---
title: "BioNLP Shared Task Workshop 2019 — accepted papers"
description: "BioNLP Shared Task Workshop 2019 — accepted papers: 3 papers in the Elamur Research library (Florence, Italy), with our summaries…"
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---
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# BioNLP Shared Task Workshop 2019 — accepted papers

BioNLP Shared Task Workshop 2019 is the 2019 edition of the BioNLP Shared Task Workshop, held in Florence, Italy, August 2019 (publisher: Association for Computational Linguistics). OpenAlex lists 59 papers of it; our library holds 3 with our summaries. Below: the most cited papers, every accepted paper, and ours with their topics, authors and institutions.

[**59** papers in the proceedings](#all) · [**3** works in our library](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2019/#works) · [**1,938** citations of these works](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2019/#works)**Florence, Italy** where it was held**August 2019** when

## Most cited papers

By their OpenAlex citations; a paper with our summary links to its page here, the others to the original.

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*

## All accepted papers (59)

The most cited first; 3 with our summary link to their page here, the others to the original.

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*

[See all 59 papers in BioNLP Shared Task Workshop 2019 — accepted papers →](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2019/papers/)

## Papers with our summary in our library (3)

The most cited first (OpenAlex citations plus our library's).

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/) [BioNLP Shared Task Workshop](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/)**Yifan Peng, Shankai Yan, Zhiyong Lu*2019 · 1,082 citations*
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/) [BioNLP Shared Task Workshop](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/)**Mark Neumann, Daniel King, Iz Beltagy, et al.*2019 · 677 citations*
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/) [BioNLP Shared Task Workshop](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/)**Asma Ben Abacha, Chaitanya Shivade, Dina Demner-Fushman*2019 · 179 citations*

## Top topics

Topics of its works in our library, with the number of works on each.

[Question answering (1)](https://md.research.elamur.ai/free/en/topics/question-answering/) · [Information extraction (1)](https://md.research.elamur.ai/free/en/topics/information-extraction/) · [Evaluation & benchmarks (1)](https://md.research.elamur.ai/free/en/topics/evaluation-benchmarks/)

## Fields

[Arts and Humanities (3)](https://md.research.elamur.ai/free/en/shelves/arts-and-humanities/) · [Biochemistry, Genetics and Molecular Biology (3)](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/) · [Computer Science (3)](https://md.research.elamur.ai/free/en/shelves/computer-science/)

## Top authors

Authors with a page who published here most often: their works here, and the citations of those works.

[🧑‍🔬**Yifan Peng**1 work here · 1,082 citations](https://md.research.elamur.ai/free/en/authors/yifan-peng/) · [🧑‍🔬**Zhiyong Lu**1 work here · 1,082 citations](https://md.research.elamur.ai/free/en/authors/zhiyong-lu/) · [🧑‍🔬**Iz Beltagy**1 work here · 677 citations](https://md.research.elamur.ai/free/en/authors/iz-beltagy/) · [🧑‍🔬**Mark Neumann**1 work here · 677 citations](https://md.research.elamur.ai/free/en/authors/mark-neumann/) · [🧑‍🔬**Waleed Ammar**1 work here · 677 citations](https://md.research.elamur.ai/free/en/authors/waleed-ammar/) · [🧑‍🔬**Asma Ben Abacha**1 work here · 179 citations](https://md.research.elamur.ai/free/en/authors/asma-ben-abacha/) · [🧑‍🔬**Chaitanya Shivade**1 work here · 179 citations](https://md.research.elamur.ai/free/en/authors/chaitanya-shivade/) · [🧑‍🔬**Dina Demner-Fushman**1 work here · 179 citations](https://md.research.elamur.ai/free/en/authors/dina-demner-fushman/)

## Top institutions

Institutions on the bylines of its works here, by the number of works.

[🏛️**National Institutes of Health** Bethesda · United States 2 works here](https://md.research.elamur.ai/free/en/government/national-institutes-of-health/) · [🔬**IBM Research - Almaden** San Jose · United States 1 work here](https://md.research.elamur.ai/free/en/labs/ibm-research-almaden/) · [🔬**National Center for Biotechnology Information** Bethesda · United States 1 work here](https://md.research.elamur.ai/free/en/labs/national-center-for-biotechnology-information/)

Place and dates from the event's site or the ACL Anthology; works and citations from OpenAlex and our library.

- [← previous BioNLP Shared Task Workshop 2011](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2011/)
- [↑ back to BioNLP Shared Task Workshop](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/)