Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor 2008-06 Association for Computational Linguistics Columbus, Ohio text conference publication ws-2008-current https://aclanthology.org/W08-0600/ A Graph Kernel for Protein-Protein Interaction Extraction Antti Airola author Sampo Pyysalo author Jari Björne author Tapio Pahikkala author Filip Ginter author Tapio Salakoski author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication airola-etal-2008-graph https://aclanthology.org/W08-0601/ 2008-06 1 9 Extracting Clinical Relationships from Patient Narratives Angus Roberts author Robert Gaizauskas author Mark Hepple author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication roberts-etal-2008-extracting https://aclanthology.org/W08-0602/ 2008-06 10 18 Using Automated Feature Optimisation to Create an Adaptable Relation Extraction System Barry Haddow author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication haddow-2008-using https://aclanthology.org/W08-0603/ 2008-06 19 27 Mining the Biomedical Literature for Genic Information Catalina O Tudor author K Vijay-Shanker author Carl J Schmidt author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication tudor-etal-2008-mining https://aclanthology.org/W08-0604/ 2008-06 28 29 Accelerating the Annotation of Sparse Named Entities by Dynamic Sentence Selection Yoshimasa Tsuruoka author Jun’ichi Tsujii author Sophia Ananiadou author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication tsuruoka-etal-2008-accelerating https://aclanthology.org/W08-0605/ 2008-06 30 37 The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts György Szarvas author Veronika Vincze author Richárd Farkas author János Csirik author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication szarvas-etal-2008-bioscope https://aclanthology.org/W08-0606/ 2008-06 38 45 Recognizing Speculative Language in Biomedical Research Articles: A Linguistically Motivated Perspective Halil Kilicoglu author Sabine Bergler author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication kilicoglu-bergler-2008-recognizing https://aclanthology.org/W08-0607/ 2008-06 46 53 Cascaded Classifiers for Confidence-Based Chemical Named Entity Recognition Peter Corbett author Ann Copestake author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication corbett-copestake-2008-cascaded https://aclanthology.org/W08-0608/ 2008-06 54 62 How to Make the Most of NE Dictionaries in Statistical NER Yutaka Sasaki author Yoshimasa Tsuruoka author John McNaught author Sophia Ananiadou author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication sasaki-etal-2008-make https://aclanthology.org/W08-0609/ 2008-06 63 70 Species Disambiguation for Biomedical Term Identification Xinglong Wang author Michael Matthews author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication wang-matthews-2008-species https://aclanthology.org/W08-0610/ 2008-06 71 79 Knowledge Sources for Word Sense Disambiguation of Biomedical Text Mark Stevenson author Yinkun Guo author Robert Gaizauskas author David Martinez author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication stevenson-etal-2008-knowledge https://aclanthology.org/W08-0611/ 2008-06 80 87 Automatic inference of indexing rules for MEDLINE Aurélie Névéol author Sonya Shooshan author Vincent Claveau author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication neveol-etal-2008-automatic https://aclanthology.org/W08-0612/ 2008-06 88 89 Prediction of Protein Sub-cellular Localization using Information from Texts and Sequences. Hong-Woo Chun author Chisato Yamasaki author Naomi Saichi author Masayuki Tanaka author Teruyoshi Hishiki author Tadashi Imanishi author Takashi Gojobori author Jin-Dong Kim author Jun’ichi Tsujii author Toshihisa Takagi author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication chun-etal-2008-prediction https://aclanthology.org/W08-0613/ 2008-06 90 91 A Pilot Annotation to Investigate Discourse Connectivity in Biomedical Text Hong Yu author Nadya Frid author Susan McRoy author Rashmi Prasad author Alan Lee author Aravind Joshi author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication yu-etal-2008-pilot https://aclanthology.org/W08-0614/ 2008-06 92 93 Conditional Random Fields and Support Vector Machines for Disorder Named Entity Recognition in Clinical Texts Dingcheng Li author Guergana Savova author Karin Kipper-Schuler author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication li-etal-2008-conditional https://aclanthology.org/W08-0615/ 2008-06 94 95 Using Natural Language Processing to Classify Suicide Notes John Pestian author Pawel Matykiewicz author Jacqueline Grupp-Phelan author Sarah Arszman Lavanier author Jennifer Combs author Robert Kowatch author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication pestian-etal-2008-using https://aclanthology.org/W08-0616/ 2008-06 96 97 Extracting Protein-Protein Interaction based on Discriminative Training of the Hidden Vector State Model Deyu Zhou author Yulan He author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication zhou-he-2008-extracting https://aclanthology.org/W08-0617/ 2008-06 98 99 A preliminary approach to extract drugs by combining UMLS resources and USAN naming conventions Isabel Segura-Bedmar author Paloma Martínez author Doaa Samy author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication segura-bedmar-etal-2008-preliminary https://aclanthology.org/W08-0618/ 2008-06 100 101 Mapping Clinical Notes to Medical Terminologies at Point of Care Yefeng Wang author Jon Patrick author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication wang-patrick-2008-mapping https://aclanthology.org/W08-0619/ 2008-06 102 103 An Approach to Reducing Annotation Costs for BioNLP Michael Bloodgood author K Vijay-Shanker author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication bloodgood-vijay-shanker-2008-approach https://aclanthology.org/W08-0620/ 2008-06 104 105 Temporal Annotation of Clinical Text Danielle Mowery author Henk Harkema author Wendy Chapman author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication mowery-etal-2008-temporal https://aclanthology.org/W08-0621/ 2008-06 106 107 CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem Mariana Neves author Monica Chagoyen author José María Carazo author Alberto Pascual-Montano author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication neves-etal-2008-cbr https://aclanthology.org/W08-0622/ 2008-06 108 109 Textual Information for Predicting Functional Properties of the Genes Oana Frunza author Diana Inkpen author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication frunza-inkpen-2008-textual https://aclanthology.org/W08-0623/ 2008-06 110 111 Determining causal and non-causal relationships in biomedical text by classifying verbs using a Naive Bayesian Classifier Pieter van der Horn author Bart Bakker author Gijs Geleijnse author Jan Korst author Sergei Kurkin author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication van-der-horn-etal-2008-determining https://aclanthology.org/W08-0624/ 2008-06 112 113 Statistical Term Profiling for Query Pattern Mining Paul Buitelaar author Pinar Oezden Wennerberg author Sonja Zillner author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication buitelaar-etal-2008-statistical https://aclanthology.org/W08-0625/ 2008-06 114 115 Using Language Models to Identify Language Impairment in Spanish-English Bilingual Children Thamar Solorio author Yang Liu author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication solorio-liu-2008-using https://aclanthology.org/W08-0626/ 2008-06 116 117 Raising the Compatibility of Heterogeneous Annotations: A Case Study on Yue Wang author Kazuhiro Yoshida author Jin-Dong Kim author Rune Saetre author Jun’ichi Tsujii author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication wang-etal-2008-raising https://aclanthology.org/W08-0627/ 2008-06 118 119 Adaptive Information Extraction for Complex Biomedical Tasks Donghui Feng author Gully Burns author Eduard Hovy author 2008-06 text Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing Dina Demner-Fushman editor Sophia Ananiadou editor Kevin Bretonnel Cohen editor John Pestian editor Jun’ichi Tsujii editor Bonnie Webber editor Association for Computational Linguistics Columbus, Ohio conference publication feng-etal-2008-adaptive https://aclanthology.org/W08-0628/ 2008-06 120 121