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Pre-trained Language Models in Biomedical Domain: A Systematic Survey

11 October 2021

Papers citing "Pre-trained Language Models in Biomedical Domain: A Systematic Survey"

50 / 223 papers shown

Title
How to Pre-Train Your Model? Comparison of Different Pre-Training Models for Biomedical Question Answering S. Kamath Brigitte Grau Yue Ma AI4MH 26 7 0 02 Nov 2019
DialoGPT: Large-Scale Generative Pre-training for Conversational Response Generation Yizhe Zhang Siqi Sun Michel Galley Yen-Chun Chen Chris Brockett Xiang Gao Jianfeng Gao Jingjing Liu W. Dolan VLM 194 1,527 0 01 Nov 2019
BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension M. Lewis Yinhan Liu Naman Goyal Marjan Ghazvininejad Abdel-rahman Mohamed Omer Levy Veselin Stoyanov Luke Zettlemoyer AIMat VLM 264 10,851 0 29 Oct 2019
Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer Colin Raffel Noam M. Shazeer Adam Roberts Katherine Lee Sharan Narang Michael Matena Yanqi Zhou Wei Li Peter J. Liu AIMat 470 20,317 0 23 Oct 2019
DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter Victor Sanh Lysandre Debut Julien Chaumond Thomas Wolf 255 7,547 0 02 Oct 2019
Biomedical relation extraction with pre-trained language representations and minimal task-specific architecture Ashok Thillaisundaram Theodosia Togia 50 17 0 26 Sep 2019
ALBERT: A Lite BERT for Self-supervised Learning of Language Representations Zhenzhong Lan Mingda Chen Sebastian Goodman Kevin Gimpel Piyush Sharma Radu Soricut SSL AIMat 373 6,467 0 26 Sep 2019
TinyBERT: Distilling BERT for Natural Language Understanding Xiaoqi Jiao Yichun Yin Lifeng Shang Xin Jiang Xiao Chen Linlin Li F. Wang Qun Liu VLM 111 1,869 0 23 Sep 2019
Representation Learning for Electronic Health Records W. Weng Peter Szolovits 65 19 0 19 Sep 2019
Pre-trained Language Model for Biomedical Question Answering Wonjin Yoon Jinhyuk Lee Donghyeon Kim Minbyul Jeong Jaewoo Kang AI4MH 62 86 0 18 Sep 2019
PubMedQA: A Dataset for Biomedical Research Question Answering Qiao Jin Bhuwan Dhingra Zhengping Liu William W. Cohen Xinghua Lu 390 912 0 13 Sep 2019
Entity, Relation, and Event Extraction with Contextualized Span Representations David Wadden Ulme Wennberg Yi Luan Hannaneh Hajishirzi 74 590 0 08 Sep 2019
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records Qingyu Chen Jingcheng Du Sun Kim W. Wilbur Zhiyong Lu 42 24 0 06 Sep 2019
Language Models as Knowledge Bases? Fabio Petroni Tim Rocktaschel Patrick Lewis A. Bakhtin Yuxiang Wu Alexander H. Miller Sebastian Riedel KELM AI4MH 576 2,674 0 03 Sep 2019
Incorporating Domain Knowledge into Medical NLI using Knowledge Graphs Soumya Sharma Bishal Santra Abhik Jana Santosh T.Y.S.S Niloy Ganguly Pawan Goyal 38 23 0 31 Aug 2019
Learning to Infer Entities, Properties and their Relations from Clinical Conversations Nan Du Mingqiu Wang Linh Tran Gang Li Izhak Shafran LRM 79 32 0 30 Aug 2019
A Survey on Bias and Fairness in Machine Learning Ninareh Mehrabi Fred Morstatter N. Saxena Kristina Lerman Aram Galstyan SyDa FaML 571 4,368 0 23 Aug 2019
Federated Learning: Challenges, Methods, and Future Directions Tian Li Anit Kumar Sahu Ameet Talwalkar Virginia Smith FedML 129 4,540 0 21 Aug 2019
Fine-tuning BERT for Joint Entity and Relation Extraction in Chinese Medical Text Kui Xue Yangming Zhou Zhiyuan Ma Tong Ruan Huanhuan Zhang Ping He 57 90 0 21 Aug 2019
LXMERT: Learning Cross-Modality Encoder Representations from Transformers Hao Hao Tan Joey Tianyi Zhou VLM MLLM 250 2,488 0 20 Aug 2019
BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks Shreyas Sharma Ron Daniel 24 33 0 13 Aug 2019
VisualBERT: A Simple and Performant Baseline for Vision and Language Liunian Harold Li Mark Yatskar Da Yin Cho-Jui Hsieh Kai-Wei Chang VLM 153 1,963 0 09 Aug 2019
Clustering of Deep Contextualized Representations for Summarization of Biomedical Texts M. Moradi Matthias Samwald 21 7 0 06 Aug 2019
RoBERTa: A Robustly Optimized BERT Pretraining Approach Yinhan Liu Myle Ott Naman Goyal Jingfei Du Mandar Joshi Danqi Chen Omer Levy M. Lewis Luke Zettlemoyer Veselin Stoyanov AIMat 677 24,541 0 26 Jul 2019
BEHRT: Transformer for Electronic Health Records Yikuan Li Shishir Rao J. R. A. Solares A. Hassaine D. Canoy Yajie Zhu K. Rahimi G. Salimi-Khorshidi OOD 110 464 0 22 Jul 2019
Mitigating Gender Bias in Natural Language Processing: Literature Review Tony Sun Andrew Gaut Shirlyn Tang Yuxin Huang Mai Elsherief Jieyu Zhao Diba Mirza E. Belding-Royer Kai-Wei Chang William Yang Wang AI4CE 108 562 0 21 Jun 2019
XLNet: Generalized Autoregressive Pretraining for Language Understanding Zhilin Yang Zihang Dai Yiming Yang J. Carbonell Ruslan Salakhutdinov Quoc V. Le AI4CE 236 8,447 0 19 Jun 2019
Evaluating Protein Transfer Learning with TAPE Roshan Rao Nicholas Bhattacharya Neil Thomas Yan Duan Xi Chen John F. Canny Pieter Abbeel Yun S. Song SSL 94 807 0 19 Jun 2019
SEntNet: Source-aware Recurrent Entity Network for Dialogue Response Selection Jiahuan Pei Arent Stienstra Julia Kiseleva Maarten de Rijke 38 6 0 16 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 71 845 0 13 Jun 2019
Extracting Symptoms and their Status from Clinical Conversations Nan Du Kai Chen Anjuli Kannan Linh Tran Yuhui Chen Izhak Shafran 46 68 0 05 Jun 2019
Pre-training of Graph Augmented Transformers for Medication Recommendation Junyuan Shang Tengfei Ma Cao Xiao Jimeng Sun 70 291 0 02 Jun 2019
How to Fine-Tune BERT for Text Classification? Chi Sun Xipeng Qiu Yige Xu Xuanjing Huang 87 1,526 0 14 May 2019
BERTScore: Evaluating Text Generation with BERT Tianyi Zhang Varsha Kishore Felix Wu Kilian Q. Weinberger Yoav Artzi 352 5,860 0 21 Apr 2019
ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission Kexin Huang Jaan Altosaar Rajesh Ranganath OOD 118 909 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 172 1,983 0 06 Apr 2019
Probing Biomedical Embeddings from Language Models Qiao Jin Bhuwan Dhingra William W. Cohen Xinghua Lu 65 116 0 03 Apr 2019
SciBERT: A Pretrained Language Model for Scientific Text Iz Beltagy Kyle Lo Arman Cohan 168 2,985 0 26 Mar 2019
SECNLP: A Survey of Embeddings in Clinical Natural Language Processing Katikapalli Subramanyam Kalyan S. Sangeetha 47 83 0 04 Mar 2019
Enhancing Clinical Concept Extraction with Contextual Embeddings Yuqi Si Jingqi Wang Hua Xu Kirk Roberts AI4MH 52 291 0 22 Feb 2019
Learning protein sequence embeddings using information from structure Tristan Bepler Bonnie Berger 76 290 0 22 Feb 2019
Federated Machine Learning: Concept and Applications Qiang Yang Yang Liu Tianjian Chen Yongxin Tong FedML 78 2,322 0 13 Feb 2019
End-to-End Knowledge-Routed Relational Dialogue System for Automatic Diagnosis Lin Xu Qixian Zhou Ke Gong Xiaodan Liang Jianheng Tang Liang Lin MedIm 91 173 0 30 Jan 2019
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 Jaewoo Kang OOD 178 5,672 0 25 Jan 2019
MIMIC-CXR-JPG, a large publicly available database of labeled chest radiographs Alistair E. W. Johnson Tom Pollard Nathaniel R. Greenbaum M. Lungren Chih-ying Deng Yifan Peng Zhiyong Lu R. Mark Seth Berkowitz Steven Horng MedIm 98 820 0 21 Jan 2019
Unsupervised Multimodal Representation Learning across Medical Images and Reports T. Hsu W. Weng Willie Boag Matthew B. A. McDermott Peter Szolovits SSL 56 35 0 21 Nov 2018
Clinical Concept Extraction with Contextual Word Embedding Henghui Zhu I. Paschalidis A. Tahmasebi 136 76 0 24 Oct 2018
BioSentVec: creating sentence embeddings for biomedical texts Qingyu Chen Yifan Peng Zhiyong Lu 62 214 0 22 Oct 2018
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.8K 95,175 0 11 Oct 2018
emrQA: A Large Corpus for Question Answering on Electronic Medical Records Anusri Pampari Preethi Raghavan Jennifer J. Liang Jian-wei Peng 63 205 0 03 Sep 2018