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Special Interest Group on Biomedical Natural Language Processing


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2015 Proceedings of BioNLP 15
2012 BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
2011 Proceedings of BioNLP 2011 Workshop
Proceedings of BioNLP Shared Task 2011 Workshop
2009 Proceedings of the BioNLP 2009 Workshop
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task


  1. Proceedings of BioNLP 15

  2. W15-38 [bib]: Entire Volume
  3. W15-3800 [bib]: Front Matter

  4. W15-3801 [bib]: James Allen; Will de Beaumont; Lucian Galescu; Choh Man Teng
    Complex Event Extraction using DRUM
  5. W15-3802 [bib]: Roland Roller; Mark Stevenson
    Making the most of limited training data using distant supervision
  6. W15-3803 [bib]: Yifan Peng; Samir Gupta; Cathy Wu; Vijay Shanker
    An extended dependency graph for relation extraction in biomedical texts
  7. W15-3804 [bib]: Chrysoula Zerva; Sophia Ananiadou
    Event Extraction in pieces:Tackling the partial event identification problem on unseen corpora
  8. W15-3805 [bib]: Michael Spranger; Sucheendra Palaniappan; Samik Ghosh
    Extracting Biological Pathway Models From NLP Event Representations
  9. W15-3806 [bib]: Ramesh Nallapati; Radu Florian
    Shallow Training is cheap but is it good enough? Experiments with Medical Fact Coding
  10. W15-3807 [bib]: Youngjun Kim; Ellen Riloff
    Stacked Generalization for Medical Concept Extraction from Clinical Notes
  11. W15-3808 [bib]: Mohsen Hassan; Olfa Makkaoui; Adrien Coulet; Yannick Toussain
    Extracting Disease-Symptom Relationships by Learning Syntactic Patterns from Dependency Graphs
  12. W15-3809 [bib]: Timothy Miller; Steven Bethard; Dmitriy Dligach; Chen Lin; Guergana Savova
    Extracting Time Expressions from Clinical Text
  13. W15-3810 [bib]: Yue Liu; Tao Ge; Kusum Mathews; Heng Ji; Deborah McGuinness
    Exploiting Task-Oriented Resources to Learn Word Embeddings for Clinical Abbreviation Expansion
  14. W15-3811 [bib]: Amy Siu; Gerhard Weikum
    Semantic Type Classification of Common Words in Biomedical Noun Phrases
  15. W15-3812 [bib]: Rize Jin; Jinseon You; Jin-Woo Chung; Hee-Jin Lee; Maria Wolters; Jong Park
    CoMAGD: Annotation of Gene-Depression Relations
  16. W15-3813 [bib]: Meizhi Ju; Haomin Li; Huilong Duan
    Lexical Characteristics Analysis of Chinese Clinical Documents
  17. W15-3814 [bib]: Chen Li; Runqing Song; Maria Liakata; Andreas Vlachos; Stephanie Seneff; Xiangrong Zhang
    Using word embedding for bio-event extraction
  18. W15-3815 [bib]: Samuel J. Severance; K. Bretonnel Cohen
    Measuring the readability of medical research journal abstracts
  19. W15-3816 [bib]: Weisong Liu; Shu Cai
    Translating Electronic Health Record Notes from English to Spanish: A Preliminary Study
  20. W15-3817 [bib]: Abdulaziz Alamri; Mark Stevenson
    Automatic Detection of Answers to Research Questions from Medline Abstracts
  21. W15-3818 [bib]: Jitendra Jonnagaddala; Hong-Jie Dai; Pradeep Ray; Siaw-Teng Liaw
    A preliminary study on automatic identification of patient smoking status in unstructured electronic health records
  22. W15-3819 [bib]: Borbála Siklósi; Attila Novák
    Restoring the intended structure of Hungarian ophthalmology documents
  23. W15-3820 [bib]: MUNEEB TH; Sunil Sahu; Ashish Anand
    Evaluating distributed word representations for capturing semantics of biomedical concepts
  24. W15-3821 [bib]: Antonio Jimeno Yepes; Andrew MacKinlay; Bo Han
    Investigating Public Health Surveillance using Twitter
  25. W15-3822 [bib]: yonghui wu; Jun Xu; Yaoyun Zhang; Hua Xu
    Clinical Abbreviation Disambiguation Using Neural Word Embeddings
  26. W15-3823 [bib] [attachment]: Na Hong; Dingcheng Li; Yue Yu; Hongfang Liu; Christopher G. Chute; Guoqian Jiang
    Representing Clinical Diagnostic Criteria in Quality Data Model Using Natural Language Processing


  1. BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing

  2. W12-24 [bib]: Entire Volume
  3. W12-2400 [bib]: Front Matter

  4. W12-2401 [bib]: Emily Prud'hommeaux; Brian Roark
    Graph-based alignment of narratives for automated neurological assessment
  5. W12-2402 [bib]: Dana Movshovitz-Attias; William W. Cohen
    Bootstrapping Biomedical Ontologies for Scientific Text using NELL
  6. W12-2403 [bib]: Marie Dupuch; Laëtitia Dupuch; Thierry Hamon; Natalia Grabar
    Semantic distance and terminology structuring methods for the detection of semantically close terms
  7. W12-2404 [bib]: Preethi Raghavan; Eric Fosler-Lussier; Albert Lai
    Temporal Classification of Medical Events
  8. W12-2405 [bib]: James Cogley; Nicola Stokes; Joe Carthy; John Dunnion
    Analyzing Patient Records to Establish If and When a Patient Suffered from a Medical Condition
  9. W12-2406 [bib]: Dana Movshovitz-Attias; William W. Cohen
    Alignment-HMM-based Extraction of Abbreviations from Biomedical Text
  10. W12-2407 [bib]: Danielle L. Mowery; Sumithra Velupillai; Wendy W. Chapman
    Medical diagnosis lost in translation – Analysis of uncertainty and negation expressions in English and Swedish clinical texts
  11. W12-2408 [bib]: Oscar Ferrandez; Brett South; Shuying Shen; Stephane Meystre
    A Hybrid Stepwise Approach for De-identifying Person Names in Clinical Documents
  12. W12-2409 [bib]: Timothy Miller; Dmitriy Dligach; Guergana Savova
    Active Learning for Coreference Resolution
  13. W12-2410 [bib]: Jari Björne; Sofie Van Landeghem; Sampo Pyysalo; Tomoko Ohta; Filip Ginter; Yves Van de Peer; Sophia Ananiadou; Tapio Salakoski
    PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations
  14. W12-2411 [bib]: Rezarta Islamaj Dogan; Zhiyong Lu
    An improved corpus of disease mentions in PubMed citations
  15. W12-2412 [bib]: Sampo Pyysalo; Pontus Stenetorp; Tomoko Ohta; Jin-Dong Kim; Sophia Ananiadou
    New Resources and Perspectives for Biomedical Event Extraction
  16. W12-2413 [bib]: Thierry Hamon; Christopher Engström; Mounira Manser; Zina Badji; Natalia Grabar; Sergei Silvestrov
    Combining Compositionality and Pagerank for the Identification of Semantic Relations between Biomedical Words
  17. W12-2414 [bib]: Emilia Apostolova; Noriko Tomuro; Pattanasak Mongkolwat; Dina Demner-Fushman
    Domain Adaptation of Coreference Resolution for Radiology Reports
  18. W12-2415 [bib]: Attapol Thamrongrattanarit; Michael Shafir; Michael Crivaro; Bensiin Borukhov; Marie Meteer
    What can NLP tell us about BioNLP?
  19. W12-2416 [bib]: Brett South; Shuying Shen; Jianwei Leng; Tyler Forbush; Scott DuVall; Wendy Chapman
    A Prototype Tool Set to Support Machine-Assisted Annotation
  20. W12-2417 [bib]: Marie Meteer; Borukhov Bensiin; Mike Crivaro; Michael Shafir; Attapol Thamrongrattanarit
    MedLingMap: A growing resource mapping the Bio-Medical NLP field
  21. W12-2418 [bib]: Shefali Sharma; Leslie Lange; Jose Luis Ambite; Yigal Arens; Chun-Nan Hsu
    Exploring Label Dependency in Active Learning for Phenotype Mapping
  22. W12-2419 [bib]: Ramnath Balasubramanyan; Kathryn Rivard; William W. Cohen; Jelena Jakovljevic; John L. Woolford
    Evaluating Joint Modeling of Yeast Biology Literature and Protein-Protein Interaction Networks
  23. W12-2420 [bib]: Catalina Oana Tudor; K Vijay-Shanker
    RankPref: Ranking Sentences Describing Relations between Biomedical Entities with an Application
  24. W12-2421 [bib]: Ying Yan; Jee-Hyub Kim; Samuel Croset; Dietrich Rebholz-Schuhmann
    Finding small molecule and protein pairs in scientific literature using a bootstrapping method
  25. W12-2422 [bib]: Binod Gyawali; Thamar Solorio; Yassine Benajiba
    Grading the Quality of Medical Evidence
  26. W12-2423 [bib]: Sun Kim; Won Kim; Don Comeau; W. John Wilbur
    Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers
  27. W12-2424 [bib]: Pawel Matykiewicz; John Pestian
    Effect of small sample size on text categorization with support vector machines
  28. W12-2425 [bib]: Jin-Dong Kim; Yue Wang
    PubAnnotation - a persistent and sharable corpus and annotation repository
  29. W12-2426 [bib]: Richard Boyce; Gregory Gardner; Henk Harkema
    Using Natural Language Processing to Extract Drug-Drug Interaction Information from Package Inserts
  30. W12-2427 [bib]: Nate Sutton; Laura Wojtulewicz; Neel Mehta; Graciela Gonzalez
    Automatic Approaches for Gene-Drug Interaction Extraction from Biomedical Text: Corpus and Comparative Evaluation
  31. W12-2428 [bib]: Yaqiang Wang; Yiguang Liu; Zhonghua Yu; Li Chen; Yongguang Jiang
    A Preliminary Work on Symptom Name Recognition from Free-Text Clinical Records of Traditional Chinese Medicine using Conditional Random Fields and Reasonable Features
  32. W12-2429 [bib]: Weiwei Cheng; Judita Preiss; Mark Stevenson
    Scaling up WSD with Automatically Generated Examples
  33. W12-2430 [bib]: Yue Wang; Jin-Dong Kim
    Boosting the protein name recognition performance by bootstrapping on selected text


  1. Proceedings of BioNLP 2011 Workshop

  2. W11-02 [bib]: Entire Volume
  3. W11-0200 [bib]: Front Matter

  4. W11-0201 [bib]: Philippe Thomas; Stefan Pietschmann; Illès Solt; Domonkos Tikk; Ulf Leser
    Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text
  5. W11-0202 [bib]: Marek Rei; Ted Briscoe
    Unsupervised Entailment Detection between Dependency Graph Fragments
  6. W11-0203 [bib]: Chun-Nan Hsu; Cheng-Ju Kuo; Congxing Cai; Sarah Pendergrass; Marylyn Ritchie; Jose Luis Ambite
    Learning Phenotype Mapping for Integrating Large Genetic Data
  7. W11-0204 [bib]: Sofie Van Landeghem; Filip Ginter; Yves Van de Peer; Tapio Salakoski
    EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions
  8. W11-0205 [bib]: K. Bretonnel Cohen; Thomas Christiansen; William Baumgartner Jr.; Karin Verspoor; Lawrence Hunter
    Fast and simple semantic class assignment for biomedical text
  9. W11-0206 [bib]: Sandeep Pokkunuri; Cartic Ramakrishnan; Ellen Riloff; Eduard Hovy; Gully Burns
    The Role of Information Extraction in the Design of a Document Triage Application for Biocuration
  10. W11-0207 [bib]: Asma Ben Abacha; Pierre Zweigenbaum
    Medical Entity Recognition: A Comparaison of Semantic and Statistical Methods
  11. W11-0208 [bib]: Yu Usami; Han-Cheol Cho; Naoaki Okazaki; Jun'ichi Tsujii
    Automatic Acquisition of Huge Training Data for Bio-Medical Named Entity Recognition
  12. W11-0209 [bib]: He Tan; Rajaram Kaliyaperumal; Nirupama Benis
    Building frame-based corpus on the basis of ontological domain knowledge
  13. W11-0210 [bib]: Riza Theresa Batista-Navarro; Sophia Ananiadou
    Building a Coreference-Annotated Corpus from the Domain of Biochemistry
  14. W11-0211 [bib]: Malgorzata Marciniak; Agnieszka Mykowiecka
    Towards Morphologically Annotated Corpus of Hospital Discharge Reports in Polish
  15. W11-0212 [bib]: Catherine Blake; Wu Zheng
    In Search of Protein Locations
  16. W11-0213 [bib]: Aurelie Neveol; W. John Wilbur; Zhiyong Lu
    Automatic extraction of data deposition statements: where do the research results go?
  17. W11-0214 [bib]: Tomoko Ohta; Sampo Pyysalo; Jun'ichi Tsujii
    From Pathways to Biomolecular Events: Opportunities and Challenges
  18. W11-0215 [bib]: Sampo Pyysalo; Tomoko Ohta; Makoto Miwa; Jun'ichi Tsujii
    Towards Exhaustive Event Extraction for Protein Modifications
  19. W11-0216 [bib]: Faisal Md. Chowdhury; Alberto Lavelli; Alessandro Moschitti
    A Study on Dependency Tree Kernels for Automatic Extraction of Protein-Protein Interaction
  20. W11-0217 [bib]: Elizabeth White; K. Bretonnel Cohen; Larry Hunter
    Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles
  21. W11-0218 [bib]: Pontus Stenetorp; Sampo Pyysalo; Jun'ichi Tsujii
    SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation
  22. W11-0219 [bib]: Hyuckchul Jung; James Allen; Nate Blaylock; William de Beaumont; Lucian Galescu; Mary Swift
    Building Timelines from Narrative Clinical Records: Initial Results Based-on Deep Natural Language Understanding
  23. W11-0220 [bib]: Lana Yeganova; Donald C. Comeau; Won Kim; W. John Wilbur
    Text Mining Techniques for Leveraging Positively Labeled Data
  24. W11-0221 [bib]: Tadayoshi Hara; Yuka Tateisi; Jin-Dong Kim; Yusuke Miyao
    Parsing Natural Language Queries for Life Science Knowledge
  25. W11-0222 [bib]: Shao Fen Liang; Donia Scott; Robert Stevens; Alan Rector
    Unlocking Medical Ontologies for Non-Ontology Experts
  26. W11-0223 [bib]: Antonio Jimeno Yepes; Alan Aronson
    Self-training and co-training in biomedical word sense disambiguation
  27. W11-0224 [bib]: Marc Verhagen; James Pustejovsky
    Medstract - The Next Generation
  28. W11-0225 [bib]: Choochart Haruechaiyasak; Jaruwat Pailai; Wasna Viratyosin; Rachada Kongkachandra
    ThaiHerbMiner: A Thai Herbal Medicine Mining and Visualizing Tool
  29. Proceedings of BioNLP Shared Task 2011 Workshop

  30. W11-18 [bib]: Entire Volume
  31. W11-1800 [bib]: Front Matter

  32. W11-1801 [bib]: Jin-Dong Kim; Sampo Pyysalo; Tomoko Ohta; Robert Bossy; Ngan Nguyen; Jun'ichi Tsujii
    Overview of BioNLP Shared Task 2011
  33. W11-1802 [bib]: Jin-Dong Kim; Yue Wang; Toshihisa Takagi; Akinori Yonezawa
    Overview of Genia Event Task in BioNLP Shared Task 2011
  34. W11-1803 [bib]: Tomoko Ohta; Sampo Pyysalo; Jun'ichi Tsujii
    Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011
  35. W11-1804 [bib]: Sampo Pyysalo; Tomoko Ohta; Rafal Rak; Dan Sullivan; Chunhong Mao; Chunxia Wang; Bruno Sobral; Jun'ichi Tsujii; Sophia Ananiadou
    Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011
  36. W11-1805 [bib]: Andreas Vlachos; Mark Craven
    Biomedical Event Extraction from Abstracts and Full Papers using Search-based Structured Prediction
  37. W11-1806 [bib]: David McClosky; Mihai Surdeanu; Christopher Manning
    Event Extraction as Dependency Parsing for BioNLP 2011
  38. W11-1807 [bib]: Sebastian Riedel; Andrew McCallum
    Robust Biomedical Event Extraction with Dual Decomposition and Minimal Domain Adaptation
  39. W11-1808 [bib]: Sebastian Riedel; David McClosky; Mihai Surdeanu; Andrew McCallum; Christopher D. Manning
    Model Combination for Event Extraction in BioNLP 2011
  40. W11-1809 [bib]: Robert Bossy; Julien Jourde; Philippe Bessières; Maarten van de Guchte; Claire Nèdellec
    BioNLP Shared Task 2011 - Bacteria Biotope
  41. W11-1810 [bib]: Julien Jourde; Alain-Pierre Manine; Philippe Veber; Karën Fort; Robert Bossy; Erick Alphonse; Philippe Bessières
    BioNLP Shared Task 2011 – Bacteria Gene Interactions and Renaming
  42. W11-1811 [bib]: Ngan Nguyen; Jin-Dong Kim; Jun'ichi Tsujii
    Overview of BioNLP 2011 Protein Coreference Shared Task
  43. W11-1812 [bib]: Sampo Pyysalo; Tomoko Ohta; Jun'ichi Tsujii
    Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011
  44. W11-1813 [bib]: Youngjun Kim; Ellen Riloff; Nathan Gilbert
    The Taming of Reconcile as a Biomedical Coreference Resolver
  45. W11-1814 [bib]: Nhung T. H. Nguyen; Yoshimasa Tsuruoka
    Extracting Bacteria Biotopes with Semi-supervised Named Entity Recognition and Coreference Resolution
  46. W11-1815 [bib]: Zorana Ratkovic; Wiktoria Golik; Pierre Warnier; Philippe Veber; Claire Nèdellec
    BioNLP 2011 Task Bacteria Biotope – The Alvis system
  47. W11-1816 [bib]: Pontus Stenetorp; Goran Topić; Sampo Pyysalo; Tomoko Ohta; Jin-Dong Kim; Jun'ichi Tsujii
    BioNLP Shared Task 2011: Supporting Resources
  48. W11-1817 [bib]: Pierre Warnier; Claire Nèdellec
    Sentence Filtering for BioNLP: Searching for Renaming Acts
  49. W11-1818 [bib]: Liam R. McGrath; Kelly Domico; Courtney D. Corley; Bobbie-Jo Webb-Robertson
    Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features
  50. W11-1819 [bib]: Arantza Casillas; Arantza Dìaz de Ilarraza; Koldo Gojenola; Maite Oronoz; German Rigau
    Using Kybots for Extracting Events in Biomedical Texts
  51. W11-1820 [bib]: Quoc-Chinh Bui; Peter. M.A. Sloot
    Extracting Biological Events from Text Using Simple Syntactic Patterns
  52. W11-1821 [bib]: Sofie Van Landeghem; Thomas Abeel; Bernard De Baets; Yves Van de Peer
    Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction
  53. W11-1822 [bib]: Quang Le Minh; Son Nguyen Truong; Quoc Ho Bao
    A Pattern Approach for Biomedical Event Annotation
  54. W11-1823 [bib]: Don Tuggener; Manfred Klenner; Gerold Schneider; Simon Clematide; Fabio Rinaldi
    An Incremental Model for the Coreference Resolution Task of BioNLP 2011
  55. W11-1824 [bib]: Ehsan Emadzadeh; Azadeh Nikfarjam; Graciela Gonzalez
    Double Layered Learning for Biological Event Extraction from Text
  56. W11-1825 [bib]: Chris Quirk; Pallavi Choudhury; Michael Gamon; Lucy Vanderwende
    MSR-NLP Entry in BioNLP Shared Task 2011
  57. W11-1826 [bib]: Haibin Liu; Ravikumar Komandur; Karin Verspoor
    From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text
  58. W11-1827 [bib]: Halil Kilicoglu; Sabine Bergler
    Adapting a General Semantic Interpretation Approach to Biological Event Extraction
  59. W11-1828 [bib]: Jari Björne; Tapio Salakoski
    Generalizing Biomedical Event Extraction


  1. Proceedings of the BioNLP 2009 Workshop

  2. W09-13 [bib]: Entire Volume
  3. W09-1300 [bib]: Front Matter

  4. W09-1301 [bib]: Sampo Pyysalo; Tomoko Ohta; Jin-Dong Kim; Jun’ichi Tsujii
    Static Relations: a Piece in the Biomedical Information Extraction Puzzle
  5. W09-1302 [bib]: Danielle Mowery; Henk Harkema; John Dowling; Jonathan Lustgarten; Wendy Chapman
    Distinguishing Historical from Current Problems in Clinical Reports – Which Textual Features Help?
  6. W09-1303 [bib]: Lee Christensen; Henk Harkema; Peter Haug; Jeannie Irwin; Wendy Chapman
    ONYX: A System for the Semantic Analysis of Clinical Text
  7. W09-1304 [bib]: Roser Morante; Walter Daelemans
    Learning the Scope of Hedge Cues in Biomedical Texts
  8. W09-1305 [bib]: Udo Hahn; Katrin Tomanek; Ekaterina Buyko; Jung-jae Kim; Dietrich Rebholz-Schuhmann
    How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions
  9. W09-1306 [bib]: Wern Wong; David Martinez; Lawrence Cavedon
    Extraction of Named Entities from Tables in Gene Mutation Literature
  10. W09-1307 [bib]: He Tan; Patrick Lambrix
    Selecting an Ontology for Biomedical Text Mining
  11. W09-1308 [bib]: Rong Xu; Alexander A. Morgan; Amar Das; Alan Garber
    Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon
  12. W09-1309 [bib]: Mark Stevenson; Yikun Guo; Abdulaziz Alamri; Robert Gaizauskas
    Disambiguation of Biomedical Abbreviations
  13. W09-1310 [bib]: Thomas Kappeler; Kaarel Kaljurand; Fabio Rinaldi
    TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
  14. W09-1311 [bib]: Thierry Hamon; Natalia Grabar
    Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology
  15. W09-1312 [bib]: Feng Jin; Minlie Huang; Zhiyong Lu; Xiaoyan Zhu
    Towards Automatic Generation of Gene Summary
  16. W09-1313 [bib]: Tomoko Ohta; Jin-Dong Kim; Sampo Pyysalo; Yue Wang; Jun’ichi Tsujii
    Incorporating GENETAG-style annotation to GENIA corpus
  17. W09-1314 [bib]: Lin Sun; Anna Korhonen; Ilona Silins; Ulla Stenius
    User-Driven Development of Text Mining Resources for Cancer Risk Assessment
  18. W09-1315 [bib]: Esra Erdem; Reyyan Yeniterzi
    Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs
  19. W09-1316 [bib]: Vijayaraghavan Bashyam; Ricky K Taira
    Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports
  20. W09-1317 [bib]: Haibin Liu; Christian Blouin; Vlado Keselj
    Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns
  21. W09-1318 [bib]: Mike Conway; Son Doan; Nigel Collier
    Using Hedges to Enhance a Disease Outbreak Report Text Mining System
  22. W09-1319 [bib]: Aurelie Neveol; Won Kim; W. John Wilbur; Zhiyong Lu
    Exploring Two Biomedical Text Genres for Disease Recognition
  23. W09-1320 [bib]: Annette Leonhard
    Towards Retrieving Relevant Information for Answering Clinical Comparison Questions
  24. W09-1321 [bib]: Sumire Uematsu; Jin-Dong Kim; Jun’ichi Tsujii
    Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics
  25. W09-1322 [bib]: Yong-Gang Cao; John Ely; Lamont Antieau; Hong Yu
    Evaluation of the Clinical Question Answering Presentation
  26. W09-1323 [bib]: Pawel Matykiewicz; Wlodzislaw Duch; John Pestian
    Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles.
  27. W09-1324 [bib]: Eiji Aramaki; Yasuhide Miura; Masatsugu Tonoike; Tomoko Ohkuma; Hiroshi Mashuichi; Kazuhiko Ohe
    TEXT2TABLE: Medical Text Summarization System Based on Named Entity Recognition and Modality Identification
  28. W09-1325 [bib]: Maria Liakata; Claire Q; Larisa N. Soldatova
    Semantic Annotation of Papers: Interface & Enrichment Tool (SAPIENT)
  29. Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task

  30. W09-14 [bib]: Entire Volume
  31. W09-1400 [bib]: Front Matter

  32. W09-1401 [bib]: Jin-Dong Kim; Tomoko Ohta; Sampo Pyysalo; Yoshinobu Kano; Jun’ichi Tsujii
    Overview of BioNLP’09 Shared Task on Event Extraction
  33. W09-1402 [bib]: Jari Björne; Juho Heimonen; Filip Ginter; Antti Airola; Tapio Pahikkala; Tapio Salakoski
    Extracting Complex Biological Events with Rich Graph-Based Feature Sets
  34. W09-1403 [bib]: Ekaterina Buyko; Erik Faessler; Joachim Wermter; Udo Hahn
    Event Extraction from Trimmed Dependency Graphs
  35. W09-1404 [bib]: Kaarel Kaljurand; Gerold Schneider; Fabio Rinaldi
    UZurich in the BioNLP 2009 Shared Task
  36. W09-1405 [bib]: Andreas Vlachos; Paula Buttery; Diarmuid Ó Séaghdha; Ted Briscoe
    Biomedical Event Extraction without Training Data
  37. W09-1406 [bib]: Sebastian Riedel; Hong-Woo Chun; Toshihisa Takagi; Jun’ichi Tsujii
    A Markov Logic Approach to Bio-Molecular Event Extraction
  38. W09-1407 [bib]: K. Bretonnel Cohen; Karin Verspoor; Helen Johnson; Chris Roeder; Philip Ogren; William Baumgartner; Elizabeth White; Lawrence Hunter
    High-precision biological event extraction with a concept recognizer
  39. W09-1408 [bib]: Roser Morante; Vincent Van Asch; Walter Daelemans
    A memory-based learning approach to event extraction in biomedical texts
  40. W09-1409 [bib]: Mariana Neves; José-María Carazo; Alberto Pascual-Montano
    Extraction of biomedical events using case-based reasoning
  41. W09-1410 [bib]: Andrew MacKinlay; David Martinez; Timothy Baldwin
    Biomedical Event Annotation with CRFs and Precision Grammars
  42. W09-1411 [bib]: Jörg Hakenberg; Illes Solt; Domonkos Tikk; Luis Tari; Astrid Rheinländer; Nguyen Quang Long; Graciela Gonzalez; Ulf Leser
    Molecular event extraction from Link Grammar parse trees
  43. W09-1412 [bib]: Georgi Georgiev; Kuzman Ganchev; Vassil Momchev; Deyan Peychev; Preslav Nakov; Angus Roberts
    Tunable Domain-Independent Event Extraction in the MIRA Framework
  44. W09-1413 [bib]: Syed Toufeeq Ahmed; Radhika Nair; Chintan Patel; Hasan Davulcu
    BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing
  45. W09-1414 [bib]: Rune Sætre; Makoto Miwa; Kazuhiro Yoshida; Jun’ichi Tsujii
    From Protein-Protein Interaction to Molecular Event Extraction
  46. W09-1415 [bib]: Hyoung-Gyu Lee; Han-Cheol Cho; Min-Jeong Kim; Joo-Young Lee; Gumwon Hong; Hae-Chang Rim
    A Multi-Phase Approach to Biomedical Event Extraction
  47. W09-1416 [bib]: Arzucan Ozgur; Dragomir Radev
    Supervised Classification for Extracting Biomedical Events
  48. W09-1417 [bib]: Farzaneh Sarafraz; James Eales; Reza Mohammadi; Jonathan Dickerson; David Robertson; Goran Nenadic
    Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances
  49. W09-1418 [bib]: Halil Kilicoglu; Sabine Bergler
    Syntactic Dependency Based Heuristics for Biological Event Extraction
  50. W09-1419 [bib]: Sofie Van Landeghem; Yvan Saeys; Bernard De Baets; Yves Van de Peer
    Analyzing text in search of bio-molecular events: a high-precision machine learning framework
  51. W09-1420 [bib]: György Móra; Richárd Farkas; György Szarvas; Zsolt Molnár
    Exploring ways beyond the simple supervised learning approach for biological event extraction