Program

BIONLP 2017 Workshop Schedule

Friday August 4, 2017
8:30–8:45 Opening remarks
8:45–10:30 Session 1: Prediction and relation extraction
8:45–9:00 Target word prediction and paraphasia classification in spoken discourse
  • Joel Adams, Steven Bedrick, Gerasimos Fergadiotis, Kyle Gorman and Jan van Santen
9:00–9:15 Extracting Drug-Drug Interactions with Attention CNNs
  • Masaki Asada, Makoto Miwa, Yutaka Sasaki
9:15–9:30 Insights into Analogy Completion from the Biomedical Domain
  • Denis Newman-Griffis, Albert Lai, Eric Fosler-Lussier
9:30–9:45 Deep learning for extracting protein-protein interactions from biomedical literature
  • Yifan Peng and Zhiyong Lu
9:45–10:00 Stacking With Auxiliary Features for Entity Linking in the Medical Domain
  • Nazneen Fatema Rajani, Mihaela Bornea, Ken Barker
10:00–10:30 Invited Talk: Results of the 5th edition of BioASQ Challenge 
Speaker: Georgios Paliouras
10:30–11:00 Coffee Break
11:00–12:30 Session 2: BioASQ 2017 and more
11:00–11:15 Tackling Biomedical Text Summarization: OAQA at BioASQ 5B
  • Khyathi Chandu, Aakanksha Naik, Aditya Chandrasekar, Zi Yang, Niloy Gupta, Eric Nyberg
11:15–11:30 Macquarie University at BioASQ 5b -- Query-based Summarisation Techniques for Selecting the Ideal Answers
  • Diego Molla
11:30–11:45 Neural Question Answering at BioASQ 5B
  • Georg Wiese, Dirk Weissenborn, Mariana Neves
11:45–12:00 End-to-End System for Bacteria Habitat Extraction
  • Farrokh Mehryary, Kai Hakala, Suwisa Kaewphan, Jari Björne, Tapio Salakoski, Filip Ginter
12:00–12:15 Creation and evaluation of a dictionary-based tagger for virus species and proteins
  • Helen Cook, Rudolfs Berzins, Cristina Leal Rodrıguez, Juan Miguel Cejuela, Lars Juhl Jensen
12:15–12:30 Representation of complex terms in a vector space structured by an ontology for a normalization task
  • Arnaud Ferré, Pierre Zweigenbaum, Claire Nédellec
12:30–14:00 Lunch break
14:00–15:30 Session 3: From bio to clinical NLP
14:00–14:15 Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second--Order Vectors
  • Bridget McInnes and Ted Pedersen
14:15–14:30 Proactive Learning for Named Entity Recognition
  • Maolin Li, Nhung Nguyen, Sophia Ananiadou
14:30–14:45 Biomedical Event Extraction using Abstract Meaning Representation
  • Sudha Rao, Daniel Marcu, Kevin Knight, Hal Daumé III
14:45–15:00 Detecting Personal Medication Intake in Twitter: An Annotated Corpus and Baseline Classification System
  • Ari Klein, Abeed Sarker, Masoud Rouhizadeh, Karen O'Connor, Graciela Gonzalez
15:00–15:15 Unsupervised Context-Sensitive Spelling Correction of Clinical Free-Text with Word and Character N-Gram Embeddings
  • Pieter Fivez, Simon Suster, Walter Daelemans
15:15–15:30 Characterization of Divergence in Impaired Speech of ALS Patients
  • Archna Bhatia, Bonnie Dorr, Kristy Hollingshead, Samuel L. Phillips, Barbara McKenzie
15:30–16:00 Coffee Break
16:00–16:30 Session 3: More clinical NLP
16:00–16:15 Deep Learning for Punctuation Restoration in Medical Reports
  • Wael Salloum, Greg Finley, Erik Edwards, Mark Miller, David Suendermann-Oeft
16:15–16:30 Unsupervised Domain Adaptation for Clinical Negation Detection
  • Timothy Miller, Steven Bethard, Hadi Amiri, Guergana Savova
16:30–18:00 Poster Session
  BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations
  • Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald Comeau, Zhiyong Lu
  Painless Relation Extraction with Kindred
  • Jake Lever and Steven Jones
  Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction
  • Gang Li, Cathy Wu, K. Vijay-Shanker
  Role-Preserving Redaction of Medical Records to Enable Ontology-Driven Processing
  • Seth Polsley, Atif Tahir, Muppala Raju, Akintayo Akinleye, Duane Steward
  Annotation of pain and anesthesia events for surgery-related processes and outcomes extraction
  • Wen-wai Yim, Dario Tedesco, Catherine Curtin, Tina Hernandez-Boussard
  Identifying Comparative Structures in Biomedical Text
  • Samir Gupta, A.S.M. Ashique Mahmood, Karen Ross, Cathy Wu, K. Vijay-Shanker
  Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models
  • Subhradeep Kayal, Zubair Afzal, George Tsatsaronis, Sophia Katrenko, Pascal Coupet, Marius Doornenbal, Michelle Gregory
  Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs
  • Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
  Detecting Dementia through Retrospective Analysis of Routine Blog Posts by Bloggers with Dementia
  • Vaden Masrani, Gabriel Murray, Thalia Field, Giuseppe Carenini
  Protein Word Detection using Text Segmentation Techniques
  • Devi Ganesan, Ashish V. Tendulkar, Sutanu Chakraborti
  External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway
  • Wojciech Kusa and Michael Spranger
  Toward Automated Early Sepsis Alerting: Identifying Infection Patients from Nursing Notes
  • Emilia Apostolova and Tom Velez
  Enhancing Automatic ICD-9-CM Code Assignment for \\Medical Texts with PubMed
  • Danchen Zhang, Daqing He, Sanqiang Zhao, Lei Li
  Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation
  • Sam Henry, Clint Cuffy, Bridget McInnes
  Investigating the Documentation of Electronic Cigarette Use in the Veteran Affairs Electronic Health Record: A Pilot Study
  • Danielle Mowery, Brett South, Olga Patterson, Shu-Hong Zhu, Mike Conway
  Automated Preamble Detection in Dictated Medical Reports
  • Wael Salloum, Greg Finley, Erik Edwards, Mark Miller, David Suendermann-Oeft
  A Biomedical Question Answering System in BioASQ 2017
  • Mourad Sarrouti and Said Ouatik El Alaoui
  Adapting Pre-trained Word Embeddings For Use In Medical Coding
  • Kevin Patel, Divya Patel, Mansi Golakiya, Pushpak Bhattacharyya, Nilesh Birari
  Initializing neural networks for hierarchical multi-label text classification
  • Simon Baker and Anna Korhonen
  Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models
  • Rahul V S S Patchigolla, Sunil Sahu, Ashish Anand
  Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks
  • Chen Lin, Timothy Miller, Dmitriy Dligach, Steven Bethard, Guergana Savova
  Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods
  • Sarvnaz Karimi, Xiang Dai, Hamedh Hassanzadeh, Anthony Nguyen
  Automatic classification of doctor-patient questions for a virtual patient record query task.
  • Leonardo Campillos Llanos, Sophie Rosset, Pierre Zweigenbaum
  Assessing the performance of Olelo, a real-time biomedical question answering application
  • Mariana Neves, Fabian Eckert, Hendrik Folkerts, Matthias Uflacker
  Clinical Event Detection with Hybrid Neural Architecture
  • Adyasha Maharana
  Extracting Personal Medical Events for User Timeline Construction using Minimal Supervision
  • Aakanksha Naik, Chris Bogart, Carolyn Rose
  Detecting mentions of pain and acute confusion in Finnish clinical text
  • Hans Moen, Kai Hakala, Farrokh Mehryary, Laura-Maria Peltonen, Tapio Salakoski, Filip Ginter, Sanna Salanterä
  A Multi-strategy Query Processing Approach for Biomedical Question Answering: USTB\_PRIR at BioASQ 2017 Task 5B
  • Zan-Xia Jin, Bo-Wen Zhang, Fan Fang, Le-Le Zhang, Xu-Cheng Yin