8:30-8:45

Introduction

9:10-9:30

Adaptive String Similarity Metrics for Biomedical Reference Resolution, article 

B.Wellner, J.Castaño, J. Pustejovsky

9:35-10:00

Unsupervised Gene/Protein Named Entity Normalization using Automatically Extracted Dictionaries, article

A.M. Cohen

10:00-10:30  Coffee Break

10:30-11:15

Invited Speaker - Dr. Judith A. Blake, The Jackson Labs
“Bioinformatics and the Biomedical Literature: Current Challenges”

11:20-11:45

A Machine Learning Approach to Acronym Generation, article
   

Y. Tsuruoka, S. Ananiadou, J. Tsujii

11:45-12:00

Scaling Up BioNLP: Application of a Text Annotation Architecture to Noun Compound Bracketing

P. Nakov, A. Schwartz, B. Wolf,
M. Hearst

12:00-13:00 Lunch

13:00-13:15

Searching for High-Utility Text in the Biomedical Literature

H. Shatkay, A. Rzhetsky, W. J. Wilbur

13:15-13:40

MedTag: a Collection of Biomedical Annotations, article
 

L.H Smith, L. Tanabe, T. Rindflesch,
W. J. Wilbur

13:45-14:10

Corpus Design for Biomedical Natural Language Processing, article

K. B. Cohen, L. Fox, P. V. Ogren,
L. Hunter

14:10-14:25

A Cross-Domain Application of Natural Language Processing in Biology

I. Chiu, L. H. Shu

14:30-15:00 Coffee Break

15:00-15:15

Functional Annotation of Genes Using Hierarchical Text Categorization, article

S. Kiritchenko, S. Matwin, 
A. F. Famili

15:15-15:30

Automatic Highlighting of Bioscience Literature, article

H. Wang, S. Bradshaw, M. Light

15:30-15:55

Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions, article

A. Ramani, E. Marcotte, R. Bunescu,
R. Mooney

15:55-16:20

InTex: A Syntactic Role Driven Protein-Protein Interaction Extractor for Bio-Medical Text, article

S. T. Ahmed, D. Chidambaram,
H. Davulcu, C. Baral

16:20-16:50

Wrap-up, announcements and discussion

16:50-17:20

Poster Boasters

17:20-18:30

Poster Session

19:00 Dinner (Informal gathering – details to be determined)

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