Day: March 16, 2012

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.

Continue Reading

Bo Yu Selected to Receives Michigan Tech SURF Award

The Michigan Technological University Department of Computer Science is proud to announce that Bo Yu, a senior in the CS, as been selected to receive the Michigan Tech SURF (Summer Undergraduate Research Fellowship) award. Bo has received the maximum award given for this fellowship – $3300.

Bo’s research, under the mentoring of Dr. Ali Ebnenasir, is titled, “Towards Designing a Fault-Tolerant Scheduler for the OkL4 Microkernal.” OkL4 is a small microkernel found within millions of smart phones. The research involves studying the task queue of the OkL4 scheduler, analyzing the impact of transient faults on the task queue, designing recovery from transient faults, and refining recovery back to the level of the OkL4 source code.

Congratulations to Bo and Dr. Ali Ebnenasir!

Continue Reading