%0 Conference Proceedings
%T Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%E Cohen, Kevin Bretonnel
%E Demner-Fushman, Dina
%E Ananiadou, Sophia
%E Tsujii, Jun-ichi
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F ws-2016-biomedical
%R 10.18653/v1/W16-29
%U https://aclanthology.org/W16-2900
%U https://doi.org/10.18653/v1/W16-29

%0 Conference Proceedings
%T A Machine Learning Approach to Clinical Terms Normalization
%A Castaño, José
%A Gambarte, María Laura
%A Park, Hee Joon
%A del Pilar Avila Williams, Maria
%A Pérez, David
%A Campos, Fernando
%A Luna, Daniel
%A Benítez, Sonia
%A Berinsky, Hernán
%A Zanetti, Sofía
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F castano-etal-2016-machine
%R 10.18653/v1/W16-2901
%U https://aclanthology.org/W16-2901
%U https://doi.org/10.18653/v1/W16-2901
%P 1-11

%0 Conference Proceedings
%T Improved Semantic Representation for Domain-Specific Entities
%A Pilehvar, Mohammad Taher
%A Collier, Nigel
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F pilehvar-collier-2016-improved
%R 10.18653/v1/W16-2902
%U https://aclanthology.org/W16-2902
%U https://doi.org/10.18653/v1/W16-2902
%P 12-16

%0 Conference Proceedings
%T Identification, characterization, and grounding of gradable terms in clinical text
%A Shivade, Chaitanya
%A de Marneffe, Marie-Catherine
%A Fosler-Lussier, Eric
%A Lai, Albert M.
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F shivade-etal-2016-identification
%R 10.18653/v1/W16-2903
%U https://aclanthology.org/W16-2903
%U https://doi.org/10.18653/v1/W16-2903
%P 17-26

%0 Conference Proceedings
%T Graph-based Semi-supervised Gene Mention Tagging
%A Sheikhshab, Golnar
%A Starks, Elizabeth
%A Karsan, Aly
%A Sarkar, Anoop
%A Birol, Inanc
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F sheikhshab-etal-2016-graph
%R 10.18653/v1/W16-2904
%U https://aclanthology.org/W16-2904
%U https://doi.org/10.18653/v1/W16-2904
%P 27-35

%0 Conference Proceedings
%T Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses
%A Freitag, Dayne
%A Niekrasz, John
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F freitag-niekrasz-2016-feature
%R 10.18653/v1/W16-2905
%U https://aclanthology.org/W16-2905
%U https://doi.org/10.18653/v1/W16-2905
%P 36-45

%0 Conference Proceedings
%T Inferring Implicit Causal Relationships in Biomedical Literature
%A Kilicoglu, Halil
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F kilicoglu-2016-inferring
%R 10.18653/v1/W16-2906
%U https://aclanthology.org/W16-2906
%U https://doi.org/10.18653/v1/W16-2906
%P 46-55

%0 Conference Proceedings
%T SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction
%A Valenzuela-Escárcega, Marco A.
%A Hahn-Powell, Gus
%A Bell, Dane
%A Surdeanu, Mihai
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F valenzuela-escarcega-etal-2016-snaptogrid
%R 10.18653/v1/W16-2907
%U https://aclanthology.org/W16-2907
%U https://doi.org/10.18653/v1/W16-2907
%P 56-65

%0 Conference Proceedings
%T Character based String Kernels for Bio-Entity Relation Detection
%A Singh, Ritambhara
%A Qi, Yanjun
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F singh-qi-2016-character
%R 10.18653/v1/W16-2908
%U https://aclanthology.org/W16-2908
%U https://doi.org/10.18653/v1/W16-2908
%P 66-71

%0 Conference Proceedings
%T Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge
%A Siu, Amy
%A Ernst, Patrick
%A Weikum, Gerhard
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F siu-etal-2016-disambiguation
%R 10.18653/v1/W16-2909
%U https://aclanthology.org/W16-2909
%U https://doi.org/10.18653/v1/W16-2909
%P 72-76

%0 Conference Proceedings
%T Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts
%A Tulkens, Stéphan
%A Suster, Simon
%A Daelemans, Walter
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F tulkens-etal-2016-using
%R 10.18653/v1/W16-2910
%U https://aclanthology.org/W16-2910
%U https://doi.org/10.18653/v1/W16-2910
%P 77-82

%0 Conference Proceedings
%T Unsupervised Document Classification with Informed Topic Models
%A Miller, Timothy
%A Dligach, Dmitriy
%A Savova, Guergana
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F miller-etal-2016-unsupervised
%R 10.18653/v1/W16-2911
%U https://aclanthology.org/W16-2911
%U https://doi.org/10.18653/v1/W16-2911
%P 83-91

%0 Conference Proceedings
%T Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes
%A Velupillai, Sumithra
%A Mowery, Danielle L.
%A Conway, Mike
%A Hurdle, John
%A Kious, Brent
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F velupillai-etal-2016-vocabulary
%R 10.18653/v1/W16-2912
%U https://aclanthology.org/W16-2912
%U https://doi.org/10.18653/v1/W16-2912
%P 92-101

%0 Conference Proceedings
%T Syntactic analyses and named entity recognition for PubMed and PubMed Central — up-to-the-minute
%A Hakala, Kai
%A Kaewphan, Suwisa
%A Salakoski, Tapio
%A Ginter, Filip
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F hakala-etal-2016-syntactic
%R 10.18653/v1/W16-2913
%U https://aclanthology.org/W16-2913
%U https://doi.org/10.18653/v1/W16-2913
%P 102-107

%0 Conference Proceedings
%T Improving Temporal Relation Extraction with Training Instance Augmentation
%A Lin, Chen
%A Miller, Timothy
%A Dligach, Dmitriy
%A Bethard, Steven
%A Savova, Guergana
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F lin-etal-2016-improving
%R 10.18653/v1/W16-2914
%U https://aclanthology.org/W16-2914
%U https://doi.org/10.18653/v1/W16-2914
%P 108-113

%0 Conference Proceedings
%T Using Centroids of Word Embeddings and Word Mover’s Distance for Biomedical Document Retrieval in Question Answering
%A Brokos, Georgios-Ioannis
%A Malakasiotis, Prodromos
%A Androutsopoulos, Ion
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F brokos-etal-2016-using
%R 10.18653/v1/W16-2915
%U https://aclanthology.org/W16-2915
%U https://doi.org/10.18653/v1/W16-2915
%P 114-118

%0 Conference Proceedings
%T Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway
%A Spranger, Michael
%A Palaniappan, Sucheendra
%A Gosh, Samik
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F spranger-etal-2016-measuring
%R 10.18653/v1/W16-2916
%U https://aclanthology.org/W16-2916
%U https://doi.org/10.18653/v1/W16-2916
%P 119-127

%0 Conference Proceedings
%T Construction of a Personal Experience Tweet Corpus for Health Surveillance
%A Jiang, Keyuan
%A Calix, Ricardo
%A Gupta, Matrika
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F jiang-etal-2016-construction
%R 10.18653/v1/W16-2917
%U https://aclanthology.org/W16-2917
%U https://doi.org/10.18653/v1/W16-2917
%P 128-135

%0 Conference Proceedings
%T Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification
%A Limsopatham, Nut
%A Collier, Nigel
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F limsopatham-collier-2016-modelling
%R 10.18653/v1/W16-2918
%U https://aclanthology.org/W16-2918
%U https://doi.org/10.18653/v1/W16-2918
%P 136-140

%0 Conference Proceedings
%T PubTermVariants: biomedical term variants and their use for PubMed search
%A Yeganova, Lana
%A Kim, Won
%A Kim, Sun
%A Islamaj Doğan, Rezarta
%A Liu, Wanli
%A Comeau, Donald C.
%A Lu, Zhiyong
%A Wilbur, W. John
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F yeganova-etal-2016-pubtermvariants
%R 10.18653/v1/W16-2919
%U https://aclanthology.org/W16-2919
%U https://doi.org/10.18653/v1/W16-2919
%P 141-145

%0 Conference Proceedings
%T This before That: Causal Precedence in the Biomedical Domain
%A Hahn-Powell, Gus
%A Bell, Dane
%A Valenzuela-Escárcega, Marco A.
%A Surdeanu, Mihai
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F hahn-powell-etal-2016-causal
%R 10.18653/v1/W16-2920
%U https://aclanthology.org/W16-2920
%U https://doi.org/10.18653/v1/W16-2920
%P 146-155

%0 Conference Proceedings
%T Syntactic methods for negation detection in radiology reports in Spanish
%A Cotik, Viviana
%A Stricker, Vanesa
%A Vivaldi, Jorge
%A Rodriguez, Horacio
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F cotik-etal-2016-syntactic
%R 10.18653/v1/W16-2921
%U https://aclanthology.org/W16-2921
%U https://doi.org/10.18653/v1/W16-2921
%P 156-165

%0 Conference Proceedings
%T How to Train good Word Embeddings for Biomedical NLP
%A Chiu, Billy
%A Crichton, Gamal
%A Korhonen, Anna
%A Pyysalo, Sampo
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F chiu-etal-2016-train
%R 10.18653/v1/W16-2922
%U https://aclanthology.org/W16-2922
%U https://doi.org/10.18653/v1/W16-2922
%P 166-174

%0 Conference Proceedings
%T An Information Foraging Approach to Determining the Number of Relevant Features
%A Connolly, Brian
%A Glass, Benjamin
%A Pestian, John
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F connolly-etal-2016-information
%R 10.18653/v1/W16-2923
%U https://aclanthology.org/W16-2923
%U https://doi.org/10.18653/v1/W16-2923
%P 175-180

%0 Conference Proceedings
%T Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians
%A Chapman, Brian E.
%A Mowery, Danielle L.
%A Narasimhan, Evan
%A Patel, Neel
%A Chapman, Wendy
%A Heilbrun, Marta
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F chapman-etal-2016-assessing
%R 10.18653/v1/W16-2924
%U https://aclanthology.org/W16-2924
%U https://doi.org/10.18653/v1/W16-2924
%P 181-185

%0 Conference Proceedings
%T Building a dictionary of lexical variants for phenotype descriptors
%A Kocbek, Simon
%A Groza, Tudor
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F kocbek-groza-2016-building
%R 10.18653/v1/W16-2925
%U https://aclanthology.org/W16-2925
%U https://doi.org/10.18653/v1/W16-2925
%P 186-190

%0 Conference Proceedings
%T Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections
%A Jacobson, Olof
%A Dalianis, Hercules
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F jacobson-dalianis-2016-applying
%R 10.18653/v1/W16-2926
%U https://aclanthology.org/W16-2926
%U https://doi.org/10.18653/v1/W16-2926
%P 191-195

%0 Conference Proceedings
%T Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning
%A Gorrell, Genevieve
%A Oduola, Sherifat
%A Roberts, Angus
%A Craig, Tom
%A Morgan, Craig
%A Stewart, Rob
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F gorrell-etal-2016-identifying
%R 10.18653/v1/W16-2927
%U https://aclanthology.org/W16-2927
%U https://doi.org/10.18653/v1/W16-2927
%P 196-205

%0 Conference Proceedings
%T Relation extraction from clinical texts using domain invariant convolutional neural network
%A Sahu, Sunil
%A Anand, Ashish
%A Oruganty, Krishnadev
%A Gattu, Mahanandeeshwar
%Y Cohen, Kevin Bretonnel
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Tsujii, Jun-ichi
%S Proceedings of the 15th Workshop on Biomedical Natural Language Processing
%D 2016
%8 August
%I Association for Computational Linguistics
%C Berlin, Germany
%F sahu-etal-2016-relation
%R 10.18653/v1/W16-2928
%U https://aclanthology.org/W16-2928
%U https://doi.org/10.18653/v1/W16-2928
%P 206-215