Table of contents

Anthology Volume Year Papers
W16-29 Proceedings of the 15th Workshop on Biomedical Natural Language Processing 2016 29
W16-30 Proceedings of the 4th BioNLP Shared Task Workshop 2016 14
W16-31 Proceedings of the Fourth BioASQ workshop 2016 8
W15-38 Proceedings of BioNLP 15 2015 24
W12-24 BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing 2012 31
W11-02 Proceedings of BioNLP 2011 Workshop 2011 26
W11-18 Proceedings of BioNLP Shared Task 2011 Workshop 2011 29
W09-13 Proceedings of the BioNLP 2009 Workshop 2009 26
W09-14 Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task 2009 21


Pdf Export Search Proceedings of the 15th Workshop on Biomedical Natural Language Processing


Pdf Export Search Proceedings of the 15th Workshop on Biomedical Natural Language Processing
[W16-2900]: Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | Jun-ichi Tsujii

Pdf Export Search A Machine Learning Approach to Clinical Terms Normalization
[W16-2901]: 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

Pdf Export Search Improved Semantic Representation for Domain-Specific Entities
[W16-2902]: Mohammad Taher Pilehvar | Nigel Collier

Pdf Export Search Identification, characterization, and grounding of gradable terms in clinical text
[W16-2903]: Chaitanya Shivade | Marie-Catherine de Marneffe | Eric Fosler-Lussier | Albert M. Lai

Pdf Export Search Graph-based Semi-supervised Gene Mention Tagging
[W16-2904]: Golnar Sheikhshab | Elizabeth Starks | Aly Karsan | Anoop Sarkar | Inanc Birol

Pdf Export Search Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses
[W16-2905]: Dayne Freitag | John Niekrasz

Pdf Export Search Inferring Implicit Causal Relationships in Biomedical Literature
[W16-2906]: Halil Kilicoglu

Pdf Export Search SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction
[W16-2907]: Marco A. Valenzuela-Escárcega | Gus Hahn-Powell | Dane Bell | Mihai Surdeanu

Pdf Export Search Character based String Kernels for Bio-Entity Relation Detection
[W16-2908]: Ritambhara Singh | Yanjun Qi

Pdf Export Search Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge
[W16-2909]: Amy Siu | Patrick Ernst | Gerhard Weikum

Pdf Export Search Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts
[W16-2910]: Stephan Tulkens | Simon Suster | Walter Daelemans

Pdf Export Search Unsupervised Document Classification with Informed Topic Models
[W16-2911]: Timothy Miller | Dmitriy Dligach | Guergana Savova

Pdf Export Search Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes
[W16-2912]: Sumithra Velupillai | Danielle L Mowery | Mike Conway | John Hurdle | Brent Kious

Pdf Export Search Syntactic analyses and named entity recognition for PubMed and PubMed Central — up-to-the-minute
[W16-2913]: Kai Hakala | Suwisa Kaewphan | Tapio Salakoski | Filip Ginter

Pdf Export Search Improving Temporal Relation Extraction with Training Instance Augmentation
[W16-2914]: Chen Lin | Timothy Miller | Dmitriy Dligach | Steven Bethard | Guergana Savova

Pdf Export Search Using Centroids of Word Embeddings and Word Mover's Distance for Biomedical Document Retrieval in Question Answering
[W16-2915]: Georgios-Ioannis Brokos | Prodromos Malakasiotis | Ion Androutsopoulos

Pdf Export Search Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway
[W16-2916]: Michael Spranger | Sucheendra Palaniappan | Samik Gosh

Pdf Export Search Construction of a Personal Experience Tweet Corpus for Health Surveillance
[W16-2917]: Keyuan Jiang | Ricardo Calix | Matrika Gupta

Pdf Export Search Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification
[W16-2918]: Nut Limsopatham | Nigel Collier

Pdf Export Search PubTermVariants: biomedical term variants and their use for PubMed search
[W16-2919]: Lana Yeganova | Won Kim | Sun Kim | Rezarta Islamaj Doğan | Wanli Liu | Donald C Comeau | Zhiyong Lu | W John Wilbur

Pdf Export Search This before That: Causal Precedence in the Biomedical Domain
[W16-2920]: Gus Hahn-Powell | Dane Bell | Marco A. Valenzuela-Escárcega | Mihai Surdeanu

Pdf Export Search Syntactic methods for negation detection in radiology reports in Spanish
[W16-2921]: Viviana Cotik | Vanesa Stricker | Jorge Vivaldi | Horacio Rodriguez

Pdf Export Search How to Train good Word Embeddings for Biomedical NLP
[W16-2922]: Billy Chiu | Gamal Crichton | Anna Korhonen | Sampo Pyysalo

Pdf Export Search An Information Foraging Approach to Determining the Number of Relevant Features
[W16-2923]: Brian Connolly | Benjamin Glass | John Pestian

Pdf Export Search Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians
[W16-2924]: Brian E. Chapman | Danielle L Mowery | Evan Narasimhan | Neel Patel | Wendy Chapman | Marta Heilbrun

Pdf Export Search Building a dictionary of lexical variants for phenotype descriptors
[W16-2925]: Simon Kocbek | Tudor Groza

Pdf Export Search Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections
[W16-2926]: Olof Jacobson | Hercules Dalianis

Pdf Export Search Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning
[W16-2927]: Genevieve Gorrell | Sherifat Oduola | Angus Roberts | Tom Craig | Craig Morgan | Rob Stewart

Pdf Export Search Relation extraction from clinical texts using domain invariant convolutional neural network
[W16-2928]: Sunil Sahu | Ashish Anand | Krishnadev Oruganty | Mahanandeeshwar Gattu



Pdf Export Search Proceedings of the 4th BioNLP Shared Task Workshop


Pdf Export Search Proceedings of the 4th BioNLP Shared Task Workshop
[W16-3000]: Claire Nėdellec | Robert Bossy | Jin-Dong Kim

Pdf Export Search Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016.
[W16-3001]: Estelle Chaix | Bertrand Dubreucq | Abdelhak Fatihi | Dialekti Valsamou | Robert Bossy | Mouhamadou Ba | Louise Delėger | Pierre Zweigenbaum | Philippe Bessières | Loïc Lepiniec | Claire Nėdellec

Pdf Export Search Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016
[W16-3002]: Louise Delėger | Robert Bossy | Estelle Chaix | Mouhamadou Ba | Arnaud Ferrė | Philippe Bessières | Claire Nėdellec

Pdf Export Search Refactoring the Genia Event Extraction Shared Task Toward a General Framework for IE-Driven KB Development
[W16-3003]: Jin-Dong Kim | Yue Wang | Nicola Colic | Seung Han Beak | Yong Hwan Kim | Min Song

Pdf Export Search LitWay, Discriminative Extraction for Different Bio-Events
[W16-3004]: Chen Li | Zhiqiang Rao | Xiangrong Zhang

Pdf Export Search VERSE: Event and Relation Extraction in the BioNLP 2016 Shared Task
[W16-3005]: Jake Lever | Steven JM Jones

Pdf Export Search A dictionary- and rule-based system for identification of bacteria and habitats in text
[W16-3006]: Helen V Cook | Evangelos Pafilis | Lars Juhl Jensen

Pdf Export Search Ontology-Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques
[W16-3007]: Mert Tiftikci | Hakan Şahin | Berfu Büyüköz | Alper Yayıkçı | Arzucan Özgür

Pdf Export Search Identification of Mentions and Relations between Bacteria and Biotope from PubMed Abstracts
[W16-3008]: Cyril Grouin

Pdf Export Search Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016
[W16-3009]: Farrokh Mehryary | Jari Björne | Sampo Pyysalo | Tapio Salakoski | Filip Ginter

Pdf Export Search SeeDev Binary Event Extraction using SVMs and a Rich Feature Set
[W16-3010]: Nagesh C. Panyam | Gitansh Khirbat | Karin Verspoor | Trevor Cohn | Kotagiri Ramamohanarao

Pdf Export Search Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision
[W16-3011]: Andre Lamurias | Miguel J. Rodrigues | Luka A. Clarke | Francisco M. Couto

Pdf Export Search DUTIR in BioNLP-ST 2016: Utilizing Convolutional Network and Distributed Representation to Extract Complicate Relations
[W16-3012]: Honglei Li | Jianhai Zhang | Jian Wang | Hongfei Lin | Zhihao Yang

Pdf Export Search Extracting Biomedical Event Using Feature Selection and Word Representation
[W16-3013]: Xinyu He | Lishuang Li | Jieqiong Zheng | Meiyue Qin



Pdf Export Search Proceedings of the Fourth BioASQ workshop


Pdf Export Search Proceedings of the Fourth BioASQ workshop
[W16-3100]: Ioannis A. Kakadiaris | George Paliouras | Anastasia Krithara

Pdf Export Search Results of the 4th edition of BioASQ Challenge
[W16-3101]: Anastasia Krithara | Anastasios Nentidis | Georgios Paliouras | Ioannis Kakadiaris

Pdf Export Search Using Learning-To-Rank to Enhance NLM Medical Text Indexer Results
[W16-3102]: Ilya Zavorin | James Mork | Dina Demner-Fushman

Pdf Export Search LABDA at the 2016 BioASQ challenge task 4a: Semantic Indexing by using ElasticSearch
[W16-3103]: Isabel Segura-Bedmar | Adrián Carruana | Paloma Martínez

Pdf Export Search Learning to Answer Biomedical Questions: OAQA at BioASQ 4B
[W16-3104]: Zi Yang | Yue Zhou | Eric Nyberg

Pdf Export Search HPI Question Answering System in BioASQ 2016
[W16-3105]: Frederik Schulze | Ricarda Schüler | Tim Draeger | Daniel Dummer | Alexander Ernst | Pedro Flemming | Cindy Perscheid | Mariana Neves

Pdf Export Search KSAnswer: Question-answering System of Kangwon National University and Sogang University in the 2016 BioASQ Challenge
[W16-3106]: Hyeon-gu Lee | Minkyoung Kim | Harksoo Kim | Juae Kim | Sunjae Kwon | Jungyun Seo | Yi-Reun Kim | Jung-Kyu Choi

Pdf Export Search Large-Scale Semantic Indexing and Question Answering in Biomedicine
[W16-3107]: Eirini Papagiannopoulou | Yiannis Papanikolaou | Dimitris Dimitriadis | Sakis Lagopoulos | Grigorios Tsoumakas | Manos Laliotis | Nikos Markantonatos | Ioannis Vlahavas



Pdf Export Search Proceedings of BioNLP 15


Pdf Export Search Proceedings of BioNLP 15
[W15-3800]: Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | Jun-ichi Tsujii

Pdf Export Search Complex Event Extraction using DRUM
[W15-3801]: James Allen | Will de Beaumont | Lucian Galescu | Choh Man Teng

Pdf Export Search Making the most of limited training data using distant supervision
[W15-3802]: Roland Roller | Mark Stevenson

Pdf Export Search An extended dependency graph for relation extraction in biomedical texts
[W15-3803]: Yifan Peng | Samir Gupta | Cathy Wu | Vijay Shanker

Pdf Export Search Event Extraction in pieces:Tackling the partial event identification problem on unseen corpora
[W15-3804]: Chrysoula Zerva | Sophia Ananiadou

Pdf Export Search Extracting Biological Pathway Models From NLP Event Representations
[W15-3805]: Michael Spranger | Sucheendra Palaniappan | Samik Ghosh

Pdf Export Search Shallow Training is cheap but is it good enough? Experiments with Medical Fact Coding
[W15-3806]: Ramesh Nallapati | Radu Florian

Pdf Export Search Stacked Generalization for Medical Concept Extraction from Clinical Notes
[W15-3807]: Youngjun Kim | Ellen Riloff

Pdf Export Search Extracting Disease-Symptom Relationships by Learning Syntactic Patterns from Dependency Graphs
[W15-3808]: Mohsen Hassan | Olfa Makkaoui | Adrien Coulet | Yannick Toussain

Pdf Export Search Extracting Time Expressions from Clinical Text
[W15-3809]: Timothy Miller | Steven Bethard | Dmitriy Dligach | Chen Lin | Guergana Savova

Pdf Export Search Exploiting Task-Oriented Resources to Learn Word Embeddings for Clinical Abbreviation Expansion
[W15-3810]: Yue Liu | Tao Ge | Kusum Mathews | Heng Ji | Deborah McGuinness

Pdf Export Search Semantic Type Classification of Common Words in Biomedical Noun Phrases
[W15-3811]: Amy Siu | Gerhard Weikum

Pdf Export Search CoMAGD: Annotation of Gene-Depression Relations
[W15-3812]: Rize Jin | Jinseon You | Jin-Woo Chung | Hee-Jin Lee | Maria Wolters | Jong Park

Pdf Export Search Lexical Characteristics Analysis of Chinese Clinical Documents
[W15-3813]: Meizhi Ju | Haomin Li | Huilong Duan

Pdf Export Search Using word embedding for bio-event extraction
[W15-3814]: Chen Li | Runqing Song | Maria Liakata | Andreas Vlachos | Stephanie Seneff | Xiangrong Zhang

Pdf Export Search Measuring the readability of medical research journal abstracts
[W15-3815]: Samuel J. Severance | K. Bretonnel Cohen

Pdf Export Search Translating Electronic Health Record Notes from English to Spanish: A Preliminary Study
[W15-3816]: Weisong Liu | Shu Cai

Pdf Export Search Automatic Detection of Answers to Research Questions from Medline Abstracts
[W15-3817]: Abdulaziz Alamri | Mark Stevenson

Pdf Export Search A preliminary study on automatic identification of patient smoking status in unstructured electronic health records
[W15-3818]: Jitendra Jonnagaddala | Hong-Jie Dai | Pradeep Ray | Siaw-Teng Liaw

Pdf Export Search Restoring the intended structure of Hungarian ophthalmology documents
[W15-3819]: Borbála Siklósi | Attila Novák

Pdf Export Search Evaluating distributed word representations for capturing semantics of biomedical concepts
[W15-3820]: MUNEEB TH | Sunil Sahu | Ashish Anand

Pdf Export Search Investigating Public Health Surveillance using Twitter
[W15-3821]: Antonio Jimeno Yepes | Andrew MacKinlay | Bo Han

Pdf Export Search Clinical Abbreviation Disambiguation Using Neural Word Embeddings
[W15-3822]: yonghui wu | Jun Xu | Yaoyun Zhang | Hua Xu

Pdf Export Search Note Representing Clinical Diagnostic Criteria in Quality Data Model Using Natural Language Processing
[W15-3823]: Na Hong | Dingcheng Li | Yue Yu | Hongfang Liu | Christopher G. Chute | Guoqian Jiang



Pdf Export Search BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing


Pdf Export Search BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
[W12-2400]: Kevin B. Cohen | Dina Demner-Fushman | Sophia Ananiadou | Bonnie Webber | Jun'ichi Tsujii | John Pestian

Pdf Export Search Graph-based alignment of narratives for automated neurological assessment
[W12-2401]: Emily Prud'hommeaux | Brian Roark

Pdf Export Search Bootstrapping Biomedical Ontologies for Scientific Text using NELL
[W12-2402]: Dana Movshovitz-Attias | William W. Cohen

Pdf Export Search Semantic distance and terminology structuring methods for the detection of semantically close terms
[W12-2403]: Marie Dupuch | Laëtitia Dupuch | Thierry Hamon | Natalia Grabar

Pdf Export Search Temporal Classification of Medical Events
[W12-2404]: Preethi Raghavan | Eric Fosler-Lussier | Albert Lai

Pdf Export Search Analyzing Patient Records to Establish If and When a Patient Suffered from a Medical Condition
[W12-2405]: James Cogley | Nicola Stokes | Joe Carthy | John Dunnion

Pdf Export Search Alignment-HMM-based Extraction of Abbreviations from Biomedical Text
[W12-2406]: Dana Movshovitz-Attias | William W. Cohen

Pdf Export Search Medical diagnosis lost in translation – Analysis of uncertainty and negation expressions in English and Swedish clinical texts
[W12-2407]: Danielle L. Mowery | Sumithra Velupillai | Wendy W. Chapman

Pdf Export Search A Hybrid Stepwise Approach for De-identifying Person Names in Clinical Documents
[W12-2408]: Oscar Ferrandez | Brett South | Shuying Shen | Stephane Meystre

Pdf Export Search Active Learning for Coreference Resolution
[W12-2409]: Timothy Miller | Dmitriy Dligach | Guergana Savova

Pdf Export Search PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations
[W12-2410]: Jari Björne | Sofie Van Landeghem | Sampo Pyysalo | Tomoko Ohta | Filip Ginter | Yves Van de Peer | Sophia Ananiadou | Tapio Salakoski

Pdf Export Search An improved corpus of disease mentions in PubMed citations
[W12-2411]: Rezarta Islamaj Dogan | Zhiyong Lu

Pdf Export Search New Resources and Perspectives for Biomedical Event Extraction
[W12-2412]: Sampo Pyysalo | Pontus Stenetorp | Tomoko Ohta | Jin-Dong Kim | Sophia Ananiadou

Pdf Export Search Combining Compositionality and Pagerank for the Identification of Semantic Relations between Biomedical Words
[W12-2413]: Thierry Hamon | Christopher Engström | Mounira Manser | Zina Badji | Natalia Grabar | Sergei Silvestrov

Pdf Export Search Domain Adaptation of Coreference Resolution for Radiology Reports
[W12-2414]: Emilia Apostolova | Noriko Tomuro | Pattanasak Mongkolwat | Dina Demner-Fushman

Pdf Export Search What can NLP tell us about BioNLP?
[W12-2415]: Attapol Thamrongrattanarit | Michael Shafir | Michael Crivaro | Bensiin Borukhov | Marie Meteer

Pdf Export Search A Prototype Tool Set to Support Machine-Assisted Annotation
[W12-2416]: Brett South | Shuying Shen | Jianwei Leng | Tyler Forbush | Scott DuVall | Wendy Chapman

Pdf Export Search MedLingMap: A growing resource mapping the Bio-Medical NLP field
[W12-2417]: Marie Meteer | Borukhov Bensiin | Mike Crivaro | Michael Shafir | Attapol Thamrongrattanarit

Pdf Export Search Exploring Label Dependency in Active Learning for Phenotype Mapping
[W12-2418]: Shefali Sharma | Leslie Lange | Jose Luis Ambite | Yigal Arens | Chun-Nan Hsu

Pdf Export Search Evaluating Joint Modeling of Yeast Biology Literature and Protein-Protein Interaction Networks
[W12-2419]: Ramnath Balasubramanyan | Kathryn Rivard | William W. Cohen | Jelena Jakovljevic | John L. Woolford

Pdf Export Search RankPref: Ranking Sentences Describing Relations between Biomedical Entities with an Application
[W12-2420]: Catalina Oana Tudor | K Vijay-Shanker

Pdf Export Search Finding small molecule and protein pairs in scientific literature using a bootstrapping method
[W12-2421]: Ying Yan | Jee-Hyub Kim | Samuel Croset | Dietrich Rebholz-Schuhmann

Pdf Export Search Grading the Quality of Medical Evidence
[W12-2422]: Binod Gyawali | Thamar Solorio | Yassine Benajiba

Pdf Export Search Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers
[W12-2423]: Sun Kim | Won Kim | Don Comeau | W. John Wilbur

Pdf Export Search Effect of small sample size on text categorization with support vector machines
[W12-2424]: Pawel Matykiewicz | John Pestian

Pdf Export Search PubAnnotation - a persistent and sharable corpus and annotation repository
[W12-2425]: Jin-Dong Kim | Yue Wang

Pdf Export Search Using Natural Language Processing to Extract Drug-Drug Interaction Information from Package Inserts
[W12-2426]: Richard Boyce | Gregory Gardner | Henk Harkema

Pdf Export Search Automatic Approaches for Gene-Drug Interaction Extraction from Biomedical Text: Corpus and Comparative Evaluation
[W12-2427]: Nate Sutton | Laura Wojtulewicz | Neel Mehta | Graciela Gonzalez

Pdf Export Search A Preliminary Work on Symptom Name Recognition from Free-Text Clinical Records of Traditional Chinese Medicine using Conditional Random Fields and Reasonable Features
[W12-2428]: Yaqiang Wang | Yiguang Liu | Zhonghua Yu | Li Chen | Yongguang Jiang

Pdf Export Search Scaling up WSD with Automatically Generated Examples
[W12-2429]: Weiwei Cheng | Judita Preiss | Mark Stevenson

Pdf Export Search Boosting the protein name recognition performance by bootstrapping on selected text
[W12-2430]: Yue Wang | Jin-Dong Kim



Pdf Export Search Proceedings of BioNLP 2011 Workshop


Pdf Export Search Proceedings of BioNLP 2011 Workshop
[W11-0200]: Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun'ichi Tsujii | Bonnie Webber

Pdf Export Search Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text
[W11-0201]: Philippe Thomas | Stefan Pietschmann | Illès Solt | Domonkos Tikk | Ulf Leser

Pdf Export Search Unsupervised Entailment Detection between Dependency Graph Fragments
[W11-0202]: Marek Rei | Ted Briscoe

Pdf Export Search Learning Phenotype Mapping for Integrating Large Genetic Data
[W11-0203]: Chun-Nan Hsu | Cheng-Ju Kuo | Congxing Cai | Sarah Pendergrass | Marylyn Ritchie | Jose Luis Ambite

Pdf Export Search EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions
[W11-0204]: Sofie Van Landeghem | Filip Ginter | Yves Van de Peer | Tapio Salakoski

Pdf Export Search Fast and simple semantic class assignment for biomedical text
[W11-0205]: K. Bretonnel Cohen | Thomas Christiansen | William Baumgartner Jr. | Karin Verspoor | Lawrence Hunter

Pdf Export Search The Role of Information Extraction in the Design of a Document Triage Application for Biocuration
[W11-0206]: Sandeep Pokkunuri | Cartic Ramakrishnan | Ellen Riloff | Eduard Hovy | Gully Burns

Pdf Export Search Medical Entity Recognition: A Comparaison of Semantic and Statistical Methods
[W11-0207]: Asma Ben Abacha | Pierre Zweigenbaum

Pdf Export Search Automatic Acquisition of Huge Training Data for Bio-Medical Named Entity Recognition
[W11-0208]: Yu Usami | Han-Cheol Cho | Naoaki Okazaki | Jun'ichi Tsujii

Pdf Export Search Building frame-based corpus on the basis of ontological domain knowledge
[W11-0209]: He Tan | Rajaram Kaliyaperumal | Nirupama Benis

Pdf Export Search Building a Coreference-Annotated Corpus from the Domain of Biochemistry
[W11-0210]: Riza Theresa Batista-Navarro | Sophia Ananiadou

Pdf Export Search Towards Morphologically Annotated Corpus of Hospital Discharge Reports in Polish
[W11-0211]: Malgorzata Marciniak | Agnieszka Mykowiecka

Pdf Export Search In Search of Protein Locations
[W11-0212]: Catherine Blake | Wu Zheng

Pdf Export Search Automatic extraction of data deposition statements: where do the research results go?
[W11-0213]: Aurelie Neveol | W. John Wilbur | Zhiyong Lu

Pdf Export Search From Pathways to Biomolecular Events: Opportunities and Challenges
[W11-0214]: Tomoko Ohta | Sampo Pyysalo | Jun'ichi Tsujii

Pdf Export Search Towards Exhaustive Event Extraction for Protein Modifications
[W11-0215]: Sampo Pyysalo | Tomoko Ohta | Makoto Miwa | Jun'ichi Tsujii

Pdf Export Search A Study on Dependency Tree Kernels for Automatic Extraction of Protein-Protein Interaction
[W11-0216]: Faisal Md. Chowdhury | Alberto Lavelli | Alessandro Moschitti

Pdf Export Search Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles
[W11-0217]: Elizabeth White | K. Bretonnel Cohen | Larry Hunter

Pdf Export Search SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation
[W11-0218]: Pontus Stenetorp | Sampo Pyysalo | Jun'ichi Tsujii

Pdf Export Search Building Timelines from Narrative Clinical Records: Initial Results Based-on Deep Natural Language Understanding
[W11-0219]: Hyuckchul Jung | James Allen | Nate Blaylock | William de Beaumont | Lucian Galescu | Mary Swift

Pdf Export Search Text Mining Techniques for Leveraging Positively Labeled Data
[W11-0220]: Lana Yeganova | Donald C. Comeau | Won Kim | W. John Wilbur

Pdf Export Search Parsing Natural Language Queries for Life Science Knowledge
[W11-0221]: Tadayoshi Hara | Yuka Tateisi | Jin-Dong Kim | Yusuke Miyao

Pdf Export Search Unlocking Medical Ontologies for Non-Ontology Experts
[W11-0222]: Shao Fen Liang | Donia Scott | Robert Stevens | Alan Rector

Pdf Export Search Self-training and co-training in biomedical word sense disambiguation
[W11-0223]: Antonio Jimeno Yepes | Alan Aronson

Pdf Export Search Medstract - The Next Generation
[W11-0224]: Marc Verhagen | James Pustejovsky

Pdf Export Search ThaiHerbMiner: A Thai Herbal Medicine Mining and Visualizing Tool
[W11-0225]: Choochart Haruechaiyasak | Jaruwat Pailai | Wasna Viratyosin | Rachada Kongkachandra



Pdf Export Search Proceedings of BioNLP Shared Task 2011 Workshop


Pdf Export Search Proceedings of BioNLP Shared Task 2011 Workshop
[W11-1800]: Jun'ichi Tsujii | Jin-Dong Kim | Sampo Pyysalo

Pdf Export Search Overview of BioNLP Shared Task 2011
[W11-1801]: Jin-Dong Kim | Sampo Pyysalo | Tomoko Ohta | Robert Bossy | Ngan Nguyen | Jun'ichi Tsujii

Pdf Export Search Overview of Genia Event Task in BioNLP Shared Task 2011
[W11-1802]: Jin-Dong Kim | Yue Wang | Toshihisa Takagi | Akinori Yonezawa

Pdf Export Search Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011
[W11-1803]: Tomoko Ohta | Sampo Pyysalo | Jun'ichi Tsujii

Pdf Export Search Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011
[W11-1804]: Sampo Pyysalo | Tomoko Ohta | Rafal Rak | Dan Sullivan | Chunhong Mao | Chunxia Wang | Bruno Sobral | Jun'ichi Tsujii | Sophia Ananiadou

Pdf Export Search Biomedical Event Extraction from Abstracts and Full Papers using Search-based Structured Prediction
[W11-1805]: Andreas Vlachos | Mark Craven

Pdf Export Search Event Extraction as Dependency Parsing for BioNLP 2011
[W11-1806]: David McClosky | Mihai Surdeanu | Christopher Manning

Pdf Export Search Robust Biomedical Event Extraction with Dual Decomposition and Minimal Domain Adaptation
[W11-1807]: Sebastian Riedel | Andrew McCallum

Pdf Export Search Model Combination for Event Extraction in BioNLP 2011
[W11-1808]: Sebastian Riedel | David McClosky | Mihai Surdeanu | Andrew McCallum | Christopher D. Manning

Pdf Export Search BioNLP Shared Task 2011 - Bacteria Biotope
[W11-1809]: Robert Bossy | Julien Jourde | Philippe Bessières | Maarten van de Guchte | Claire Nèdellec

Pdf Export Search BioNLP Shared Task 2011 – Bacteria Gene Interactions and Renaming
[W11-1810]: Julien Jourde | Alain-Pierre Manine | Philippe Veber | Karën Fort | Robert Bossy | Erick Alphonse | Philippe Bessières

Pdf Export Search Overview of BioNLP 2011 Protein Coreference Shared Task
[W11-1811]: Ngan Nguyen | Jin-Dong Kim | Jun'ichi Tsujii

Pdf Export Search Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011
[W11-1812]: Sampo Pyysalo | Tomoko Ohta | Jun'ichi Tsujii

Pdf Export Search The Taming of Reconcile as a Biomedical Coreference Resolver
[W11-1813]: Youngjun Kim | Ellen Riloff | Nathan Gilbert

Pdf Export Search Extracting Bacteria Biotopes with Semi-supervised Named Entity Recognition and Coreference Resolution
[W11-1814]: Nhung T. H. Nguyen | Yoshimasa Tsuruoka

Pdf Export Search BioNLP 2011 Task Bacteria Biotope – The Alvis system
[W11-1815]: Zorana Ratkovic | Wiktoria Golik | Pierre Warnier | Philippe Veber | Claire Nèdellec

Pdf Export Search BioNLP Shared Task 2011: Supporting Resources
[W11-1816]: Pontus Stenetorp | Goran Topić | Sampo Pyysalo | Tomoko Ohta | Jin-Dong Kim | Jun'ichi Tsujii

Pdf Export Search Sentence Filtering for BioNLP: Searching for Renaming Acts
[W11-1817]: Pierre Warnier | Claire Nèdellec

Pdf Export Search Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features
[W11-1818]: Liam R. McGrath | Kelly Domico | Courtney D. Corley | Bobbie-Jo Webb-Robertson

Pdf Export Search Using Kybots for Extracting Events in Biomedical Texts
[W11-1819]: Arantza Casillas | Arantza Dìaz de Ilarraza | Koldo Gojenola | Maite Oronoz | German Rigau

Pdf Export Search Extracting Biological Events from Text Using Simple Syntactic Patterns
[W11-1820]: Quoc-Chinh Bui | Peter. M.A. Sloot

Pdf Export Search Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction
[W11-1821]: Sofie Van Landeghem | Thomas Abeel | Bernard De Baets | Yves Van de Peer

Pdf Export Search A Pattern Approach for Biomedical Event Annotation
[W11-1822]: Quang Le Minh | Son Nguyen Truong | Quoc Ho Bao

Pdf Export Search An Incremental Model for the Coreference Resolution Task of BioNLP 2011
[W11-1823]: Don Tuggener | Manfred Klenner | Gerold Schneider | Simon Clematide | Fabio Rinaldi

Pdf Export Search Double Layered Learning for Biological Event Extraction from Text
[W11-1824]: Ehsan Emadzadeh | Azadeh Nikfarjam | Graciela Gonzalez

Pdf Export Search MSR-NLP Entry in BioNLP Shared Task 2011
[W11-1825]: Chris Quirk | Pallavi Choudhury | Michael Gamon | Lucy Vanderwende

Pdf Export Search From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text
[W11-1826]: Haibin Liu | Ravikumar Komandur | Karin Verspoor

Pdf Export Search Adapting a General Semantic Interpretation Approach to Biological Event Extraction
[W11-1827]: Halil Kilicoglu | Sabine Bergler

Pdf Export Search Generalizing Biomedical Event Extraction
[W11-1828]: Jari Björne | Tapio Salakoski



Pdf Export Search Proceedings of the BioNLP 2009 Workshop


Pdf Export Search Proceedings of the BioNLP 2009 Workshop
[W09-1300]: K. Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii | Bonnie Webber

Pdf Export Search Static Relations: a Piece in the Biomedical Information Extraction Puzzle
[W09-1301]: Sampo Pyysalo | Tomoko Ohta | Jin-Dong Kim | Jun’ichi Tsujii

Pdf Export Search Distinguishing Historical from Current Problems in Clinical Reports – Which Textual Features Help?
[W09-1302]: Danielle Mowery | Henk Harkema | John Dowling | Jonathan Lustgarten | Wendy Chapman

Pdf Export Search ONYX: A System for the Semantic Analysis of Clinical Text
[W09-1303]: Lee Christensen | Henk Harkema | Peter Haug | Jeannie Irwin | Wendy Chapman

Pdf Export Search Learning the Scope of Hedge Cues in Biomedical Texts
[W09-1304]: Roser Morante | Walter Daelemans

Pdf Export Search How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions
[W09-1305]: Udo Hahn | Katrin Tomanek | Ekaterina Buyko | Jung-jae Kim | Dietrich Rebholz-Schuhmann

Pdf Export Search Extraction of Named Entities from Tables in Gene Mutation Literature
[W09-1306]: Wern Wong | David Martinez | Lawrence Cavedon

Pdf Export Search Selecting an Ontology for Biomedical Text Mining
[W09-1307]: He Tan | Patrick Lambrix

Pdf Export Search Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon
[W09-1308]: Rong Xu | Alexander A. Morgan | Amar Das | Alan Garber

Pdf Export Search Disambiguation of Biomedical Abbreviations
[W09-1309]: Mark Stevenson | Yikun Guo | Abdulaziz Alamri | Robert Gaizauskas

Pdf Export Search TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
[W09-1310]: Thomas Kappeler | Kaarel Kaljurand | Fabio Rinaldi

Pdf Export Search Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology
[W09-1311]: Thierry Hamon | Natalia Grabar

Pdf Export Search Towards Automatic Generation of Gene Summary
[W09-1312]: Feng Jin | Minlie Huang | Zhiyong Lu | Xiaoyan Zhu

Pdf Export Search Incorporating GENETAG-style annotation to GENIA corpus
[W09-1313]: Tomoko Ohta | Jin-Dong Kim | Sampo Pyysalo | Yue Wang | Jun’ichi Tsujii

Pdf Export Search User-Driven Development of Text Mining Resources for Cancer Risk Assessment
[W09-1314]: Lin Sun | Anna Korhonen | Ilona Silins | Ulla Stenius

Pdf Export Search Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs
[W09-1315]: Esra Erdem | Reyyan Yeniterzi

Pdf Export Search Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports
[W09-1316]: Vijayaraghavan Bashyam | Ricky K Taira

Pdf Export Search Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns
[W09-1317]: Haibin Liu | Christian Blouin | Vlado Keselj

Pdf Export Search Using Hedges to Enhance a Disease Outbreak Report Text Mining System
[W09-1318]: Mike Conway | Son Doan | Nigel Collier

Pdf Export Search Exploring Two Biomedical Text Genres for Disease Recognition
[W09-1319]: Aurelie Neveol | Won Kim | W. John Wilbur | Zhiyong Lu

Pdf Export Search Towards Retrieving Relevant Information for Answering Clinical Comparison Questions
[W09-1320]: Annette Leonhard

Pdf Export Search Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics
[W09-1321]: Sumire Uematsu | Jin-Dong Kim | Jun’ichi Tsujii

Pdf Export Search Evaluation of the Clinical Question Answering Presentation
[W09-1322]: Yong-Gang Cao | John Ely | Lamont Antieau | Hong Yu

Pdf Export Search Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles.
[W09-1323]: Pawel Matykiewicz | Wlodzislaw Duch | John Pestian

Pdf Export Search TEXT2TABLE: Medical Text Summarization System Based on Named Entity Recognition and Modality Identification
[W09-1324]: Eiji Aramaki | Yasuhide Miura | Masatsugu Tonoike | Tomoko Ohkuma | Hiroshi Mashuichi | Kazuhiko Ohe

Pdf Export Search Semantic Annotation of Papers: Interface & Enrichment Tool (SAPIENT)
[W09-1325]: Maria Liakata | Claire Q | Larisa N. Soldatova



Pdf Export Search Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task


Pdf Export Search Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task
[W09-1400]: Jun’ichi Tsujii

Pdf Export Search Overview of BioNLP’09 Shared Task on Event Extraction
[W09-1401]: Jin-Dong Kim | Tomoko Ohta | Sampo Pyysalo | Yoshinobu Kano | Jun’ichi Tsujii

Pdf Export Search Extracting Complex Biological Events with Rich Graph-Based Feature Sets
[W09-1402]: Jari Björne | Juho Heimonen | Filip Ginter | Antti Airola | Tapio Pahikkala | Tapio Salakoski

Pdf Export Search Event Extraction from Trimmed Dependency Graphs
[W09-1403]: Ekaterina Buyko | Erik Faessler | Joachim Wermter | Udo Hahn

Pdf Export Search UZurich in the BioNLP 2009 Shared Task
[W09-1404]: Kaarel Kaljurand | Gerold Schneider | Fabio Rinaldi

Pdf Export Search Biomedical Event Extraction without Training Data
[W09-1405]: Andreas Vlachos | Paula Buttery | Diarmuid Ó Séaghdha | Ted Briscoe

Pdf Export Search A Markov Logic Approach to Bio-Molecular Event Extraction
[W09-1406]: Sebastian Riedel | Hong-Woo Chun | Toshihisa Takagi | Jun’ichi Tsujii

Pdf Export Search High-precision biological event extraction with a concept recognizer
[W09-1407]: K. Bretonnel Cohen | Karin Verspoor | Helen Johnson | Chris Roeder | Philip Ogren | William Baumgartner | Elizabeth White | Lawrence Hunter

Pdf Export Search A memory-based learning approach to event extraction in biomedical texts
[W09-1408]: Roser Morante | Vincent Van Asch | Walter Daelemans

Pdf Export Search Extraction of biomedical events using case-based reasoning
[W09-1409]: Mariana Neves | José-María Carazo | Alberto Pascual-Montano

Pdf Export Search Biomedical Event Annotation with CRFs and Precision Grammars
[W09-1410]: Andrew MacKinlay | David Martinez | Timothy Baldwin

Pdf Export Search Molecular event extraction from Link Grammar parse trees
[W09-1411]: Jörg Hakenberg | Illes Solt | Domonkos Tikk | Luis Tari | Astrid Rheinländer | Nguyen Quang Long | Graciela Gonzalez | Ulf Leser

Pdf Export Search Tunable Domain-Independent Event Extraction in the MIRA Framework
[W09-1412]: Georgi Georgiev | Kuzman Ganchev | Vassil Momchev | Deyan Peychev | Preslav Nakov | Angus Roberts

Pdf Export Search BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing
[W09-1413]: Syed Toufeeq Ahmed | Radhika Nair | Chintan Patel | Hasan Davulcu

Pdf Export Search From Protein-Protein Interaction to Molecular Event Extraction
[W09-1414]: Rune Sætre | Makoto Miwa | Kazuhiro Yoshida | Jun’ichi Tsujii

Pdf Export Search A Multi-Phase Approach to Biomedical Event Extraction
[W09-1415]: Hyoung-Gyu Lee | Han-Cheol Cho | Min-Jeong Kim | Joo-Young Lee | Gumwon Hong | Hae-Chang Rim

Pdf Export Search Supervised Classification for Extracting Biomedical Events
[W09-1416]: Arzucan Ozgur | Dragomir Radev

Pdf Export Search Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances
[W09-1417]: Farzaneh Sarafraz | James Eales | Reza Mohammadi | Jonathan Dickerson | David Robertson | Goran Nenadic

Pdf Export Search Syntactic Dependency Based Heuristics for Biological Event Extraction
[W09-1418]: Halil Kilicoglu | Sabine Bergler

Pdf Export Search Analyzing text in search of bio-molecular events: a high-precision machine learning framework
[W09-1419]: Sofie Van Landeghem | Yvan Saeys | Bernard De Baets | Yves Van de Peer

Pdf Export Search Exploring ways beyond the simple supervised learning approach for biological event extraction
[W09-1420]: György Móra | Richárd Farkas | György Szarvas | Zsolt Molnár