---
title: "BioNLP Shared Task Workshop 2019 — all accepted papers"
description: "All 59 papers of BioNLP Shared Task Workshop 2019, the most cited first; those with our summary link to it."
canonical: "https://research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2019/papers/"
---
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# BioNLP Shared Task Workshop 2019: all accepted papers

59 papers · the most cited first · [← BioNLP Shared Task Workshop 2019](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2019/)

1. **[Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://md.research.elamur.ai/free/en/papers/peng-2019-transfer-learning-biomedical-natural-language/)**Yifan Peng, Shankai Yan, Zhiyong Lu*868 citations · our summary*
2. **[ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://md.research.elamur.ai/free/en/papers/neumann-2019-scispacy-fast-robust-models-biomedical/)**Mark Neumann, Daniel King, Iz Beltagy et al.*488 citations · our summary*
3. **[Overview of the MEDIQA 2019 Shared Task on Textual Inference, Question Entailment and Question Answering](https://md.research.elamur.ai/free/en/papers/abacha-2019-overview-mediqa-2019-shared-task/)**Asma Ben Abacha, Chaitanya Shivade, Dina Demner-Fushman*116 citations · our summary*
4. **[Two-stage Federated Phenotyping and Patient Representation Learning ↗](https://aclanthology.org/W19-5030/)**Dianbo Liu, Dmitriy Dligach, Timothy Miller*98 citations*
5. **[Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings ↗](https://aclanthology.org/W19-5035/)**Zenan Zhai, Dat Quoc Nguyen, Saber Akhondi et al.*40 citations*
6. **[Deep Contextualized Biomedical Abbreviation Expansion ↗](https://aclanthology.org/W19-5010/)**Qiao Jin, Jinling Liu, Xinghua Lu*33 citations*
7. **[ChiMed: A Chinese Medical Corpus for Question Answering ↗](https://aclanthology.org/W19-5027/)**Yuanhe Tian, Weicheng Ma, Fei Xia et al.*31 citations*
8. **[Improving classification of Adverse Drug Reactions through Using Sentiment Analysis and Transfer Learning ↗](https://aclanthology.org/W19-5036/)**Hassan Alhuzali, Sophia Ananiadou*29 citations*
9. **[Transfer Learning for Causal Sentence Detection ↗](https://aclanthology.org/W19-5031/)**Manolis Kyriakakis, Ion Androutsopoulos, Artur Saudabayev et al.*26 citations*
10. **[PANLP at MEDIQA 2019: Pre-trained Language Models, Transfer Learning and Knowledge Distillation ↗](https://aclanthology.org/W19-5040/)**Wei Zhu, Xiaofeng Zhou, Keqiang Wang et al.*25 citations*
11. **[NCUEE at MEDIQA 2019: Medical Text Inference Using Ensemble BERT-BiLSTM-Attention Model ↗](https://aclanthology.org/W19-5058/)**Lung-Hao Lee, Yi Lu, Po-Han Chen et al.*23 citations*
12. **[Constructing large scale biomedical knowledge bases from scratch with rapid annotation of interpretable patterns ↗](https://aclanthology.org/W19-5016/)**Julien Fauqueur, Ashok Thillaisundaram, Theodosia Togia*22 citations*
13. **[A Comparison of Word-based and Context-based Representations for Classification Problems in Health Informatics ↗](https://aclanthology.org/W19-5015/)**Aditya Joshi, Sarvnaz Karimi, Ross Sparks et al.*20 citations*
14. **[Contributions to Clinical Named Entity Recognition in Portuguese ↗](https://aclanthology.org/W19-5024/)**Fábio Lopes, César Teixeira, Hugo Gonçalo Oliveira*20 citations*
15. **[A Paraphrase Generation System for EHR Question Answering ↗](https://aclanthology.org/W19-5003/)**Sarvesh Soni, Kirk Roberts*18 citations*
16. **[BioRelEx 1.0: Biological Relation Extraction Benchmark ↗](https://aclanthology.org/W19-5019/)**Hrant Khachatrian, Lilit Nersisyan, Karen Hambardzumyan et al.*17 citations*
17. **[LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition ↗](https://aclanthology.org/W19-5057/)**Andre Lamurias, Francisco M Couto*17 citations*
18. **[DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain ↗](https://aclanthology.org/W19-5042/)**Yichong Xu, Xiaodong Liu, Chunyuan Li et al.*14 citations*
19. **[Embedding Biomedical Ontologies by Jointly Encoding Network Structure and Textual Node Descriptors ↗](https://aclanthology.org/W19-5032/)**Sotiris Kotitsas, Dimitris Pappas, Ion Androutsopoulos et al.*14 citations*
20. **[Pentagon at MEDIQA 2019: Multi-task Learning for Filtering and Re-ranking Answers using Language Inference and Question Entailment ↗](https://aclanthology.org/W19-5041/)**Hemant Pugaliya, Karan Saxena, Shefali Garg et al.*12 citations*
21. **[ARS_NITK at MEDIQA 2019:Analysing Various Methods for Natural Language Inference, Recognising Question Entailment and Medical Question Answering System ↗](https://aclanthology.org/W19-5059/)**Anumeha Agrawal, Rosa Anil George, Selvan Suntiha Ravi et al.*11 citations*
22. **[MoNERo: a Biomedical Gold Standard Corpus for the Romanian Language ↗](https://aclanthology.org/W19-5008/)**Maria Mitrofan, Verginica Barbu Mititelu, Grigorina Mitrofan*11 citations*
23. **[WTMED at MEDIQA 2019: A Hybrid Approach to Biomedical Natural Language Inference ↗](https://aclanthology.org/W19-5044/)**Zhaofeng Wu, Yan Song, Sicong Huang et al.*11 citations*
24. **[Can Character Embeddings Improve Cause-of-Death Classification for Verbal Autopsy Narratives? ↗](https://aclanthology.org/W19-5025/)**Zhaodong Yan, Serena Jeblee, Graeme Hirst*10 citations*
25. **[Classifying the reported ability in clinical mobility descriptions ↗](https://aclanthology.org/W19-5001/)**Denis Newman-Griffis, Ayah Zirikly, Guy Divita et al.*10 citations*
26. **[Clinical Concept Extraction for Document-Level Coding ↗](https://aclanthology.org/W19-5028/)**Sarah Wiegreffe, Edward Choi, Sherry Yan et al.*10 citations*
27. **[A distantly supervised dataset for automated data extraction from diagnostic studies ↗](https://aclanthology.org/W19-5012/)**Christopher Norman, Mariska Leeflang, René Spijker et al.*9 citations*
28. **[First Steps towards Building a Medical Lexicon for Spanish with Linguistic and Semantic Information ↗](https://aclanthology.org/W19-5017/)**Leonardo Campillos-Llanos*9 citations*
29. **[Is artificial data useful for biomedical Natural Language Processing algorithms? ↗](https://aclanthology.org/W19-5026/)**Zixu Wang, Julia Ive, Sumithra Velupillai et al.*9 citations*
30. **[Combining Structured and Free-text Electronic Medical Record Data for Real-time Clinical Decision Support ↗](https://aclanthology.org/W19-5007/)**Emilia Apostolova, Tony Wang, Tim Tschampel et al.*7 citations*
31. **[DUT-NLP at MEDIQA 2019: An Adversarial Multi-Task Network to Jointly Model Recognizing Question Entailment and Question Answering ↗](https://aclanthology.org/W19-5046/)**Huiwei Zhou, Xuefei Li, Weihong Yao et al.*7 citations*
32. **[Enhancing biomedical word embeddings by retrofitting to verb clusters ↗](https://aclanthology.org/W19-5014/)**Billy Chiu, Simon Baker, Martha Palmer et al.*7 citations*
33. **[IIT-KGP at MEDIQA 2019: Recognizing Question Entailment using Sci-BERT stacked with a Gradient Boosting Classifier ↗](https://aclanthology.org/W19-5050/)**Prakhar Sharma, Sumegh Roychowdhury*7 citations*
34. **[KU_ai at MEDIQA 2019: Domain-specific Pre-training and Transfer Learning for Medical NLI ↗](https://aclanthology.org/W19-5045/)**Cemil Cengiz, Ulaş Sert, Deniz Yuret*7 citations*
35. **[Saama Research at MEDIQA 2019: Pre-trained BioBERT with Attention Visualisation for Medical Natural Language Inference ↗](https://aclanthology.org/W19-5055/)**Kamal raj Kanakarajan, Suriyadeepan Ramamoorthy, Vaidheeswaran Archana et al.*7 citations*
36. **[Sieg at MEDIQA 2019: Multi-task Neural Ensemble for Biomedical Inference and Entailment ↗](https://aclanthology.org/W19-5049/)**Sai Abishek Bhaskar, Rashi Rungta, James Route et al.*7 citations*
37. **[Simplification-induced transformations: typology and some characteristics ↗](https://aclanthology.org/W19-5033/)**Anaïs Koptient, Rémi Cardon, Natalia Grabar*7 citations*
38. **[UU_TAILS at MEDIQA 2019: Learning Textual Entailment in the Medical Domain ↗](https://aclanthology.org/W19-5053/)**Noha Tawfik, Marco Spruit*7 citations*
39. **[Enhancing PIO Element Detection in Medical Text Using Contextualized Embedding ↗](https://aclanthology.org/W19-5023/)**Hichem Mezaoui, Isuru Gunasekara, Aleksandr Gontcharov*6 citations*
40. **[Extracting relations between outcomes and significance levels in Randomized Controlled Trials (RCTs) publications ↗](https://aclanthology.org/W19-5038/)**Anna Koroleva, Patrick Paroubek*5 citations*
41. **[MSIT_SRIB at MEDIQA 2019: Knowledge Directed Multi-task Framework for Natural Language Inference in Clinical Domain. ↗](https://aclanthology.org/W19-5052/)**Sahil Chopra, Ankita Gupta, Anupama Kaushik*5 citations*
42. **[RNN Embeddings for Identifying Difficult to Understand Medical Words ↗](https://aclanthology.org/W19-5011/)**Hanna Pylieva, Artem Chernodub, Natalia Grabar et al.*5 citations*
43. **[ANU-CSIRO at MEDIQA 2019: Question Answering Using Deep Contextual Knowledge ↗](https://aclanthology.org/W19-5051/)**Vincent Nguyen, Sarvnaz Karimi, Zhenchang Xing*4 citations*
44. **[Analysing Representations of Memory Impairment in a Clinical Notes Classification Model ↗](https://aclanthology.org/W19-5005/)**Mark Ormerod, Jesús Martínez-del-Rincón, Neil Robertson et al.*4 citations*
45. **[Clinical Case Reports for NLP ↗](https://aclanthology.org/W19-5029/)**Cyril Grouin, Natalia Grabar, Vincent Claveau et al.*4 citations*
46. **[DUT-BIM at MEDIQA 2019: Utilizing Transformer Network and Medical Domain-Specific Contextualized Representations for Question Answering ↗](https://aclanthology.org/W19-5047/)**Huiwei Zhou, Bizun Lei, Zhe Liu et al.*4 citations*
47. **[UW-BHI at MEDIQA 2019: An Analysis of Representation Methods for Medical Natural Language Inference ↗](https://aclanthology.org/W19-5054/)**William Kearns, Wilson Lau, Jason Thomas*4 citations*
48. **[Domain Adaptation of SRL Systems for Biological Processes ↗](https://aclanthology.org/W19-5009/)**Dheeraj Rajagopal, Nidhi Vyas, Aditya Siddhant et al.*3 citations*
49. **[Dr.Quad at MEDIQA 2019: Towards Textual Inference and Question Entailment using contextualized representations ↗](https://aclanthology.org/W19-5048/)**Vinayshekhar Bannihatti Kumar, Ashwin Srinivasan, Aditi Chaudhary et al.*3 citations*
50. **[IITP at MEDIQA 2019: Systems Report for Natural Language Inference, Question Entailment and Question Answering ↗](https://aclanthology.org/W19-5056/)**Dibyanayan Bandyopadhyay, Baban Gain, Tanik Saikh et al.*3 citations*
51. **[Learning from the Experience of Doctors: Automated Diagnosis of Appendicitis Based on Clinical Notes ↗](https://aclanthology.org/W19-5002/)**Steven Kester Yuwono, Hwee Tou Ng, Kee Yuan Ngiam*3 citations*
52. **[Leveraging Sublanguage Features for the Semantic Categorization of Clinical Terms ↗](https://aclanthology.org/W19-5022/)**Leonie Grön, Ann Bertels, Kris Heylen*3 citations*
53. **[Query selection methods for automated corpora construction with a use case in food-drug interactions ↗](https://aclanthology.org/W19-5013/)**Georgeta Bordea, Tsanta Randriatsitohaina, Fleur Mougin et al.*3 citations*
54. **[Annotating Temporal Information in Clinical Notes for Timeline Reconstruction: Towards the Definition of Calendar Expressions ↗](https://aclanthology.org/W19-5021/)**Natalia Viani, Hegler Tissot, Ariane Bernardino et al.*2 citations*
55. **[Exploring Diachronic Changes of Biomedical Knowledge using Distributed Concept Representations ↗](https://aclanthology.org/W19-5037/)**Gaurav Vashisth, Jan-Niklas Voigt-Antons, Michael Mikhailov et al.*2 citations*
56. **[Extraction of Lactation Frames from Drug Labels and LactMed ↗](https://aclanthology.org/W19-5020/)**Heath Goodrum, Meghana Gudala, Ankita Misra et al.*2 citations*
57. **[Surf at MEDIQA 2019: Improving Performance of Natural Language Inference in the Clinical Domain by Adopting Pre-trained Language Model ↗](https://aclanthology.org/W19-5043/)**Jiin Nam, Seunghyun Yoon, Kyomin Jung*2 citations*
58. **[Incorporating Figure Captions and Descriptive Text in MeSH Term Indexing ↗](https://aclanthology.org/W19-5018/)**Xindi Wang, Robert E. Mercer*1 citation*
59. **[REflex: Flexible Framework for Relation Extraction in Multiple Domains ↗](https://aclanthology.org/W19-5004/)**Geeticka Chauhan, Matthew B.A. McDermott, Peter Szolovits
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