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Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Karin Verspoor | Kevin Bretonnel Cohen | Ben Goertzel | Inderjeet Mani

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The Semantics of a Definiendum Constrains both the Lexical Semantics and the Lexicosyntactic Patterns in the Definiens
Hong Yu | Ying Wei

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Ontology-Based Natural Language Query Processing for the Biological Domain
Jisheng Liang | Thien Nguyen | Krzysztof Koperski | Giovanni Marchisio

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Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction
Alona Fyshe | Duane Szafron

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Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity
Antonio Sanfilippo | Christian Posse | Banu Gopalan | Stephen Tratz | Michelle Gregory

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A Priority Model for Named Entities
Lorraine Tanabe | W. John Wilbur

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Human Gene Name Normalization using Text Matching with Automatically Extracted Synonym Dictionaries
Haw-ren Fang | Kevin Murphy | Yang Jin | Jessica Kim | Peter White

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Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline
Razvan Bunescu | Raymond Mooney | Arun Ramani | Edward Marcotte

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BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs:
Richard Tzong-Han Tsai | Wen-Chi Chou | Yu-Chun Lin | Cheng-Lung Sung | Wei Ku | Ying-Shan Su | Ting-Yi Sung | Wen-Lian Hsu

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Generative Content Models for Structural Analysis of Medical Abstracts
Jimmy Lin | Damianos Karakos | Dina Demner-Fushman | Sanjeev Khudanpur

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Exploring Text and Image Features to Classify Images in Bioscience Literature
Barry Rafkind | Minsuk Lee | Shih-Fu Chang | Hong Yu

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Mining biomedical texts for disease-related pathways
Andrey Rzhetsky

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Postnominal Prepositional Phrase Attachment in Proteomics
Jonathan Schuman | Sabine Bergler

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BioKI:Enzymes - an adaptable system to locate low-frequency information in full-text proteomics articles
Sabine Bergler | Jonathan Schuman | Julien Dubuc | Alexandr Lebedev

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A Graph-Search Framework for GeneId Ranking
William Cohen

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Semi-supervised anaphora resolution in biomedical texts
Caroline Gasperin

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Using Dependency Parsing and Probabilistic Inference to Extract Relationships between Genes, Proteins and Malignancies Implicit Among Multiple Biomedical Research Abstracts
Ben Goertzel | Hugo Pinto | Ari Heljakka | Michael Ross | Cassio Pennachin | Izabela Goertzel

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Recognizing Nested Named Entities in GENIA corpus
Baohua Gu

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Biomedical Term Recognition with the Perceptron HMM Algorithm
Sittichai Jiampojamarn | Grzegorz Kondrak | Colin Cherry

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Refactoring Corpora
Helen L. Johnson | William A. Baumgartner Jr. | Martin Krallinger | K. Bretonnel Cohen | Lawrence Hunter

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Rapid Adaptation of POS Tagging for Domain Specific Uses
John E. Miller | Michael Bloodgood | Manabu Torii | K. Vijay-Shanker

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Extracting Protein-Protein interactions using simple contextual features
Leif Arda Nielsen

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Identifying Experimental Techniques in Biomedical Literature
Meeta Oberoi | Craig A. Struble | Sonia L. Sugg

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A Pragmatic Approach to Summary Extraction in Clinical Trials
Graciela Rosemblat | Laurel Graham

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The Difficulties of Taxonomic Name Extraction and a Solution
Guido Sautter | Klemens Böhm

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Summarizing Key Concepts using Citation Sentences
Ariel S. Schwartz | Marti Hearst

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Subdomain adaptation of a POS tagger with a small corpus
Yuka Tateisi | Yoshimasa Tsuruoka | Jun’ichi Tsujii

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Bootstrapping and Evaluating Named Entity Recognition in the Biomedical Domain
Andreas Vlachos | Caroline Gasperin