BioNLP Workshop

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An ACL 2016 Workshop associated with the SIGBIOMED special interest group Featuring two associated tasks: BioASQ ( and BioNLP-ST (

Berlin, Germany, August 12 -13, 2016


  • BioNLP workshop: Friday, August 12, 2016
  • BioNLP-ST and BioASQ workshop: Saturday August 13, 2016

BIONLP 2016 Workshop Schedule

Friday August 12, 2016
8:30–8:40Opening remarks
8:40–10:30Session 1: Entity extraction and representation
8:40–9:00A Machine Learning Approach to Clinical Terms Normalization
Jose Castano, María Laura Gambarte, Hee Joon Park, Maria del Pilar Avila Williams, David Perez, Fernando Campos, Daniel Luna, Sonia Benitez, Hernan Berinsky and Sofía Zanetti
9:00–9:20Improved Semantic Representation for Domain-Specific Entities
Mohammad Taher Pilehvar and Nigel Collier
9:20–9:40Identification, characterization, and grounding of gradable terms in clinical text
Chaitanya Shivade, Marie-Catherine de Marneffe, Eric Fosler-Lussier and Albert M. Lai
9:40–10:00Graph-based Semi-supervised Gene Mention Tagging
Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Anoop Sarkar and Inanc Birol
10:00–10:30Invited Talk: The BioNLP-ST challenges on information extraction and knowledge acquisition in biology
Speakers: Robert Bossy and Jin-Dong Kim
10:30–11:00Coffee Break
11:00–12:30Session 2: Event and Relation Extraction
11:00–11:20Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses
Dayne Freitag and John Niekrasz
11:40–12:00Inferring Implicit Causal Relationships in Biomedical Literature
Halil Kilicoglu
12:00–12:20SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction
Marco A. Valenzuela-Escárcega, Gus Hahn-Powell, Dane Bell and Mihai Surdeanu
12:20–12:40Character based String Kernels for Bio-Entity Relation Detection
Ritambhara Singh and Yanjun Qi
12:40–14:00Lunch break
14:00–15:40Session 3: Disambiguation, Classification, and more
14:00–14:20Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge
Amy Siu, Patrick Ernst and Gerhard Weikum
14:20–14:40Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts
Stephan Tulkens, Simon Suster and Walter Daelemans
14:40–15:00Unsupervised Document Classification with Informed Topic Models
Timothy Miller, Dmitriy Dligach and Guergana Savova
15:00–15:20Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes
Sumithra Velupillai, Danielle L Mowery, Mike Conway, John Hurdle and Brent Kious
15:20–15:40Syntactic analyses and named entity recognition for PubMed and PubMed Central __ up-to-the-minute
Kai Hakala, Suwisa Kaewphan, Tapio Salakoski and Filip Ginter
15:40–16:00Coffee Break
16:00–16:30Invited Talk: BioASQ: A challenge on large-scale biomedical semantic indexing and question answering
Speaker: Anastasia Krithara
16:30–17:30Poster Session
 Improving Temporal Relation Extraction with Training Instance Augmentation
Chen Lin, Timothy Miller, Dmitriy Dligach, Steven Bethard and Guergana Savova
 Using Centroids of Word Embeddings and Word Mover’s Distance for Biomedical Document Retrieval in Question Answering
Georgios-Ioannis Brokos, Prodromos Malakasiotis and Ion Androutsopoulos
 Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway
Michael Spranger, Sucheendra Palaniappan and Samik Gosh
 Construction of a Personal Experience Tweet Corpus for Health Surveillance
Keyuan Jiang, Ricardo Calix and Matrika Gupta
 Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification
Nut Limsopatham and Nigel Collier
 PubTermVariants: biomedical term variants and their use for PubMed search
Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Doğan, Wanli Liu, Donald C Comeau, Zhiyong Lu and W John Wilbur
 This before That: Causal Precedence in the Biomedical Domain
Gus Hahn-Powell, Dane Bell, Marco A. Valenzuela-Escárcega and Mihai Surdeanu
 Syntactic methods for negation detection in radiology reports in Spanish
Viviana Cotik, Vanesa Stricker, Jorge Vivaldi and Horacio Rodriguez
 How to Train good Word Embeddings for Biomedical NLP
Billy Chiu, Gamal Crichton, Anna Korhonen and Sampo Pyysalo
 An Information Foraging Approach to Determining the Number of Relevant Features
Brian Connolly, Benjamin Glass and John Pestian
 Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians
Brian E. Chapman, Danielle L Mowery, Evan Narasimhan, Neel Patel, Wendy Chapman and Marta Heilbrun
 Building a dictionary of lexical variants for phenotype descriptors
Simon Kocbek and Tudor Groza
 Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections
Olof Jacobson and Hercules Dalianis
 Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning
Genevieve Gorrell, Sherifat Oduola, Angus Roberts, Tom Craig, Craig Morgan and Rob Stewart
 Relation extraction from clinical texts using domain invariant convolutional neural network
Sunil Sahu, Ashish Anand, Krishnadev Oruganty and Mahanandeeshwar Gattu
 Results of the 4th edition of BioASQ Challenge
Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras and Ioannis Kakadiaris
  All August 13 talks are also presented as posters on August 12 and August 13

BioASQ / BioNLP-ST Workshop Program, August 13

9:00-9:15 Welcome
9:15-10:15 Invited speaker: Sherri Matis-Mitchell
Solving Problems and Supporting Decisions in Pharma R&D using Text Analytics: A Recent History
10:15-10:30 Overview of BioASQ
10:30-11:00 Coffee break
11:00-12:30 BioASQ participant session
11:00-11:15 Using Learning-To-Rank to Enhance NLM Medical Text Indexer Results
Ilya Zavorin, James Mork and Dina Demner-Fushman
11:15-11:30 LABDA at the 2016 BioASQ challenge task 4a: Semantic Indexing by using ElasticSearch
Isabel Segura-Bedmar, Adrián Carruana and Paloma Martínez
11:30-11:45 Learning to Answer Biomedical Questions: OAQA at BioASQ 4B
Zi Yang, Yue Zhou and Eric Nyberg
11:45-12:00 HPI Question Answering System in BioASQ 2016
Frederik Schulze, Ricarda Schuler, Tim Draeger, Daniel Dummer, Alexander Ernst, Pedro Flemming, Cindy Perscheid, Mariana Neves
12:00-12:15 KSAnswer: Question-answering System of Kangwon National University and Sogang University in the 2016 BioASQ Challenge
Hyeon-gu Lee, Minkyoung Kim, Harksoo Kim, Juae Kim, Sunjae Kwon, Jungyun Seo, Yi-Reun Kim and Jung-Kyu Choi
12:15-12:30 Large-Scale Semantic Indexing and Question Answering in Biomedicine
Eirini Papagiannopoulou, Yiannis Papanikolaou, Dimitris Dimitriadis, Sakis Lagopoulos, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos and Ioannis Vlahavas
12:30-14:00 Lunch break
14:00-14:15 Overview of BioNLP-ST
14:15-15:30 BioNLP-ST participant session 1
14:15-14:30 LitWay, discriminative extraction for different bio-events
Chen Li, Zhiqiang Rao and Xiangrong Zhang
14:30-14:45 VERSE: Event and relation extraction in the BioNLP 2016 Shared Task
Jake Lever and Steven JM Jones
14:45-15:00 A dictionary- and rule-based system for identification of bacteria and habitats in text
Helen Cook, Evangelos Pafilis and Lars Juhl Jensen
15:00-15:15 Extraction of Regulatory Events Using Kernel-based Classifiers and Distant Supervision
Andre Lamurias, Miguel J. Rodrigues, Luka A. Clarke and Francisco M Couto
15:15-15:30 Deep Learning With Minimal Training Data: TurkuNLP Entry in The BioNLP Shared Task 2016
Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski and Filip Ginter
15:30-16:00 Coffee break
16:00-17:00 BioNLP-ST participant session 2
16:00-16:15Identification of mentions and relations between bacteria and biotope from PubMed abstracts
Cyril Grouin
16:15-16:30 SeeDev Binary Event Extraction Using SVMs and a Rich Feature set
Nagesh Panyam Chandrasekarasastry, Gitansh Khirbat, Karin Verspoor, Trevor Cohn and Kotagiri Ramamohanarao
16:30-16:45 Ontology Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques
Mert Tiftikci, Hakan Şahin, Berfu Büyüköz, Alper Yayıkçı and Arzucan Özgür
16:45-17:00 DUTIR in BioNLP-ST 2016: Utilizing convolutional network and distributed representation to extract complicate relations
Honglei Li, Jianhai Zhang, Jian Wang, Hongfei Lin and Zhihao Yang
17:00-17:30 Closing session