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  • CS Department Seminar – Dr. Timothy Havens, Speaker

    Department of Computer Science Seminar
    February 27, 2012 – 4:04 PM – Room G005 – Rekhi Hall
    Title: “Fuzzy Kernel Clustering of Large Scale Biomedical and Bioinformatics Data”

    Dr. Timothy Havens

    Since the early 1990’s, the ubiquity of personal computing technology has produced an abundance of staggeringly large data sets—it is estimated that Facebook alone logs over 25 terabytes of data per day and large bioinformatics data sets that integrate microarrays, sequences, and ontology annotations continue to grow. To compound this fact, these data sets are populated from disparate, often unknown, sources and are in a wide-range of formats. There is a great need for systems by which one can elucidate the similarity among and between groups in these data sets and produce easy-to-understand visualizations of the results. In this talk, I will discuss a method for efficiently and accurately approximating the solution of the kernel c-means clustering algorithm, specifically focusing on the fuzzy variant. Kernel clustering has been shown to be effective for data sets where the groups are not linearly separable in the input space or are high-dimensional. However, kernel fuzzy c-means (kFCM) presents computation and storage requirement challenges: clustering 500,000 objects requires 1 terabyte of main memory. I will show that on medium scale data (~50,000 objects) the approximate kFCM (akFCM) algorithm gives up to three orders of magnitude speed-up and a constant factor reduction in memory footprint with little-to-no degradation in performance, as compared to literal kFCM. I also demonstrate that akFCM performs well on large-scale data (>500,000 objects), including magnetic resonance imaging volumes. Last, I will apply the clustering method to bioinformatics data composed of genes described by Gene Ontology annotations to show how akFCM can be used for comparative genomics.

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