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Background: Biomedical event extraction has attracted substantial attention as it can assist researchers in understanding the plethora of interactions among genes that are described in publications in molecular biology. While most recent work has focused on abstracts, the BioNLP 2011 shared task evaluated the submitted systems on both abstracts and full papers. In this article, we describe our submission to the shared task which decomposes event extraction into a set of classification tasks that can be learned either independently or jointly using the search-based structured prediction framework. Our intention is to explore how these two learning paradigms compare in the context of the shared task. Results: We report that models learned using search-based structured prediction exceed the accuracy of independently learned classifiers by 8.3 points in F-score, with the gains being more pronounced on the more complex Regulation events (13.23 points). Furthermore, we show how the trade-off between recall and precision can be adjusted in both learning paradigms and that search-based structured prediction achieves better recall at all precision points. Finally, we report on experiments with a simple domain-adaptation method, resulting in the second-best performance achieved by a single system. Conclusions: We demonstrate that joint inference using the search-based structured prediction framework can achieve better performance than independently learned classifiers, thus demonstrating the potential of this learning paradigm for event extraction and other similarly complex information-extraction tasks. [ABSTRACT FROM AUTHOR]

Papers from the 2010 American Medical Informatics Association (AMIA) Summit on Translational Bioinformatics held from March 10-12, 2010 in San Francisco, California are presented including "Mapping Transcription Mechanisms from Multimodal Genomic Data," "Using Gene Co-Expression Network Analysis to Predict Biomarkers for Chronic Lymphocytic Leukemia," and "Mining Multi-Item Drug Adverse Effect Associations in Spontaneous Reporting Systems."

Papers from the 9th International Conference on Bioinformatics, held September 26-28, 2010 in Tokyo, Japan are presented including "Robust and Accurate Prediction of Noncoding RNAs from Aligned Sequences," "Integrating Diverse Biological and Computational sources for Reliable Protein-Protein Interactions," and "DiScRIBinATE: A Rapid Method for Accurate Taxonomic Classification of Metagenomic Sequences."

Papers from the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference, held February 19-20, 2010 in Jonesboro, Arkansas are presented including "Analysis of Bovine Viral Diarrhea Viruses-Infected Monocytes: Identification of Cytopathic and Noncytopathic Biotype Differences," "Enzyme Structure Dynamics of Xylanase I from Trichoderma Longibrachiatum," and "Comparative Genome Analysis of PHB Gene Family Reveals Deep Evolutionary Origins and Diverse Gene Function."