Biomedical Natural Language Processing Workshop (2011)

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bib (full) Proceedings of BioNLP 2011 Workshop

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Proceedings of BioNLP 2011 Workshop
Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii | Bonnie Webber

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Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text
Philippe Thomas | Stefan Pietschmann | Illés Solt | Domonkos Tikk | Ulf Leser

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Unsupervised Entailment Detection between Dependency Graph Fragments
Marek Rei | Ted Briscoe

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Learning Phenotype Mapping for Integrating Large Genetic Data
Chun-Nan Hsu | Cheng-Ju Kuo | Congxing Cai | Sarah Pendergrass | Marylyn Ritchie | Jose Luis Ambite

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EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions
Sofie Van Landeghem | Filip Ginter | Yves Van de Peer | Tapio Salakoski

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Fast and simple semantic class assignment for biomedical text
K. Bretonnel Cohen | Thomas Christiansen | William Baumgartner Jr. | Karin Verspoor | Lawrence Hunter

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The Role of Information Extraction in the Design of a Document Triage Application for Biocuration
Sandeep Pokkunuri | Cartic Ramakrishnan | Ellen Riloff | Eduard Hovy | Gully Burns

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Medical Entity Recognition: A Comparaison of Semantic and Statistical Methods
Asma Ben Abacha | Pierre Zweigenbaum

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Automatic Acquisition of Huge Training Data for Bio-Medical Named Entity Recognition
Yu Usami | Han-Cheol Cho | Naoaki Okazaki | Jun’ichi Tsujii

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Building frame-based corpus on the basis of ontological domain knowledge
He Tan | Rajaram Kaliyaperumal | Nirupama Benis

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Building a Coreference-Annotated Corpus from the Domain of Biochemistry
Riza Theresa Batista-Navarro | Sophia Ananiadou

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Towards Morphologically Annotated Corpus of Hospital Discharge Reports in Polish
Malgorzata Marciniak | Agnieszka Mykowiecka

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In Search of Protein Locations
Catherine Blake | Wu Zheng

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Automatic extraction of data deposition statements: where do the research results go?
Aurélie Névéol | W. John Wilbur | Zhiyong Lu

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From Pathways to Biomolecular Events: Opportunities and Challenges
Tomoko Ohta | Sampo Pyysalo | Jun’ichi Tsujii

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Towards Exhaustive Event Extraction for Protein Modifications
Sampo Pyysalo | Tomoko Ohta | Makoto Miwa | Jun’ichi Tsujii

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A Study on Dependency Tree Kernels for Automatic Extraction of Protein-Protein Interaction
Faisal Md. Chowdhury | Alberto Lavelli | Alessandro Moschitti

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Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles
Elizabeth White | K. Bretonnel Cohen | Larry Hunter

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SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation
Pontus Stenetorp | Sampo Pyysalo | Jun’ichi Tsujii

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

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Text Mining Techniques for Leveraging Positively Labeled Data
Lana Yeganova | Donald C. Comeau | Won Kim | W. John Wilbur

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Parsing Natural Language Queries for Life Science Knowledge
Tadayoshi Hara | Yuka Tateisi | Jin-Dong Kim | Yusuke Miyao

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Unlocking Medical Ontologies for Non-Ontology Experts
Shao Fen Liang | Donia Scott | Robert Stevens | Alan Rector

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Self-training and co-training in biomedical word sense disambiguation
Antonio Jimeno-Yepes | Alan Aronson

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Medstract - The Next Generation
Marc Verhagen | James Pustejovsky

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ThaiHerbMiner: A Thai Herbal Medicine Mining and Visualizing Tool
Choochart Haruechaiyasak | Jaruwat Pailai | Wasna Viratyosin | Rachada Kongkachandra

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pdf (full)
bib (full) Proceedings of BioNLP Shared Task 2011 Workshop

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Proceedings of BioNLP Shared Task 2011 Workshop
Jun’ichi Tsujii | Jin-Dong Kim | Sampo Pyysalo

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Overview of BioNLP Shared Task 2011
Jin-Dong Kim | Sampo Pyysalo | Tomoko Ohta | Robert Bossy | Ngan Nguyen | Jun’ichi Tsujii

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Overview of Genia Event Task in BioNLP Shared Task 2011
Jin-Dong Kim | Yue Wang | Toshihisa Takagi | Akinori Yonezawa

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Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011
Tomoko Ohta | Sampo Pyysalo | Jun’ichi Tsujii

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Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011
Sampo Pyysalo | Tomoko Ohta | Rafal Rak | Dan Sullivan | Chunhong Mao | Chunxia Wang | Bruno Sobral | Jun’ichi Tsujii | Sophia Ananiadou

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Biomedical Event Extraction from Abstracts and Full Papers using Search-based Structured Prediction
Andreas Vlachos | Mark Craven

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Event Extraction as Dependency Parsing for BioNLP 2011
David McClosky | Mihai Surdeanu | Christopher Manning

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Robust Biomedical Event Extraction with Dual Decomposition and Minimal Domain Adaptation
Sebastian Riedel | Andrew McCallum

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Model Combination for Event Extraction in BioNLP 2011
Sebastian Riedel | David McClosky | Mihai Surdeanu | Andrew McCallum | Christopher D. Manning

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BioNLP Shared Task 2011 - Bacteria Biotope
Robert Bossy | Julien Jourde | Philippe Bessières | Maarten van de Guchte | Claire Nédellec

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BioNLP Shared Task 2011 – Bacteria Gene Interactions and Renaming
Julien Jourde | Alain-Pierre Manine | Philippe Veber | Karën Fort | Robert Bossy | Erick Alphonse | Philippe Bessières

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Overview of BioNLP 2011 Protein Coreference Shared Task
Ngan Nguyen | Jin-Dong Kim | Jun’ichi Tsujii

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Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011
Sampo Pyysalo | Tomoko Ohta | Jun’ichi Tsujii

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The Taming of Reconcile as a Biomedical Coreference Resolver
Youngjun Kim | Ellen Riloff | Nathan Gilbert

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Extracting Bacteria Biotopes with Semi-supervised Named Entity Recognition and Coreference Resolution
Nhung T. H. Nguyen | Yoshimasa Tsuruoka

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BioNLP 2011 Task Bacteria Biotope – The Alvis system
Zorana Ratkovic | Wiktoria Golik | Pierre Warnier | Philippe Veber | Claire Nédellec

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BioNLP Shared Task 2011: Supporting Resources
Pontus Stenetorp | Goran Topić | Sampo Pyysalo | Tomoko Ohta | Jin-Dong Kim | Jun’ichi Tsujii

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Sentence Filtering for BioNLP: Searching for Renaming Acts
Pierre Warnier | Claire Nédellec

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Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features
Liam R. McGrath | Kelly Domico | Courtney D. Corley | Bobbie-Jo Webb-Robertson

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Using Kybots for Extracting Events in Biomedical Texts
Arantza Casillas | Arantza Díaz de Ilarraza | Koldo Gojenola | Maite Oronoz | German Rigau

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Extracting Biological Events from Text Using Simple Syntactic Patterns
Quoc-Chinh Bui | Peter M.A. Sloot

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Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction
Sofie Van Landeghem | Thomas Abeel | Bernard De Baets | Yves Van de Peer

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A Pattern Approach for Biomedical Event Annotation
Quang Le Minh | Son Nguyen Truong | Quoc Ho Bao

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An Incremental Model for the Coreference Resolution Task of BioNLP 2011
Don Tuggener | Manfred Klenner | Gerold Schneider | Simon Clematide | Fabio Rinaldi

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Double Layered Learning for Biological Event Extraction from Text
Ehsan Emadzadeh | Azadeh Nikfarjam | Graciela Gonzalez

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MSR-NLP Entry in BioNLP Shared Task 2011
Chris Quirk | Pallavi Choudhury | Michael Gamon | Lucy Vanderwende

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From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text
Haibin Liu | Ravikumar Komandur | Karin Verspoor

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Adapting a General Semantic Interpretation Approach to Biological Event Extraction
Halil Kilicoglu | Sabine Bergler

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Generalizing Biomedical Event Extraction
Jari Björne | Tapio Salakoski