The 3rd Clinical Natural Language Processing Workshop

At EMNLP 2020. November 19, 2020.

Attending Online

Clinical NLP will be held online at EMNLP 2020. We will be using the tools recommended by EMNLP, specifically:

  • Zoom: we will be playing a stream of the pre-recorded talks and hosting Q&A using Zoom.
  • Rocket Chat: we will be distributing information and engaging with participants via chat using Rocket Chat.
  • we will be hosting the poster session and informal coffee breaks using Coffee breaks will be in Room L. The poster session will be in both Room L and Room M.

In sum, the workshop will be hosted on Zoom. Q&A sessions will also be in Zoom, but questions should be posted to the rocket chat. Posters will be in Gather.Town. If in doubt, join the Zoom session linked above at the beginning of the day, and check out the Rocket Chat for clarifications.

NOTE: It is possible to be logged in to both and Zoom at the same time, but participants should ensure that they set themselves to "red"/busy mode status in to avoid audio feedback issues.

Workshop Program

19 Nov 2020 (all times EST)

08:45–10:00Opening Session
08:45–09:00Opening Remarks
09:00–09:45Keynote Talk: Deep Learning is Conquering Human Tasks. How Far Can it Go in Medicine? Advances, Challenges, and Future Directions
Hong Yu
09:45–10:00Keynote Q&A
Hong Yu
10:00–10:40Oral Session 1
10:00–10:05Various Approaches for Predicting Stroke Prognosis using Magnetic Resonance Imaging Text Records
Tak-Sung Heo, Chulho Kim, Jeong-Myeong Choi, Yeong-Seok Jeong and Yu-Seop Kim
10:05–10:15Multiple Sclerosis Severity Classification From Clinical Text
Alister D’Costa, Stefan Denkovski, Michal Malyska, Sae Young Moon, Brandon Rufino, Zhen Yang, Taylor Killian and Marzyeh Ghassemi
10:15–10:25BERT-XML: Large Scale Automated ICD Coding Using BERT Pretraining
Zachariah Zhang, Jingshu Liu and Narges Razavian
10:25–10:40Oral Session 1: Q&A
10:40–10:50Coffee Break
10:50–11:40Oral Session 2
10:50–10:55Incorporating Risk Factor Embeddings in Pre-trained Transformers Improves Sentiment Prediction in Psychiatric Discharge Summaries
Xiyu Ding, Mei-Hua Hall and Timothy Miller
10:55–11:05Information Extraction from Swedish Medical Prescriptions with Sig-Transformer Encoder
John Pougué Biyong, Bo Wang, Terry Lyons and Alejo Nevado-Holgado
11:05–11:15Evaluation of Transfer Learning for Adverse Drug Event (ADE) and Medication Entity Extraction
Sankaran Narayanan, Kaivalya Mannam, Sreeranga P Rajan and P Venkat Rangan
11:15–11:25BioBERTpt - A Portuguese Neural Language Model for Clinical Named Entity Recognition
Elisa Terumi Rubel Schneider, João Vitor Andrioli de Souza, Julien Knafou, Lucas Emanuel Silva e Oliveira, Jenny Copara, Yohan Bonescki Gumiel, Lucas Ferro Antunes de Oliveira, Emerson Cabrera Paraiso, Douglas Teodoro and Cláudia Maria Cabral Moro Barra
11:25–11:40Oral Session 2: Q&A
11:40–12:00Poster Teasers
11:40–11:41Dilated Convolutional Attention Network for Medical Code Assignment from Clinical Text
Shaoxiong Ji, Erik Cambria and Pekka Marttinen
11:41–11:42Classification of Syncope Cases in Norwegian Medical Records
Ildiko Pilan, Pål H. Brekke, Fredrik A. Dahl, Tore Gundersen, Haldor Husby, Øystein Nytrø and Lilja Øvrelid
11:42–11:43Comparison of Machine Learning Methods for Multi-label Classification of Nursing Education and Licensure Exam Questions
John Langton, Krishna Srihasam and Junlin Jiang
11:43–11:44Clinical XLNet: Modeling Sequential Clinical Notes and Predicting Prolonged Mechanical Ventilation
Kexin Huang, Abhishek Singh, Sitong Chen, Edward Moseley, Chih-Ying Deng, Naomi George and Charolotta Lindvall
11:44–11:45Automatic recognition of abdominal lymph nodes from clinical text
Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas Shen, Yu-xing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald Summers and Zhiyong Lu
11:45–11:46How You Ask Matters: The Effect of Paraphrastic Questions to BERT Performance on a Clinical SQuAD Dataset
Sungrim (Riea) Moon and Jungwei Fan
11:46–11:47Relative and Incomplete Time Expression Anchoring for Clinical Text
Louise Dupuis, Nicol Bergou, Hegler Tissot and Sumithra Velupillai
11:47–11:48MeDAL: Medical Abbreviation Disambiguation Dataset for Natural Language Understanding Pretraining
Zhi Wen, Xing Han Lu and Siva Reddy
11:48–11:49Knowledge Grounded Conversational Symptom Detection with Graph Memory Networks
Hongyin Luo, Shang-Wen Li and James Glass
11:49–11:50Pretrained Language Models for Biomedical and Clinical Tasks: Understanding and Extending the State-of-the-Art
Patrick Lewis, Myle Ott, Jingfei Du and Veselin Stoyanov
11:50–11:51Assessment of DistilBERT performance on Named Entity Recognition task for the detection of Protected Health Information and medical concepts
Macarious Abadeer
11:51–11:52Distinguishing between Dementia with Lewy bodies (DLB) and Alzheimer’s Disease (AD) using Mental Health Records: a Classification Approach
Zixu Wang, Julia Ive, Sinead Moylett, Christoph Mueller, Rudolf Cardinal, Sumithra Velupillai, John O’Brien and Robert Stewart
11:52–11:53Weakly Supervised Medication Regimen Extraction from Medical Conversations
Dhruvesh Patel, Sandeep Konam and Sai Prabhakar
11:53–11:54Extracting Relations between Radiotherapy Treatment Details
Danielle Bitterman, Timothy Miller, David Harris, Chen Lin, Sean Finan, Jeremy Warner, Raymond Mak and Guergana Savova
11:54–11:55Cancer Registry Information Extraction via Transfer Learning
Yan-Jie Lin, Hong-Jie Dai, You-Chen Zhang, Chung-Yang Wu, Yu-Cheng Chang, Pin-Jou Lu, Chih-Jen Huang, Yu-Tsang Wang, Hui-Min Hsieh, Kun-San Chao, Tsang-Wu Liu, I-Shou Chang, Yi-Hsin Connie Yang, Ti-Hao Wang, Ko-Jiunn Liu, Li-Tzong Chen and Sheau-Fang Yang
11:55–11:56PHICON: Improving Generalization of Clinical Text De-identification Models via Data Augmentation
Xiang Yue and Shuang Zhou
11:56–11:57Where’s the Question? A Multi-channel Deep Convolutional Neural Network for Question Identification in Textual Data
George Michalopoulos, Helen Chen and Alexander Wong
11:57–11:58Learning from Unlabelled Data for Clinical Semantic Textual Similarity
Yuxia Wang, Karin Verspoor and Timothy Baldwin
11:58–11:59Joint Learning with Pre-trained Transformer on Named Entity Recognition and Relation Extraction Tasks for Clinical Analytics
Miao Chen, Ganhui Lan, Fang Du and Victor Lobanov
12:00–13:20Poster Session & Lunch
13:20–14:10Oral Session 3
13:20–13:25Extracting Semantic Aspects for Structured Representation of Clinical Trial Eligibility Criteria
Tirthankar Dasgupta, Ishani Mondal, abir naskar and Lipika Dey
13:25–13:35An Ensemble Approach to Automatic Structuring of Radiology Reports
Morteza Pourreza Shahri, Amir Tahmasebi, Bingyang Ye, Henghui Zhu, Javed Aslam and Timothy Ferris
13:35–13:45Utilizing Multimodal Feature Consistency to Detect Adversarial Examples on Clinical Summaries
Wenjie Wang, Youngja Park, Taesung Lee, Ian Molloy, Pengfei Tang and Li Xiong
13:45–13:55Advancing Seq2seq with Joint Paraphrase Learning
So Yeon Min, Preethi Raghavan and Peter Szolovits
13:55–14:10Oral Session 3: Q&A
14:10–14:55EMNLP Findings Session 1
14:10–14:15Learning to Generate Clinically Coherent Chest X-Ray Reports
Justin Lovelace, Bobak Mortazavi
14:15–14:20Learning Visual-Semantic Embeddings for Reporting Abnormal Findings on Chest X-rays
Jianmo Ni, Chun-Nan Hsu, Amilcare Gentili, Julian McAuley
14:20–14:30Characterizing the Value of Information in Medical Notes
Chao-Chun Hsu, Shantanu Karnwal, Sendhil Mullainathan, Ziad Obermeyer, Chenhao Tan
14:30–14:40PharmMT: A Neural Machine Translation Approach to Simplify Prescription Directions
Jiazhao Li, Corey Lester, Xinyan Zhao, Yuting Ding, Yun Jiang, V.G.Vinod Vydiswaran
14:40–14:55EMNLP Findings Session 1: Q&A
14:55–15:05Coffee Break
15:05–15:50EMNLP Findings Session 2
15:05–15:15A Dual-Attention Network for Joint Named Entity Recognition and Sentence Classification of Adverse Drug Events
Susmitha Wunnava, Xiao Qin, Tabassum Kakar, Xiangnan Kong, Elke A. Rundensteiner
15:15–15:25Dr. Summarize: Global Summarization of Medical Dialogue by Exploiting Local Structures
Anirudh Joshi, Namit Katariya, Xavier Amatriain, Anitha Kannan
15:25–15:35Generating Accurate Electronic Health Assessment from Medical Graph
Zhichao Yang, Hong Yu
15:35–15:50EMNLP Findings Session 2: Q&A
15:50–16:35Best Paper Session
15:50–16:00On the diminishing return of labeling clinical reports
Jean-Baptiste Lamare, Oloruntobiloba Olatunji and Li Yao
16:00–16:10The Chilean Waiting List Corpus: a new resource for clinical Named Entity Recognition in Spanish
Pablo Báez, Fabián Villena, Matías Rojas, Manuel Durán and Jocelyn Dunstan
16:10–16:20Analyzing Text Specific vs Blackbox Fairness Algorithms in Multimodal Clinical NLP
John Chen, Ian Berlot-Attwell, Xindi Wang, Safwan Hossain and Frank Rudzicz
16:20–16:35Best Paper Session: Q&A
16:35–16:50Concluding Session