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BioBERT: a pre-trained biomedical language representation model for biomedical text mining

25 January 2019

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Papers citing "BioBERT: a pre-trained biomedical language representation model for biomedical text mining"

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Title
A Neural Topic-Attention Model for Medical Term Abbreviation Disambiguation Irene Li Michihiro Yasunaga Muhammed Yavuz Nuzumlali C. Caraballo S. Mahajan H. Krumholz Dragomir R. Radev 122 29 0 30 Oct 2019
Attention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels Tung Tran Ramakanth Kavuluru H. Kilicoglu GNN 153 5 0 28 Oct 2019
Keyphrase Extraction from Scholarly Articles as Sequence Labeling using Contextualized Embeddings Dhruva Sahrawat Debanjan Mahata Mayank Kulkarni Haimin Zhang Rakesh Gosangi Amanda Stent Agniv Sharma Yaman Kumar Singla R. Shah Roger Zimmermann 92 32 0 19 Oct 2019
Domain-Relevant Embeddings for Medical Question Similarity Clara H. McCreery Namit Katariya A. Kannan Manish Chablani X. Amatriain 127 9 0 09 Oct 2019
Extracting UMLS Concepts from Medical Text Using General and Domain-Specific Deep Learning ModelsConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Sicong Tang Feitong Tan Berry de Bruijn Muqun Li A. LaPlante P. Tan 147 14 0 03 Oct 2019
Cracking the Contextual Commonsense Code: Understanding Commonsense Reasoning Aptitude of Deep Contextual RepresentationsConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Jeff Da Jungo Kasai LRM 155 41 0 02 Oct 2019
BillSum: A Corpus for Automatic Summarization of US LegislationConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Anastassia Kornilova Vladimir Eidelman AILaw 249 177 0 01 Oct 2019
On the use of BERT for Neural Machine TranslationConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Stéphane Clinchant K. Jung Vassilina Nikoulina 195 96 0 27 Sep 2019
Biomedical relation extraction with pre-trained language representations and minimal task-specific architectureConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Ashok Thillaisundaram Theodosia Togia 96 17 0 26 Sep 2019
Does BERT Make Any Sense? Interpretable Word Sense Disambiguation with Contextualized EmbeddingsConference on Natural Language Processing (NLP), 2019 Gregor Wiedemann Steffen Remus Avi Chawla Chris Biemann 249 191 0 23 Sep 2019
Biomedical Mention Disambiguation using a Deep Learning ApproachACM International Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), 2019 Chih-Hsuan Wei Kyubum Lee Robert Leaman Zhiyong Lu MedIm 75 16 0 23 Sep 2019
Representation Learning for Electronic Health Records W. Weng Peter Szolovits 154 20 0 19 Sep 2019
Pre-trained Language Model for Biomedical Question Answering Wonjin Yoon Jinhyuk Lee Donghyeon Kim Minbyul Jeong Jaewoo Kang AI4MH 176 88 0 18 Sep 2019
SUPP.AI: Finding Evidence for Supplement-Drug Interactions Lucy Lu Wang Oyvind Tafjord Arman Cohan Sarthak Jain Sam Skjonsberg Carissa Schoenick Nick Botner Bridger Waleed Ammar 120 2 0 17 Sep 2019
Bridging the domain gap in cross-lingual document classification Guokun Lai Barlas Oğuz Yiming Yang Veselin Stoyanov VLM 206 16 0 16 Sep 2019
PubMedQA: A Dataset for Biomedical Research Question AnsweringConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Qiao Jin Bhuwan Dhingra Zhengping Liu William W. Cohen Xinghua Lu 719 1,255 0 13 Sep 2019
Measuring Domain Portability and ErrorPropagation in Biomedical QA Stefan Hosein D. Andor Ryan T. McDonald 124 9 0 12 Sep 2019
Scientific Discourse Tagging for Evidence ExtractionConference of the European Chapter of the Association for Computational Linguistics (EACL), 2019 Xiangci Li Gully A. Burns Nanyun Peng 212 5 0 10 Sep 2019
Pretrained AI Models: Performativity, Mobility, and Change Lav Varshney N. Keskar R. Socher 91 21 0 07 Sep 2019
Specializing Unsupervised Pretraining Models for Word-Level Semantic SimilarityInternational Conference on Computational Linguistics (COLING), 2019 Anne Lauscher Ivan Vulić Edoardo Ponti Anna Korhonen Goran Glavaš SSL 275 59 0 05 Sep 2019
Incorporating Domain Knowledge into Medical NLI using Knowledge GraphsConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Soumya Sharma Bishal Santra Abhik Jana Santosh T.Y.S.S Niloy Ganguly Pawan Goyal 182 25 0 31 Aug 2019
Learning to Transfer Learn: Reinforcement Learning-Based Selection for Adaptive Transfer Learning Linchao Zhu Sercan O. Arik Yezhou Yang Tomas Pfister 193 5 0 29 Aug 2019
HARE: a Flexible Highlighting Annotator for Ranking and ExplorationConference on Empirical Methods in Natural Language Processing (EMNLP), 2019 Denis R. Newman-Griffis Eric Fosler-Lussier 103 11 0 29 Aug 2019
Question Answering based Clinical Text Structuring Using Pre-trained Language ModelIEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2019 Jiahui Qiu Yangming Zhou Zhiyuan Ma Tong Ruan Jinlin Liu Jing Sun 162 4 0 19 Aug 2019
Learning Conceptual-Contextual Embeddings for Medical TextAAAI Conference on Artificial Intelligence (AAAI), 2019 Xiao Zhang Dejing Dou Ji Wu BDL 214 17 0 16 Aug 2019
BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks Shreyas Sharma Ron Daniel 112 33 0 13 Aug 2019
Understanding Spatial Language in Radiology: Representation Framework, Annotation, and Spatial Relation Extraction from Chest X-ray Reports using Deep LearningJournal of Biomedical Informatics (JBI), 2019 Surabhi Datta Yuqi Si Laritza M. Rodriguez S. E. Shooshan Dina Demner-Fushman Kirk Roberts MedIm 160 36 0 13 Aug 2019
TAPER: Time-Aware Patient EHR RepresentationIEEE journal of biomedical and health informatics (IEEE JBHI), 2019 Sajad Darabi Mohammad Kachuee Shayan Fazeli Majid Sarrafzadeh 173 63 0 11 Aug 2019
BERT-based Ranking for Biomedical Entity Normalization Zongcheng Ji Qiang Wei Hua Xu OOD MedIm 134 137 0 09 Aug 2019
Attention-Wrapped Hierarchical BLSTMs for DDI Extraction Vahab Mostafapour Oguz Dikenelli BDL 84 7 0 31 Jul 2019
Lexical Simplification with Pretrained Encoders Jipeng Qiang Yun Li Yi Zhu Yunhao Yuan Xindong Wu 344 11 0 14 Jul 2019
UW-BHI at MEDIQA 2019: An Analysis of Representation Methods for Medical Natural Language Inference William R. Kearns Wilson Lau Jason Thomas 106 3 0 09 Jul 2019
Enhancing PIO Element Detection in Medical Text Using Contextualized Embedding H. Mezaoui A. Gontcharov Isuru Gunasekara 59 5 0 26 Jun 2019
REflex: Flexible Framework for Relation Extraction in Multiple Domains Geeticka Chauhan Matthew B. A. McDermott Peter Szolovits 293 12 0 19 Jun 2019
Surf at MEDIQA 2019: Improving Performance of Natural Language Inference in the Clinical Domain by Adopting Pre-trained Language Model Jiin Nam Seunghyun Yoon Kyomin Jung LM&MA 122 3 0 19 Jun 2019
Transfer Learning for Causal Sentence Detection Manolis Kyriakakis Ion Androutsopoulos Joan Ginés i Ametllé Artur Saudabayev 143 28 0 18 Jun 2019
IITP at MEDIQA 2019: Systems Report for Natural Language Inference, Question Entailment and Question Answering Dibyanayan Bandyopadhyay Baban Gain Tanik Saikh Asif Ekbal 67 4 0 14 Jun 2019
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets Yifan Peng Shankai Yan Zhiyong Lu LM&MA AI4MH 345 925 0 13 Jun 2019
Using Neural Networks for Relation Extraction from Biomedical Literature Diana Sousa Andre Lamurias Francisco M. Couto 130 12 0 27 May 2019
MetaPred: Meta-Learning for Clinical Risk Prediction with Limited Patient Electronic Health RecordsKnowledge Discovery and Data Mining (KDD), 2019 Xi Sheryl Zhang Fengyi Tang H. H. Dodge Jiayu Zhou Fei Wang 102 114 0 08 May 2019
ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission Kexin Huang Jaan Altosaar Rajesh Ranganath OOD 353 1,099 0 10 Apr 2019
Publicly Available Clinical BERT Embeddings Emily Alsentzer John R. Murphy Willie Boag W. Weng Di Jin Tristan Naumann Matthew B. A. McDermott AI4MH 631 2,314 0 06 Apr 2019
Unsupervised Domain Adaptation of Contextualized Embeddings for Sequence Labeling Xiaochuang Han Jacob Eisenstein 121 20 0 04 Apr 2019
Probing Biomedical Embeddings from Language Models Qiao Jin Bhuwan Dhingra William W. Cohen Xinghua Lu 190 123 0 03 Apr 2019
A Silver Standard Corpus of Human Phenotype-Gene Relations Diana Sousa Andre Lamurias Francisco M. Couto 113 37 0 26 Mar 2019
SciBERT: A Pretrained Language Model for Scientific Text Iz Beltagy Kyle Lo Arman Cohan 515 3,437 0 26 Mar 2019
Enhancing Clinical Concept Extraction with Contextual Embeddings Yuqi Si Jingqi Wang Hua Xu Kirk Roberts AI4MH 354 314 0 22 Feb 2019
NSEEN: Neural Semantic Embedding for Entity Normalization Shobeir Fakhraei Joel Mathew J. Ambite 124 19 0 19 Nov 2018
Advancing PICO Element Detection in Biomedical Text via Deep Neural Networks Di Jin Peter Szolovits 192 35 0 30 Oct 2018