Proceedings of the 20th Workshop on Biomedical Language Processing

Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor 2021-06 Association for Computational Linguistics Online text conference publication bionlp-2021-biomedical https://aclanthology.org/2021.bionlp-1.0/ Improving BERT Model Using Contrastive Learning for Biomedical Relation Extraction Peng Su author Yifan Peng author K Vijay-Shanker author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication su-etal-2021-improving 10.18653/v1/2021.bionlp-1.1 https://aclanthology.org/2021.bionlp-1.1/ 2021-06 1 10 Triplet-Trained Vector Space and Sieve-Based Search Improve Biomedical Concept Normalization Dongfang Xu author Steven Bethard author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication xu-bethard-2021-triplet 10.18653/v1/2021.bionlp-1.2 https://aclanthology.org/2021.bionlp-1.2/ 2021-06 11 22 Scalable Few-Shot Learning of Robust Biomedical Name Representations Pieter Fivez author Simon Suster author Walter Daelemans author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication fivez-etal-2021-scalable 10.18653/v1/2021.bionlp-1.3 https://aclanthology.org/2021.bionlp-1.3/ 2021-06 23 29 SAFFRON: tranSfer leArning For Food-disease RelatiOn extractioN Gjorgjina Cenikj author Tome Eftimov author Barbara Koroušić Seljak author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication cenikj-etal-2021-saffron 10.18653/v1/2021.bionlp-1.4 https://aclanthology.org/2021.bionlp-1.4/ 2021-06 30 40 Are we there yet? Exploring clinical domain knowledge of BERT models Madhumita Sushil author Simon Suster author Walter Daelemans author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication sushil-etal-2021-yet 10.18653/v1/2021.bionlp-1.5 https://aclanthology.org/2021.bionlp-1.5/ 2021-06 41 53 Towards BERT-based Automatic ICD Coding: Limitations and Opportunities Damian Pascual author Sandro Luck author Roger Wattenhofer author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication pascual-etal-2021-towards 10.18653/v1/2021.bionlp-1.6 https://aclanthology.org/2021.bionlp-1.6/ 2021-06 54 63 emrKBQA: A Clinical Knowledge-Base Question Answering Dataset Preethi Raghavan author Jennifer J Liang author Diwakar Mahajan author Rachita Chandra author Peter Szolovits author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication raghavan-etal-2021-emrkbqa 10.18653/v1/2021.bionlp-1.7 https://aclanthology.org/2021.bionlp-1.7/ 2021-06 64 73 Overview of the MEDIQA 2021 Shared Task on Summarization in the Medical Domain Asma Ben Abacha author Yassine Mrabet author Yuhao Zhang author Chaitanya Shivade author Curtis Langlotz author Dina Demner-Fushman author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication ben-abacha-etal-2021-overview 10.18653/v1/2021.bionlp-1.8 https://aclanthology.org/2021.bionlp-1.8/ 2021-06 74 85 WBI at MEDIQA 2021: Summarizing Consumer Health Questions with Generative Transformers Mario Sänger author Leon Weber author Ulf Leser author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication sanger-etal-2021-wbi 10.18653/v1/2021.bionlp-1.9 https://aclanthology.org/2021.bionlp-1.9/ 2021-06 86 95 paht_nlp @ MEDIQA 2021: Multi-grained Query Focused Multi-Answer Summarization Wei Zhu author Yilong He author Ling Chai author Yunxiao Fan author Yuan Ni author Guotong Xie author Xiaoling Wang author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication zhu-etal-2021-paht 10.18653/v1/2021.bionlp-1.10 https://aclanthology.org/2021.bionlp-1.10/ 2021-06 96 102 BDKG at MEDIQA 2021: System Report for the Radiology Report Summarization Task Songtai Dai author Quan Wang author Yajuan Lyu author Yong Zhu author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication dai-etal-2021-bdkg 10.18653/v1/2021.bionlp-1.11 https://aclanthology.org/2021.bionlp-1.11/ 2021-06 103 111 damo_nlp at MEDIQA 2021: Knowledge-based Preprocessing and Coverage-oriented Reranking for Medical Question Summarization Yifan He author Mosha Chen author Songfang Huang author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication he-etal-2021-damo 10.18653/v1/2021.bionlp-1.12 https://aclanthology.org/2021.bionlp-1.12/ 2021-06 112 118 Stress Test Evaluation of Biomedical Word Embeddings Vladimir Araujo author Andrés Carvallo author Carlos Aspillaga author Camilo Thorne author Denis Parra author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication araujo-etal-2021-stress 10.18653/v1/2021.bionlp-1.13 https://aclanthology.org/2021.bionlp-1.13/ 2021-06 119 125 BLAR: Biomedical Local Acronym Resolver William Hogan author Yoshiki Vazquez Baeza author Yannis Katsis author Tyler Baldwin author Ho-Cheol Kim author Chun-Nan Hsu author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication hogan-etal-2021-blar 10.18653/v1/2021.bionlp-1.14 https://aclanthology.org/2021.bionlp-1.14/ 2021-06 126 130 Claim Detection in Biomedical Twitter Posts Amelie Wührl author Roman Klinger author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication wuhrl-klinger-2021-claim 10.18653/v1/2021.bionlp-1.15 https://aclanthology.org/2021.bionlp-1.15/ 2021-06 131 142 BioELECTRA:Pretrained Biomedical text Encoder using Discriminators Kamal raj Kanakarajan author Bhuvana Kundumani author Malaikannan Sankarasubbu author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication kanakarajan-etal-2021-bioelectra 10.18653/v1/2021.bionlp-1.16 https://aclanthology.org/2021.bionlp-1.16/ 2021-06 143 154 Word centrality constrained representation for keyphrase extraction Zelalem Gero author Joyce Ho author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication gero-ho-2021-word 10.18653/v1/2021.bionlp-1.17 https://aclanthology.org/2021.bionlp-1.17/ 2021-06 155 161 End-to-end Biomedical Entity Linking with Span-based Dictionary Matching Shogo Ujiie author Hayate Iso author Shuntaro Yada author Shoko Wakamiya author Eiji Aramaki author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication ujiie-etal-2021-end 10.18653/v1/2021.bionlp-1.18 https://aclanthology.org/2021.bionlp-1.18/ 2021-06 162 167 Word-Level Alignment of Paper Documents with their Electronic Full-Text Counterparts Mark-Christoph Müller author Sucheta Ghosh author Ulrike Wittig author Maja Rey author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication muller-etal-2021-word 10.18653/v1/2021.bionlp-1.19 https://aclanthology.org/2021.bionlp-1.19/ 2021-06 168 179 Improving Biomedical Pretrained Language Models with Knowledge Zheng Yuan author Yijia Liu author Chuanqi Tan author Songfang Huang author Fei Huang author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication yuan-etal-2021-improving 10.18653/v1/2021.bionlp-1.20 https://aclanthology.org/2021.bionlp-1.20/ 2021-06 180 190 EntityBERT: Entity-centric Masking Strategy for Model Pretraining for the Clinical Domain Chen Lin author Timothy Miller author Dmitriy Dligach author Steven Bethard author Guergana Savova author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication lin-etal-2021-entitybert 10.18653/v1/2021.bionlp-1.21 https://aclanthology.org/2021.bionlp-1.21/ 2021-06 191 201 Contextual explanation rules for neural clinical classifiers Madhumita Sushil author Simon Suster author Walter Daelemans author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication sushil-etal-2021-contextual 10.18653/v1/2021.bionlp-1.22 https://aclanthology.org/2021.bionlp-1.22/ 2021-06 202 212 Exploring Word Segmentation and Medical Concept Recognition for Chinese Medical Texts Yang Liu author Yuanhe Tian author Tsung-Hui Chang author Song Wu author Xiang Wan author Yan Song author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication liu-etal-2021-exploring 10.18653/v1/2021.bionlp-1.23 https://aclanthology.org/2021.bionlp-1.23/ 2021-06 213 220 BioM-Transformers: Building Large Biomedical Language Models with BERT, ALBERT and ELECTRA Sultan Alrowili author K Vijay-Shanker author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication alrowili-shanker-2021-biom 10.18653/v1/2021.bionlp-1.24 https://aclanthology.org/2021.bionlp-1.24/ 2021-06 221 227 Semi-Supervised Language Models for Identification of Personal Health Experiential from Twitter Data: A Case for Medication Effects Minghao Zhu author Keyuan Jiang author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication zhu-jiang-2021-semi 10.18653/v1/2021.bionlp-1.25 https://aclanthology.org/2021.bionlp-1.25/ 2021-06 228 237 Context-aware query design combines knowledge and data for efficient reading and reasoning Emilee Holtzapple author Brent Cochran author Natasa Miskov-Zivanov author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication holtzapple-etal-2021-context 10.18653/v1/2021.bionlp-1.26 https://aclanthology.org/2021.bionlp-1.26/ 2021-06 238 246 Measuring the relative importance of full text sections for information retrieval from scientific literature. Lana Yeganova author Won Gyu Kim author Donald Comeau author W John Wilbur author Zhiyong Lu author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication yeganova-etal-2021-measuring 10.18653/v1/2021.bionlp-1.27 https://aclanthology.org/2021.bionlp-1.27/ 2021-06 247 256 UCSD-Adobe at MEDIQA 2021: Transfer Learning and Answer Sentence Selection for Medical Summarization Khalil Mrini author Franck Dernoncourt author Seunghyun Yoon author Trung Bui author Walter Chang author Emilia Farcas author Ndapa Nakashole author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication mrini-etal-2021-ucsd 10.18653/v1/2021.bionlp-1.28 https://aclanthology.org/2021.bionlp-1.28/ 2021-06 257 262 ChicHealth @ MEDIQA 2021: Exploring the limits of pre-trained seq2seq models for medical summarization Liwen Xu author Yan Zhang author Lei Hong author Yi Cai author Szui Sung author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication xu-etal-2021-chichealth 10.18653/v1/2021.bionlp-1.29 https://aclanthology.org/2021.bionlp-1.29/ 2021-06 263 267 NCUEE-NLP at MEDIQA 2021: Health Question Summarization Using PEGASUS Transformers Lung-Hao Lee author Po-Han Chen author Yu-Xiang Zeng author Po-Lei Lee author Kuo-Kai Shyu author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication lee-etal-2021-ncuee 10.18653/v1/2021.bionlp-1.30 https://aclanthology.org/2021.bionlp-1.30/ 2021-06 268 272 SB_NITK at MEDIQA 2021: Leveraging Transfer Learning for Question Summarization in Medical Domain Spandana Balumuri author Sony Bachina author Sowmya Kamath S author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication balumuri-etal-2021-sb 10.18653/v1/2021.bionlp-1.31 https://aclanthology.org/2021.bionlp-1.31/ 2021-06 273 279 Optum at MEDIQA 2021: Abstractive Summarization of Radiology Reports using simple BART Finetuning Ravi Kondadadi author Sahil Manchanda author Jason Ngo author Ronan McCormack author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication kondadadi-etal-2021-optum 10.18653/v1/2021.bionlp-1.32 https://aclanthology.org/2021.bionlp-1.32/ 2021-06 280 284 QIAI at MEDIQA 2021: Multimodal Radiology Report Summarization Jean-Benoit Delbrouck author Cassie Zhang author Daniel Rubin author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication delbrouck-etal-2021-qiai 10.18653/v1/2021.bionlp-1.33 https://aclanthology.org/2021.bionlp-1.33/ 2021-06 285 290 NLM at MEDIQA 2021: Transfer Learning-based Approaches for Consumer Question and Multi-Answer Summarization Shweta Yadav author Mourad Sarrouti author Deepak Gupta author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication yadav-etal-2021-nlm 10.18653/v1/2021.bionlp-1.34 https://aclanthology.org/2021.bionlp-1.34/ 2021-06 291 301 IBMResearch at MEDIQA 2021: Toward Improving Factual Correctness of Radiology Report Abstractive Summarization Diwakar Mahajan author Ching-Huei Tsou author Jennifer J Liang author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication mahajan-etal-2021-ibmresearch 10.18653/v1/2021.bionlp-1.35 https://aclanthology.org/2021.bionlp-1.35/ 2021-06 302 310 UETrice at MEDIQA 2021: A Prosper-thy-neighbour Extractive Multi-document Summarization Model Duy-Cat Can author Quoc-An Nguyen author Quoc-Hung Duong author Minh-Quang Nguyen author Huy-Son Nguyen author Linh Nguyen Tran Ngoc author Quang-Thuy Ha author Mai-Vu Tran author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication can-etal-2021-uetrice 10.18653/v1/2021.bionlp-1.36 https://aclanthology.org/2021.bionlp-1.36/ 2021-06 311 319 MNLP at MEDIQA 2021: Fine-Tuning PEGASUS for Consumer Health Question Summarization Jooyeon Lee author Huong Dang author Ozlem Uzuner author Sam Henry author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication lee-etal-2021-mnlp 10.18653/v1/2021.bionlp-1.37 https://aclanthology.org/2021.bionlp-1.37/ 2021-06 320 327 UETfishes at MEDIQA 2021: Standing-on-the-Shoulders-of-Giants Model for Abstractive Multi-answer Summarization Hoang-Quynh Le author Quoc-An Nguyen author Quoc-Hung Duong author Minh-Quang Nguyen author Huy-Son Nguyen author Tam Doan Thanh author Hai-Yen Thi Vuong author Trang M Nguyen author 2021-06 text Proceedings of the 20th Workshop on Biomedical Language Processing Dina Demner-Fushman editor Kevin Bretonnel Cohen editor Sophia Ananiadou editor Junichi Tsujii editor Association for Computational Linguistics Online conference publication le-etal-2021-uetfishes 10.18653/v1/2021.bionlp-1.38 https://aclanthology.org/2021.bionlp-1.38/ 2021-06 328 335