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Objective: The majority of detailed patient information in real-world data (RWD) is only consistently available in free-text clinical documents.
Accelerating literature curation with text-mining tools: a case study of using pubtator to curate genes in pubmed abstracts
Chih-Hsuan Wei, Bethany R Harris, Donghui Li, Tanya Z Berardini, Eva Huala, Hung-Yu Kao, and Zhiyong Lu · 2012
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Distributed representations of words and phrases and their compositionality
Tomas Mikolov, Ilya Sutskever, Kai Chen, Greg Corrado, and Jeffrey Dean · 2013
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Learning phrase representations using RNN encoder–decoder for statistical machine translation
Kyunghyun Cho, Bart van Merriënboer, Caglar Gulcehre, Dzmitry Bahdanau, Fethi Bougares, Holger Schwenk, and Yoshua Bengio · 2014
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GloVe: Global vectors for word representation
Jeffrey Pennington, Richard Socher, and Christopher Manning · 2014
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Data programming: Creating large training sets, quickly
Alexander J Ratner, Christopher M De Sa, Sen Wu, Daniel Selsam, and Christopher Ré · 2016
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Neural machine translation of rare words with subword units
Rico Sennrich, Barry Haddow, and Alexandra Birch · 2016
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Hierarchical Attention Networks for Document Classification
Zichao Yang, Diyi Yang, Chris Dyer, Xiaodong He, Alex Smola, and Eduard Hovy · 2016
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Natural language processing in oncology: A review
Wen-Wai Yim, Meliha Yetisgen, William P Harris, and Sharon W Kwan · 2016
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
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Deriving machine attention from human rationales
Yujia Bao, Shiyu Chang, Mo Yu, and Regina Barzilay · 2018
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SentencePiece: A simple and language independent subword tokenizer and detokenizer for neural text processing
Taku Kudo and John Richardson · 2018
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Deep contextualized word representations
Matthew E. Peters, Mark Neumann, Mohit Iyyer, Matt Gardner, Christopher Clark, Kenton Lee, and Luke Zettlemoyer · 2018
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Deep probabilistic logic: A unifying framework for indirect supervision
Hai Wang and Hoifung Poon · 2018
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Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova · 2019
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Classifying cancer pathology reports with hierarchical self-attention networks
Shang Gao, John X. Qiu, Mohammed Alawad, Jacob D. Hinkle, Noah Schaefferkoetter, Hong Jun Yoon, Blair Christian, Paul A. Fearn, Lynne Penberthy, Xiao Cheng Wu, Linda Coyle, Georgia Tourassi, and Arvind Ramanathan · 2019
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Attention is not explanation
Sarthak Jain and Byron C. Wallace · 2019
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Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes from Radiology Reports
Deep learning in clinical natural language processing: a methodical review
Stephen Wu, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, and Hua Xu · 2020
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Layoutlm: Pre-training of text and layout for document image understanding
Yiheng Xu, Minghao Li, Lei Cui, Shaohan Huang, Furu Wei, and Ming Zhou · 2020
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Clinically relevant pretraining is all you need
Oliver J Bear Don’t Walk IV, Tony Sun, Adler Perotte, and Noémie Elhadad · 2021
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Limitations of Transformers on Clinical Text Classification
Shang Gao, Mohammed Alawad, Michael Todd Young, John Gounley, Noah Schaefferkoetter, Hong Jun Yoon, Xiao Cheng Wu, Eric B. Durbin, Jennifer Doherty, Antoinette Stroup, Linda Coyle, and Georgia D. Tourassi · 2021
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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 · 2021
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Kenneth L. Kehl, Haitham Elmarakeby, Mizuki Nishino, Eliezer M. Van Allen, Eva M. Lepisto, Michael J. Hassett, Bruce E. Johnson, and Deborah Schrag · 2019
Cited alongside, same era.
Roberta: A robustly optimized bert pretraining approach
Yinhan Liu, Myle Ott, Naman Goyal, Jingfei Du, Mandar Joshi, Danqi Chen, Omer Levy, Mike Lewis, Luke Zettlemoyer, and Veselin Stoyanov · 2019
Cited alongside, same era.
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
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Enhancing clinical BERT embedding using a biomedical knowledge base
Boran Hao, Henghui Zhu, and Ioannis Paschalidis · 2020
Cited alongside, same era.
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
Cited alongside, same era.
Opportunities and challenges in using real-world data for health care
Vivek A. Rudrapatna and Atul J. Butte · 2020
Cited alongside, same era.
Self-supervised self-supervision by combining deep learning and probabilistic logic
Hunter Lang and Hoifung Poon · 2021
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Natural language processing enabling COVID-19 predictive analytics to support data-driven patient advising and pooled testing
Stéphane M Meystre, Paul M Heider, Youngjun Kim, Matthew Davis, Jihad Obeid, James Madory, and Alexander V Alekseyenko · 2021
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Natural language inference for curation of structured clinical registries from unstructured text
Bethany Percha, Kereeti Pisapati, Cynthia Gao, and Hank Schmidt · 2021
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Knowledge-rich self-supervised entity linking
Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, and Hoifung Poon · 2021
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Modular self-supervision for document-level relation extraction
Sheng Zhang, Cliff Wong, Naoto Usuyama, Sarthak Jain, Tristan Naumann, and Hoifung Poon · 2021
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Distantly supervised biomedical relation extraction using piecewise attentive convolutional neural network and reinforcement learning
Tiantian Zhu, Yang Qin, Yang Xiang, Baotian Hu, Qingcai Chen, and Weihua Peng · 2021
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