|BIOKDD '10 Workshop, "Mining BioComplexity: From Molecular Systems to Health"|
Bioinformatics is the science of managing, mining, and interpreting information from biological data. Various genome projects have contributed to an exponential growth in DNA and protein sequence databases. Advances in high-throughput technology such as microarrays and mass spectrometry have further created the fields of functional genomics and proteomics, in which one can monitor quantitatively the presence of multiple genes, proteins, metabolites, and compounds in a given biological state. The ongoing influx of these data, the inherent uncertainties in data collection processes, and the gap between data collection and knowledge curation have collectively created exciting opportunities for data mining researchers.
While tremendous progress has been made over the years, many of the fundamental problems in bioinformatics, such as protein structure prediction, gene-environment interaction, and regulatory pathway mapping, are still open. Data mining will play essential roles in understanding these fundamental problems and development of novel therapeutic/diagnostic solutions in post-genome medicine.
Data Mining approaches seem ideally suited for Bioinformatics, since they are data-driven and do not require a comprehensive theory of life's organization at the molecular level. The extensive databases of biological information create both challenges and opportunities for developing novel KDD methods. To highlight these avenues we organized the Workshops on Data Mining in Bioinformatics (BIOKDD 2001-2009), held annually or biannually in conjunction with the ACM SIGKDD Conference. This will be the 9th year for the workshop.
Past workshops attracted 50-100 participants, from academia, industry and government labs, underscoring the surge of interest in this exciting and rapidly expanding field. The program of the workshops included 10-11 contributed papers, and a panel/invited talk.
Information on past workshops is available at:
The goal of this workshop is to encourage KDD researchers and practitioners to take on the numerous challenges that Bioinformatics offers. This year the workshop will feature the theme of “Mining biocomplexity: From Molecular Systems to Health”. Complex biological systems consist of components that are in themselves complex and interacting with each other. Understanding how the various components work in concert, using modern high-throughput biology and data mining methods, is crucial to the ultimate goal of genome-based economy such as genome medicine and new agricultural and energy solutions. Applying the study of complex biological systems, health informatics aims to discover novel and useful patterns in large volumes of health care related data and to explore the links between disease physiology and molecular bio-sciences. BIOKDD offers a premier forum of presenting data mining concepts and tools for integrating data from heterogeneous multimedia sources, especially those from new high-throughput experimental data collection technologies, and expediting knowledge discovery in a wide range of areas including biological, biomedical, pharmaceutical, nursing, clinical care, dentistry, and public health research.
We encourage papers that propose novel data mining techniques for post-genome bioinformatics studies in areas such as:
Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides. Paper should be submitted in PDF/PS format through Easychar at the following link: http://www.easychair.org/conferences?conf=biokdd10
Camera-ready format papers may be referenced from previous BIOKDD conference proceedings (e.g., BIOKDD08)
All papers will be published at the workshop proceedings and at the ACM digital library.
Submission of accepted papers. For accepted workshop papers, we require that each camera-ready paper be formatted strictly according to the official ACM Proceedings Format. Please submit PDF file only. To prepare for the camera-ready PDF file submission, you may use either the Microsoft word template or the Latex files preparation instructions found here. All final camera-ready submissions must be accompanied by a completed digital copy (scanned Okay) of the ACM copyright transfer form, or else the paper cannot be included in the final workshop proceedings.
Publication of proceeding and expanded papers. Expanded version of selected high-quality papers from the workshop will be invited for publication in a special issue of a major bioinformatics/biocomputing journal (in 2007, it was Journal of Bioinformatics and Computational Biology; in 2008, it was ACM/IEEE Transactions on Computational Biology and Bioinformatics). Details of the journal/book publication will be announced online after the workshop.
To register officially for the workshop, please use the following Google Checkout to pay the fees.
8:25 8:30: Opening Remarks
8:30-8:45 Discovery of Error-tolerant Biclusters from Noisy Gene Expression Data
8:45-9:00 Systematic Construction and Analysis of Co-expression Networks for Identification of Functional Modules and cis-regulatory Elements
9:00- 9:15 A Fast Markov Blankets Method for Epistatic Interactions Detection in Genome-wide Association Studies
9:15 – 9:30 Combining Active Learning and Semi-supervised Learning Techniques to Extract Protein Interaction Sentences
9:30-10:30: Keynote Speech
10:30-11:15 Coffee Break & Poster Session
11:15-11:30 Efficient Motif Finding Algorithms for Large-Alphabet Inputs
11:15 – 11:45 Planning Combinatorial Disulfide Cross-links for Protein Fold Determination
11:45 – 12:00 A New Approach for Detecting Bivariate Interactions in High Dimensional Data using Quadratic Discriminant Analysis
12:00 – 1:00: Panel Discussion