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Program, talks, and posters
| 09:00-10:30
| Session 1: Linking NLP and biology
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| 09:00-09:10
| Welcome and introduction
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| 09:10-09:30
| Definitional-term semantics constrain both the lexical semantics and the lexicosyntactic patterns in definitional sentences.
Hong Yu and Ying Wei
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| 09:30-09:50
| Ontology-based natural language query processing for the biological domain.
Jisheng Liang, Thien Nguyen, and Kris Koperski
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| 09:50-10:10
| Term generalization and synonym resolution for biological abstracts: using the Gene Ontology as a source of expert knowledge.
Alona Fyshe and Duane Szafron
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| 10:10-10:30
| Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity.
Antonio Sanfilippo, Christian Posse, Banu Gopalan,
Stephen Tratz, and Michelle Gregory
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| 10:30-11:00
| Break
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| 11:00-12:30
| Session 2: Towards deeper biological literature analysis
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| 11:00-11:20
| A priority model for named entities.
Lorraine Tanabe and W. John Wilbur
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| 11:20-11:40
| Human gene name normalization using text matching with automatically extracted synonym dictionaries.
Haw-ren Fang, Kevin Murphy, Yang Jin, Jessica Kim, and Peter White
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| 11:40-12:00
| Integrating co-occurrence statistics with information extraction for robust retrieval of protein interactions from MEDLINE.
Razvan Bunescu, Raymond Mooney, Arun Ramani, and Edward Marcotte
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| 12:00-12:20
| SEROW: Adapting semantic role labeling for biomedical verbs: an exponential model coupled with automatically generated template features.
Tzong-Han Tsai, Wen-Chi Chou, Yu-Chun Lin, Wei Ku,
Ying-Shan Su, Ting-Yi Sung, and Wen-Lian Hsu
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| 12:30-14:00
| Lunch
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| 14:00-14:40
| Session 3: Exploring document properties
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| 14:00-14:20
| Generative content models for structural analysis of medical abstracts.
Jimmy Lin, Dina Demner-Fushman, Damianos Karakos, and
Sanjeev Khudanpur
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| 14:20-14:40
| Exploring text and image features to classify images in bioscience literature.
Barry Rafkind, Minsuk Lee, Hong Yu, and Shih-Fu Chang
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| 14:40-15:30
| The Procter and Gamble Keynote Speech: Mining biomedical texts for disease-related pathways
Andrey Rzhetsky, Columbia University
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| 15:30-16:00
| Break
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| 16:00-17:30
| Session 4: Insights from corpus analysis
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| 16:00-16:20
| Postnominal Prepositional Phrase Attachment in Proteomics.
Jonathan Schuman and Sabine Bergler
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| 16:20-16:30
| Wrap-up and discussion
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| 16:30-18:00
| Poster session
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Posters
BioKI:Enzymes - an adaptable system to locate
low-frequency information in full-text proteomics articles.
Sabine Bergler, Jonathan Schuman, Julien Dubuc, and Alexandr
Lebedev
| A graph-search framework for GeneId ranking.
William Cohen
| Semi-supervised anaphora resolution in biomedical texts.
Caroline Gasperin
| 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, and Izabela Goertzel
| Recognizing nested named entities in GENIA corpus.
Baohua Gu
| Biomedical term recognition with the perceptron HMM
algorithm.
Sittichai Jiampojamarn, Grzegorz Kondrak, and Colin Cherry
| Refactoring corpora.
Helen L. Johnson, William A. Baumgartner Jr.,
Martin Krallinger, K. Bretonnel Cohen, and Lawrence Hunter
| Rapid adaptation of POS tagging for domain specific uses.
John Miller, Michael Bloodgood, Manabu Torii, and Vijay Shanker
| Extracting protein-protein interactions using simple
contextual features.
Leif Arda Nielsen
| Identifying experimental techniques in biomedical
literature.
Meeta Oberoi, Craig A. Struble, and Sonia L. Sugg
| A pragmatic approach to summary extraction in clinical
trials.
Graciela Rosemblat and Laurel Graham
| The difficulties of taxonomic name extraction and a
solution.
Guido Sautter and Klemens Boehm
| Summarizing key concepts using citation sentences.
Ariel Schwartz, Preslav Nakov, and Marti Hearst
| Subdomain adaptation of a POS tagger with a small corpus.
Yuka Tateisi, Yoshimasa Tsuruoka, and Jun'ichi Tsujii
| Bootstrapping and evaluating named entity recognition in
the biomedical domain.
Andreas Vlachos and Caroline Gasperin
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