Proceedings of the 15th Workshop on Biomedical Natural Language Processing

Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor 2016-08 Association for Computational Linguistics Berlin, Germany text conference publication ws-2016-biomedical https://aclanthology.org/W16-2900/ A Machine Learning Approach to Clinical Terms Normalization José Castaño author María Laura Gambarte author Hee Joon Park author Maria del Pilar Avila Williams author David Pérez author Fernando Campos author Daniel Luna author Sonia Benítez author Hernán Berinsky author Sofía Zanetti author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication castano-etal-2016-machine 10.18653/v1/W16-2901 https://aclanthology.org/W16-2901/ 2016-08 1 11 Improved Semantic Representation for Domain-Specific Entities Mohammad Taher Pilehvar author Nigel Collier author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication pilehvar-collier-2016-improved 10.18653/v1/W16-2902 https://aclanthology.org/W16-2902/ 2016-08 12 16 Identification, characterization, and grounding of gradable terms in clinical text Chaitanya Shivade author Marie-Catherine de Marneffe author Eric Fosler-Lussier author Albert M Lai author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication shivade-etal-2016-identification 10.18653/v1/W16-2903 https://aclanthology.org/W16-2903/ 2016-08 17 26 Graph-based Semi-supervised Gene Mention Tagging Golnar Sheikhshab author Elizabeth Starks author Aly Karsan author Anoop Sarkar author Inanc Birol author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication sheikhshab-etal-2016-graph 10.18653/v1/W16-2904 https://aclanthology.org/W16-2904/ 2016-08 27 35 Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses Dayne Freitag author John Niekrasz author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication freitag-niekrasz-2016-feature 10.18653/v1/W16-2905 https://aclanthology.org/W16-2905/ 2016-08 36 45 Inferring Implicit Causal Relationships in Biomedical Literature Halil Kilicoglu author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication kilicoglu-2016-inferring 10.18653/v1/W16-2906 https://aclanthology.org/W16-2906/ 2016-08 46 55 SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction Marco A Valenzuela-Escárcega author Gus Hahn-Powell author Dane Bell author Mihai Surdeanu author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication valenzuela-escarcega-etal-2016-snaptogrid 10.18653/v1/W16-2907 https://aclanthology.org/W16-2907/ 2016-08 56 65 Character based String Kernels for Bio-Entity Relation Detection Ritambhara Singh author Yanjun Qi author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication singh-qi-2016-character 10.18653/v1/W16-2908 https://aclanthology.org/W16-2908/ 2016-08 66 71 Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge Amy Siu author Patrick Ernst author Gerhard Weikum author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication siu-etal-2016-disambiguation 10.18653/v1/W16-2909 https://aclanthology.org/W16-2909/ 2016-08 72 76 Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts Stéphan Tulkens author Simon Suster author Walter Daelemans author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication tulkens-etal-2016-using 10.18653/v1/W16-2910 https://aclanthology.org/W16-2910/ 2016-08 77 82 Unsupervised Document Classification with Informed Topic Models Timothy Miller author Dmitriy Dligach author Guergana Savova author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication miller-etal-2016-unsupervised 10.18653/v1/W16-2911 https://aclanthology.org/W16-2911/ 2016-08 83 91 Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes Sumithra Velupillai author Danielle L Mowery author Mike Conway author John Hurdle author Brent Kious author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication velupillai-etal-2016-vocabulary 10.18653/v1/W16-2912 https://aclanthology.org/W16-2912/ 2016-08 92 101 Syntactic analyses and named entity recognition for PubMed and PubMed Central — up-to-the-minute Kai Hakala author Suwisa Kaewphan author Tapio Salakoski author Filip Ginter author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication hakala-etal-2016-syntactic 10.18653/v1/W16-2913 https://aclanthology.org/W16-2913/ 2016-08 102 107 Improving Temporal Relation Extraction with Training Instance Augmentation Chen Lin author Timothy Miller author Dmitriy Dligach author Steven Bethard author Guergana Savova author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication lin-etal-2016-improving 10.18653/v1/W16-2914 https://aclanthology.org/W16-2914/ 2016-08 108 113 Using Centroids of Word Embeddings and Word Mover’s Distance for Biomedical Document Retrieval in Question Answering Georgios-Ioannis Brokos author Prodromos Malakasiotis author Ion Androutsopoulos author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication brokos-etal-2016-using 10.18653/v1/W16-2915 https://aclanthology.org/W16-2915/ 2016-08 114 118 Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway Michael Spranger author Sucheendra Palaniappan author Samik Gosh author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication spranger-etal-2016-measuring 10.18653/v1/W16-2916 https://aclanthology.org/W16-2916/ 2016-08 119 127 Construction of a Personal Experience Tweet Corpus for Health Surveillance Keyuan Jiang author Ricardo Calix author Matrika Gupta author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication jiang-etal-2016-construction 10.18653/v1/W16-2917 https://aclanthology.org/W16-2917/ 2016-08 128 135 Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification Nut Limsopatham author Nigel Collier author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication limsopatham-collier-2016-modelling 10.18653/v1/W16-2918 https://aclanthology.org/W16-2918/ 2016-08 136 140 PubTermVariants: biomedical term variants and their use for PubMed search Lana Yeganova author Won Kim author Sun Kim author Rezarta Islamaj Doğan author Wanli Liu author Donald C Comeau author Zhiyong Lu author W John Wilbur author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication yeganova-etal-2016-pubtermvariants 10.18653/v1/W16-2919 https://aclanthology.org/W16-2919/ 2016-08 141 145 This before That: Causal Precedence in the Biomedical Domain Gus Hahn-Powell author Dane Bell author Marco A Valenzuela-Escárcega author Mihai Surdeanu author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication hahn-powell-etal-2016-causal 10.18653/v1/W16-2920 https://aclanthology.org/W16-2920/ 2016-08 146 155 Syntactic methods for negation detection in radiology reports in Spanish Viviana Cotik author Vanesa Stricker author Jorge Vivaldi author Horacio Rodriguez author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication cotik-etal-2016-syntactic 10.18653/v1/W16-2921 https://aclanthology.org/W16-2921/ 2016-08 156 165 How to Train good Word Embeddings for Biomedical NLP Billy Chiu author Gamal Crichton author Anna Korhonen author Sampo Pyysalo author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication chiu-etal-2016-train 10.18653/v1/W16-2922 https://aclanthology.org/W16-2922/ 2016-08 166 174 An Information Foraging Approach to Determining the Number of Relevant Features Brian Connolly author Benjamin Glass author John Pestian author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication connolly-etal-2016-information 10.18653/v1/W16-2923 https://aclanthology.org/W16-2923/ 2016-08 175 180 Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians Brian E Chapman author Danielle L Mowery author Evan Narasimhan author Neel Patel author Wendy Chapman author Marta Heilbrun author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication chapman-etal-2016-assessing 10.18653/v1/W16-2924 https://aclanthology.org/W16-2924/ 2016-08 181 185 Building a dictionary of lexical variants for phenotype descriptors Simon Kocbek author Tudor Groza author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication kocbek-groza-2016-building 10.18653/v1/W16-2925 https://aclanthology.org/W16-2925/ 2016-08 186 190 Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections Olof Jacobson author Hercules Dalianis author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication jacobson-dalianis-2016-applying 10.18653/v1/W16-2926 https://aclanthology.org/W16-2926/ 2016-08 191 195 Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning Genevieve Gorrell author Sherifat Oduola author Angus Roberts author Tom Craig author Craig Morgan author Rob Stewart author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication gorrell-etal-2016-identifying 10.18653/v1/W16-2927 https://aclanthology.org/W16-2927/ 2016-08 196 205 Relation extraction from clinical texts using domain invariant convolutional neural network Sunil Sahu author Ashish Anand author Krishnadev Oruganty author Mahanandeeshwar Gattu author 2016-08 text Proceedings of the 15th Workshop on Biomedical Natural Language Processing Kevin Bretonnel Cohen editor Dina Demner-Fushman editor Sophia Ananiadou editor Jun-ichi Tsujii editor Association for Computational Linguistics Berlin, Germany conference publication sahu-etal-2016-relation 10.18653/v1/W16-2928 https://aclanthology.org/W16-2928/ 2016-08 206 215