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Special Interest Group on Biomedical Natural Language Processing

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2016 Proceedings of the 15th Workshop on Biomedical Natural Language Processing
Proceedings of the 4th BioNLP Shared Task Workshop
Proceedings of the Fourth BioASQ workshop
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

2016

  1. Proceedings of the 15th Workshop on Biomedical Natural Language Processing

  2. W16-29 [bib]: Entire Volume
  3. W16-2900 [bib]: Front Matter

  4. W16-2901 [bib]: Jose Castano; María Laura Gambarte; Hee Joon Park; Maria del Pilar Avila Williams; David Perez; Fernando Campos; Daniel Luna; Sonia Benitez; Hernan Berinsky; Sofía Zanetti
    A Machine Learning Approach to Clinical Terms Normalization
  5. W16-2902 [bib]: Mohammad Taher Pilehvar; Nigel Collier
    Improved Semantic Representation for Domain-Specific Entities
  6. W16-2903 [bib]: Chaitanya Shivade; Marie-Catherine de Marneffe; Eric Fosler-Lussier; Albert M. Lai
    Identification, characterization, and grounding of gradable terms in clinical text
  7. W16-2904 [bib]: Golnar Sheikhshab; Elizabeth Starks; Aly Karsan; Anoop Sarkar; Inanc Birol
    Graph-based Semi-supervised Gene Mention Tagging
  8. W16-2905 [bib]: Dayne Freitag; John Niekrasz
    Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses
  9. W16-2906 [bib]: Halil Kilicoglu
    Inferring Implicit Causal Relationships in Biomedical Literature
  10. W16-2907 [bib]: Marco A. Valenzuela-Escárcega; Gus Hahn-Powell; Dane Bell; Mihai Surdeanu
    SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction
  11. W16-2908 [bib]: Ritambhara Singh; Yanjun Qi
    Character based String Kernels for Bio-Entity Relation Detection
  12. W16-2909 [bib]: Amy Siu; Patrick Ernst; Gerhard Weikum
    Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge
  13. W16-2910 [bib]: Stephan Tulkens; Simon Suster; Walter Daelemans
    Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts
  14. W16-2911 [bib]: Timothy Miller; Dmitriy Dligach; Guergana Savova
    Unsupervised Document Classification with Informed Topic Models
  15. W16-2912 [bib]: Sumithra Velupillai; Danielle L Mowery; Mike Conway; John Hurdle; Brent Kious
    Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes
  16. W16-2913 [bib]: Kai Hakala; Suwisa Kaewphan; Tapio Salakoski; Filip Ginter
    Syntactic analyses and named entity recognition for PubMed and PubMed Central — up-to-the-minute
  17. W16-2914 [bib]: Chen Lin; Timothy Miller; Dmitriy Dligach; Steven Bethard; Guergana Savova
    Improving Temporal Relation Extraction with Training Instance Augmentation
  18. W16-2915 [bib]: Georgios-Ioannis Brokos; Prodromos Malakasiotis; Ion Androutsopoulos
    Using Centroids of Word Embeddings and Word Mover's Distance for Biomedical Document Retrieval in Question Answering
  19. W16-2916 [bib]: Michael Spranger; Sucheendra Palaniappan; Samik Gosh
    Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway
  20. W16-2917 [bib]: Keyuan Jiang; Ricardo Calix; Matrika Gupta
    Construction of a Personal Experience Tweet Corpus for Health Surveillance
  21. W16-2918 [bib]: Nut Limsopatham; Nigel Collier
    Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification
  22. W16-2919 [bib]: Lana Yeganova; Won Kim; Sun Kim; Rezarta Islamaj Doğan; Wanli Liu; Donald C Comeau; Zhiyong Lu; W John Wilbur
    PubTermVariants: biomedical term variants and their use for PubMed search
  23. W16-2920 [bib]: Gus Hahn-Powell; Dane Bell; Marco A. Valenzuela-Escárcega; Mihai Surdeanu
    This before That: Causal Precedence in the Biomedical Domain
  24. W16-2921 [bib]: Viviana Cotik; Vanesa Stricker; Jorge Vivaldi; Horacio Rodriguez
    Syntactic methods for negation detection in radiology reports in Spanish
  25. W16-2922 [bib]: Billy Chiu; Gamal Crichton; Anna Korhonen; Sampo Pyysalo
    How to Train good Word Embeddings for Biomedical NLP
  26. W16-2923 [bib]: Brian Connolly; Benjamin Glass; John Pestian
    An Information Foraging Approach to Determining the Number of Relevant Features
  27. W16-2924 [bib]: Brian E. Chapman; Danielle L Mowery; Evan Narasimhan; Neel Patel; Wendy Chapman; Marta Heilbrun
    Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians
  28. W16-2925 [bib]: Simon Kocbek; Tudor Groza
    Building a dictionary of lexical variants for phenotype descriptors
  29. W16-2926 [bib]: Olof Jacobson; Hercules Dalianis
    Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections
  30. W16-2927 [bib]: Genevieve Gorrell; Sherifat Oduola; Angus Roberts; Tom Craig; Craig Morgan; Rob Stewart
    Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning
  31. W16-2928 [bib]: Sunil Sahu; Ashish Anand; Krishnadev Oruganty; Mahanandeeshwar Gattu
    Relation extraction from clinical texts using domain invariant convolutional neural network
  32. Proceedings of the 4th BioNLP Shared Task Workshop

  33. W16-30 [bib]: Entire Volume
  34. W16-3000 [bib]: Front Matter

  35. W16-3001 [bib]: Estelle Chaix; Bertrand Dubreucq; Abdelhak Fatihi; Dialekti Valsamou; Robert Bossy; Mouhamadou Ba; Louise Delėger; Pierre Zweigenbaum; Philippe Bessières; Loïc Lepiniec; Claire Nėdellec
    Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016.
  36. W16-3002 [bib]: Louise Delėger; Robert Bossy; Estelle Chaix; Mouhamadou Ba; Arnaud Ferrė; Philippe Bessières; Claire Nėdellec
    Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016
  37. W16-3003 [bib]: Jin-Dong Kim; Yue Wang; Nicola Colic; Seung Han Beak; Yong Hwan Kim; Min Song
    Refactoring the Genia Event Extraction Shared Task Toward a General Framework for IE-Driven KB Development
  38. W16-3004 [bib]: Chen Li; Zhiqiang Rao; Xiangrong Zhang
    LitWay, Discriminative Extraction for Different Bio-Events
  39. W16-3005 [bib]: Jake Lever; Steven JM Jones
    VERSE: Event and Relation Extraction in the BioNLP 2016 Shared Task
  40. W16-3006 [bib]: Helen V Cook; Evangelos Pafilis; Lars Juhl Jensen
    A dictionary- and rule-based system for identification of bacteria and habitats in text
  41. W16-3007 [bib]: Mert Tiftikci; Hakan Şahin; Berfu Büyüköz; Alper Yayıkçı; Arzucan Özgür
    Ontology-Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques
  42. W16-3008 [bib]: Cyril Grouin
    Identification of Mentions and Relations between Bacteria and Biotope from PubMed Abstracts
  43. W16-3009 [bib]: Farrokh Mehryary; Jari Björne; Sampo Pyysalo; Tapio Salakoski; Filip Ginter
    Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016
  44. W16-3010 [bib]: Nagesh C. Panyam; Gitansh Khirbat; Karin Verspoor; Trevor Cohn; Kotagiri Ramamohanarao
    SeeDev Binary Event Extraction using SVMs and a Rich Feature Set
  45. W16-3011 [bib]: Andre Lamurias; Miguel J. Rodrigues; Luka A. Clarke; Francisco M. Couto
    Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision
  46. W16-3012 [bib]: Honglei Li; Jianhai Zhang; Jian Wang; Hongfei Lin; Zhihao Yang
    DUTIR in BioNLP-ST 2016: Utilizing Convolutional Network and Distributed Representation to Extract Complicate Relations
  47. W16-3013 [bib]: Xinyu He; Lishuang Li; Jieqiong Zheng; Meiyue Qin
    Extracting Biomedical Event Using Feature Selection and Word Representation
  48. Proceedings of the Fourth BioASQ workshop

  49. W16-31 [bib]: Entire Volume
  50. W16-3101 [bib]: Anastasia Krithara; Anastasios Nentidis; Georgios Paliouras; Ioannis Kakadiaris
    Results of the 4th edition of BioASQ Challenge
  51. W16-3102 [bib]: Ilya Zavorin; James Mork; Dina Demner-Fushman
    Using Learning-To-Rank to Enhance NLM Medical Text Indexer Results
  52. W16-3103 [bib]: Isabel Segura-Bedmar; Adrián Carruana; Paloma Martínez
    LABDA at the 2016 BioASQ challenge task 4a: Semantic Indexing by using ElasticSearch
  53. W16-3104 [bib]: Zi Yang; Yue Zhou; Eric Nyberg
    Learning to Answer Biomedical Questions: OAQA at BioASQ 4B
  54. W16-3105 [bib]: Frederik Schulze; Ricarda Schüler; Tim Draeger; Daniel Dummer; Alexander Ernst; Pedro Flemming; Cindy Perscheid; Mariana Neves
    HPI Question Answering System in BioASQ 2016
  55. W16-3106 [bib]: Hyeon-gu Lee; Minkyoung Kim; Harksoo Kim; Juae Kim; Sunjae Kwon; Jungyun Seo; Yi-Reun Kim; Jung-Kyu Choi
    KSAnswer: Question-answering System of Kangwon National University and Sogang University in the 2016 BioASQ Challenge
  56. W16-3107 [bib]: Eirini Papagiannopoulou; Yiannis Papanikolaou; Dimitris Dimitriadis; Sakis Lagopoulos; Grigorios Tsoumakas; Manos Laliotis; Nikos Markantonatos; Ioannis Vlahavas
    Large-Scale Semantic Indexing and Question Answering in Biomedicine

2015

  1. Proceedings of BioNLP 15

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

2012

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

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

2011

  1. Proceedings of BioNLP 2011 Workshop

  2. W11-0201: 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
  3. W11-0202: Marek Rei; Ted Briscoe
    Unsupervised Entailment Detection between Dependency Graph Fragments
  4. W11-0203: Chun-Nan Hsu; Cheng-Ju Kuo; Congxing Cai; Sarah Pendergrass; Marylyn Ritchie; Jose Luis Ambite
    Learning Phenotype Mapping for Integrating Large Genetic Data
  5. W11-0204: Sofie Van Landeghem; Filip Ginter; Yves Van de Peer; Tapio Salakoski
    EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions
  6. W11-0205: K. Bretonnel Cohen; Thomas Christiansen; William Baumgartner Jr.; Karin Verspoor; Lawrence Hunter
    Fast and simple semantic class assignment for biomedical text
  7. W11-0206: 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
  8. W11-0207: Asma Ben Abacha; Pierre Zweigenbaum
    Medical Entity Recognition: A Comparaison of Semantic and Statistical Methods
  9. W11-0208: Yu Usami; Han-Cheol Cho; Naoaki Okazaki; Jun'ichi Tsujii
    Automatic Acquisition of Huge Training Data for Bio-Medical Named Entity Recognition
  10. W11-0209: He Tan; Rajaram Kaliyaperumal; Nirupama Benis
    Building frame-based corpus on the basis of ontological domain knowledge
  11. W11-0210: Riza Theresa Batista-Navarro; Sophia Ananiadou
    Building a Coreference-Annotated Corpus from the Domain of Biochemistry
  12. W11-0211: Malgorzata Marciniak; Agnieszka Mykowiecka
    Towards Morphologically Annotated Corpus of Hospital Discharge Reports in Polish
  13. W11-0212: Catherine Blake; Wu Zheng
    In Search of Protein Locations
  14. W11-0213: Aurelie Neveol; W. John Wilbur; Zhiyong Lu
    Automatic extraction of data deposition statements: where do the research results go?
  15. W11-0214: Tomoko Ohta; Sampo Pyysalo; Jun'ichi Tsujii
    From Pathways to Biomolecular Events: Opportunities and Challenges
  16. W11-0215: Sampo Pyysalo; Tomoko Ohta; Makoto Miwa; Jun'ichi Tsujii
    Towards Exhaustive Event Extraction for Protein Modifications
  17. W11-0216: Faisal Md. Chowdhury; Alberto Lavelli; Alessandro Moschitti
    A Study on Dependency Tree Kernels for Automatic Extraction of Protein-Protein Interaction
  18. W11-0217: Elizabeth White; K. Bretonnel Cohen; Larry Hunter
    Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles
  19. W11-0218: Pontus Stenetorp; Sampo Pyysalo; Jun'ichi Tsujii
    SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation
  20. W11-0219: 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
  21. W11-0220: Lana Yeganova; Donald C. Comeau; Won Kim; W. John Wilbur
    Text Mining Techniques for Leveraging Positively Labeled Data
  22. W11-0221: Tadayoshi Hara; Yuka Tateisi; Jin-Dong Kim; Yusuke Miyao
    Parsing Natural Language Queries for Life Science Knowledge
  23. W11-0222: Shao Fen Liang; Donia Scott; Robert Stevens; Alan Rector
    Unlocking Medical Ontologies for Non-Ontology Experts
  24. W11-0223: Antonio Jimeno Yepes; Alan Aronson
    Self-training and co-training in biomedical word sense disambiguation
  25. W11-0224: Marc Verhagen; James Pustejovsky
    Medstract - The Next Generation
  26. W11-0225: Choochart Haruechaiyasak; Jaruwat Pailai; Wasna Viratyosin; Rachada Kongkachandra
    ThaiHerbMiner: A Thai Herbal Medicine Mining and Visualizing Tool
  27. Proceedings of BioNLP Shared Task 2011 Workshop

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

2009

  1. Proceedings of the BioNLP 2009 Workshop

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

  28. W09-1401: Jin-Dong Kim; Tomoko Ohta; Sampo Pyysalo; Yoshinobu Kano; Jun’ichi Tsujii
    Overview of BioNLP’09 Shared Task on Event Extraction
  29. W09-1402: Jari Björne; Juho Heimonen; Filip Ginter; Antti Airola; Tapio Pahikkala; Tapio Salakoski
    Extracting Complex Biological Events with Rich Graph-Based Feature Sets
  30. W09-1403: Ekaterina Buyko; Erik Faessler; Joachim Wermter; Udo Hahn
    Event Extraction from Trimmed Dependency Graphs
  31. W09-1404: Kaarel Kaljurand; Gerold Schneider; Fabio Rinaldi
    UZurich in the BioNLP 2009 Shared Task
  32. W09-1405: Andreas Vlachos; Paula Buttery; Diarmuid Ó Séaghdha; Ted Briscoe
    Biomedical Event Extraction without Training Data
  33. W09-1406: Sebastian Riedel; Hong-Woo Chun; Toshihisa Takagi; Jun’ichi Tsujii
    A Markov Logic Approach to Bio-Molecular Event Extraction
  34. W09-1407: 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
  35. W09-1408: Roser Morante; Vincent Van Asch; Walter Daelemans
    A memory-based learning approach to event extraction in biomedical texts
  36. W09-1409: Mariana Neves; José-María Carazo; Alberto Pascual-Montano
    Extraction of biomedical events using case-based reasoning
  37. W09-1410: Andrew MacKinlay; David Martinez; Timothy Baldwin
    Biomedical Event Annotation with CRFs and Precision Grammars
  38. W09-1411: 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
  39. W09-1412: Georgi Georgiev; Kuzman Ganchev; Vassil Momchev; Deyan Peychev; Preslav Nakov; Angus Roberts
    Tunable Domain-Independent Event Extraction in the MIRA Framework
  40. W09-1413: Syed Toufeeq Ahmed; Radhika Nair; Chintan Patel; Hasan Davulcu
    BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing
  41. W09-1414: Rune Sætre; Makoto Miwa; Kazuhiro Yoshida; Jun’ichi Tsujii
    From Protein-Protein Interaction to Molecular Event Extraction
  42. W09-1415: 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
  43. W09-1416: Arzucan Ozgur; Dragomir Radev
    Supervised Classification for Extracting Biomedical Events
  44. W09-1417: Farzaneh Sarafraz; James Eales; Reza Mohammadi; Jonathan Dickerson; David Robertson; Goran Nenadic
    Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances
  45. W09-1418: Halil Kilicoglu; Sabine Bergler
    Syntactic Dependency Based Heuristics for Biological Event Extraction
  46. W09-1419: 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
  47. W09-1420: György Móra; Richárd Farkas; György Szarvas; Zsolt Molnár
    Exploring ways beyond the simple supervised learning approach for biological event extraction