roman Klinger, Christoph M Friedrich, Kuzman Ganchev, et al. 2008 · 2008
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Coder: Knowledge infused cross-lingual medical term embedding for term normalization
Zheng Yuan, Zhengyun Zhao, and Sheng Yu. 2020 · 2011
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Translating embeddings for modeling multi-relational data
Antoine Bordes, Nicolas Usunier, Alberto Garcia-Duran, Jason Weston, and Oksana Yakhnenko. 2013 · 2013
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The ddi corpus: An annotated corpus with pharmacological substances and drug–drug interactions
María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, and Thierry Declerck. 2013 · 2013
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Ncbi disease corpus: a resource for disease name recognition and concept normalization
Rezarta Islamaj Doğan, Robert Leaman, and Zhiyong Lu. 2014 · 2014
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Adam: A method for stochastic optimization
Diederik P Kingma and Jimmy Ba. 2014 · 2014
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Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research
Àlex Bravo, Janet Piñero, Núria Queralt-Rosinach, Michael Rautschka, and Laura I Furlong. 2015 · 2015
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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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Google’s neural machine translation system: Bridging the gap between human and machine translation
ScispaCy: Fast and robust models for biomedical natural language processing
Mark Neumann, Daniel King, Iz Beltagy, and Waleed Ammar. 2019 · 2019
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Transfer learning in biomedical natural language processing: An evaluation of BERT and ELMo on ten benchmarking datasets
Yifan Peng, Shankai Yan, and Zhiyong Lu. 2019 · 2019
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Knowledge enhanced contextual word representations
Matthew E. Peters, Mark Neumann, Robert Logan, Roy Schwartz, Vidur Joshi, Sameer Singh, and Noah A. Smith. 2019 · 2019
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Language models as knowledge bases?
Fabio Petroni, Tim Rocktäschel, Sebastian Riedel, Patrick Lewis, Anton Bakhtin, Yuxiang Wu, and Alexander Miller. 2019 · 2019
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ERNIE: Enhanced language representation with informative entities
Zhengyan Zhang, Xu Han, Zhiyuan Liu, Xin Jiang, Maosong Sun, and Qun Liu. 2019 · 2019
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Yonghui Wu, Mike Schuster, Zhifeng Chen, Quoc V Le, Mohammad Norouzi, Wolfgang Macherey, Maxim Krikun, Yuan Cao, Qin Gao, Klaus Macherey, et al. 2016 · 2016
Cited alongside, same era.
Overview of the biocreative vi chemical-protein interaction track
Martin Krallinger, Obdulia Rabal, Saber A Akhondi, Martın Pérez Pérez, Jesús Santamaría, Gael Pérez Rodríguez, et al. 2017 · 2017
Cited alongside, same era.
Decoupled weight decay regularization
Ilya Loshchilov and Frank Hutter. 2017 · 2017
Cited alongside, same era.
Deep contextualized word representations
Matthew Peters, Mark Neumann, Mohit Iyyer, Matt Gardner, Christopher Clark, Kenton Lee, and Luke Zettlemoyer. 2018 · 2018
Cited alongside, same era.
Leveraging biomedical resources in bi-lstm for drug-drug interaction extraction
B. Xu, X. Shi, Z. Zhao, and W. Zheng. 2018 · 2018
Cited alongside, same era.
Publicly available clinical BERT embeddings
Emily Alsentzer, John Murphy, William Boag, Wei-Hung Weng, Di Jindi, Tristan Naumann, and Matthew McDermott. 2019 · 2019
Cited alongside, same era.
SciBERT: A pretrained language model for scientific text
Iz Beltagy, Kyle Lo, and Arman Cohan. 2019 · 2019
Cited alongside, same era.
BERT: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2019 · 2019
Cited alongside, same era.
Entities as experts: Sparse memory access with entity supervision
Thibault Févry, Livio Baldini Soares, Nicholas FitzGerald, Eunsol Choi, and Tom Kwiatkowski. 2020 · 2020
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Infusing Disease Knowledge into BERT for Health Question Answering, Medical Inference and Disease Name Recognition
Yun He, Ziwei Zhu, Yin Zhang, Qin Chen, and James Caverlee. 2020 · 2020
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X-FACTR: Multilingual factual knowledge retrieval from pretrained language models
Zhengbao Jiang, Antonios Anastasopoulos, Jun Araki, Haibo Ding, and Graham Neubig. 2020 · 2020
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Biobert: a pre-trained biomedical language representation model for biomedical text mining
Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, and Jaewoo Kang. 2020 · 2020
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Pretrained language models for biomedical and clinical tasks: Understanding and extending the state-of-the-art
Patrick Lewis, Myle Ott, Jingfei Du, and Veselin Stoyanov. 2020 · 2020
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K-bert: Enabling language representation with knowledge graph
Weijie Liu, Peng Zhou, Zhe Zhao, Zhiruo Wang, Qi Ju, Haotang Deng, and Ping Wang. 2020 · 2020
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George Michalopoulos, Yuanxin Wang, Hussam Kaka, Helen Chen, and Alex Wong. 2020 · 2020
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BioMegatron: Larger biomedical domain language model
Hoo-Chang Shin, Yang Zhang, Evelina Bakhturina, Raul Puri, Mostofa Patwary, Mohammad Shoeybi, and Raghav Mani. 2020 · 2020
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