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.

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!

Computer Science Department Scholar Announced

John Bush has been selected as the Department Scholar for 2012. At the 18th Annual Student Leadership Awards Ceremony being held on Friday, April 13, 2012, John will be recognized as the Computer Science Departmental Scholar and will receive a $200 cash award, along with a student from each academic department at Michigan Technological University.

In addition, one of the Departmental Scholars will be selected as as the Provost’s Award for Scholarship recipient and receive an additional $800 cash award. The Department congratulates you on your hard work.

CS Department Scholar 2012 Nominations

At the 18th Annual Student Leadership Awards Ceremony being held on April 13, 2012, our department will recognize one CS student as its 2012 Department Scholar. This student will receive a $200 cash award from the university. In addition, from the collective 2012 department scholars, one student will be selected to receive the Provost’s Award for Scholarship. This is an additional $800 cash award.

Our department has selected the following nominees for the CS Department Scholar: John Bush, Jeanette Head, Sonya Hochkammer, Keith Jurek, Paul LaMotte and Zachary Wolberg

Each nominee has been selected by the CS faculty because the CS department sees them as meeting the criteria specified by the university in choosing one Department Scholar. The Department Scholar receives recognition based on these criteria: excellent academic performance, research and/or scholarly activities, intellectual curiosity, creativity and good communication skills. Even though only one CS student is chosen for this award, the CS department wishes to recognize all six CS students and congratulate them on their hard work and scholarly success at Michigan Tech.

CS Creativity Contest

The Computer Science Department is hosting a Creativity Contest, looking for artwork, designs, and anything creative to adorn the walls of Rekhi Hall. The contest is open to Software Engineering, Computer Science, Computer Systems Science, and Computer Engineering students of all levels, as well as department faculty and staff. Any questions can be sent to csdept@mtu.edu or posted on the Michigan Tech CSCC Facebook wall (http://www.facebook.com/MTUCSCC).

Submissions will be accepted until November 27th at 11:59pm. When submitting a piece, the following will need to be provided:

* Name of Student, Faculty or Staff Member
* Major of Student, or Faculty/Staff title
* Name of Piece/Entry
* Category for Entry to be placed in: Artwork, Digital Artwork, Computer Art, Photography, and Other Pieces.
* A short description of the piece.
* Finally a Thumbnail, snapshot, or photograph of the piece. The actual piece does not have to be scanned in to be submitted. For example: Photographs of paintings are acceptable for submission.

Winning entries will be placed throughout Rekhi Hall to help bring a more creative and inspirational mood to the Computer Science building!

All entries, including those sent to csdept@mtu.edu, will be placed in albums on the Facebook page. Judging for entries will be both based on the amount of “Likes” the entry receives from Michigan Tech Students and the collaborative opinions of the CS Department Faculty and Staff.  All entries will receive a free MTU/CS Dept T-shirt.

WiCs Receives $500 NCWIT/Return Path Inc. Award

Women in Computing Science (WiCS), a student organization supported by the Department of Computer Science (CS) recently received a $500 award from the National Center for Women in Information Technology and Return Path, Inc. through the NCWIT Academic Alliance Student Seed Fund program. The purpose of these awards are to help student-run programs and initiatives that promote increased participation of women in computing and IT programs. WiCS is developing outreach programs for high school students with the purpose of raising their interest in computing especially among pre-college age girls.

The WiCS program is being designed to provide high school students with specific examples of the career opportunities available to them with a degree in CS. Many high school students, especially those who may be interested in a career in computing, have minimal or incorrect knowledge about the career opportunities in CS-related fields. WiCS is working closely with Michigan Tech Computer Science alumni to gather information about the broad range of fields that use computer science skills, including technology, health care, design and manufacturing, financial, and entertainment.

WiCS expects to present their program to both local and downstate high schools. Downstate visits to high schools will primarily occur during the break between semesters.

GPU “Just in Time” Compiler (aka “Shader Compiler”)

The Computer Science Department & the Center for Computer Systems Research will sponsor a seminar Friday, November 4, 2011, in Rekhi Hall, Room 214 featuring  Dr. Gang Chen.  Dr. Chen from AMD Boston Design Center,  will talk about the just-in-time compiler shipped with every AMD GPU and APU product, what it is and why it is an essential component of the GPU. The talk will include a brief overview of GPU architecture, focusing on the differences from CPU, a brief overview of the JIT’s internal structure, and interesting compiler issues that may not be seen with a typical CPU compiler along with some tips about performance tuning, and some of our ongoing and future works.

Gang Chen is currently the lead engineer for AMD’s GPU just-in-time compiler, and responsible for developing a new compiler for AMD’s next-generation GPU. He has been working in this field for AMD/ATI since 2002. Before that, he worked on a DSP C compiler at StarCore Technology Center for Agere from 2001 to 2002. He received his Ph.D in Computer Science in 2001 from Harvard University, his BE and ME in 1991 and 1993 from Tsinghua University, Beijing.

CS Professors Pastel and Wallace Involved in NSF-sponsored Citizen Science Project

Dr. Robert Pastel and Dr. Charles Wallace
Dr. Robert Pastel and Dr. Charles Wallace

Dr. Robert Pastel and Dr. Charles Wallace of the Computer Science Department are co-principal investigators on a $249,840 award from the National Science Foundation (NSF) titled “Environmental Cyber Citizens: Engaging Citizen Scientists in Global Environmental Change through Crowdsensing and Visualization”.

Citizen science aims to bring citizen scientists, ordinary individuals and groups, directly into the scientific inquiry process through legitimate and meaningful activities that are useful to the scientific community. The goal of the NSF-sponsored project is to use current computing technology to develop tools for environmental citizen scientists. A multi-disciplinary team of faculty and undergraduate students will collaborate with citizen scientist end users to develop and deploy data collection and visualization tools to monitor the critical ecosystems of Lightfoot Bay in the Upper Peninsula of Michigan. These users will effectively engage in crowdsensing: supplying useful data over space and time through “strength in numbers” that would be difficult for individual scientists to collect.

One goal is to develop and use smartphone applications that make it easy to acquire environmental information: e.g., digital images, in-situ measurements of water quality parameters, and personal narratives. In addition, applications will be developed for transferring the acquired data synchronously or asynchronously to an interactive visualization website. On the visualization website, users will combine quantitative data in meaningful ways while framing or annotating it with qualitative data. The smartphone applications and visualization tools will be developed in undergraduate design courses within the Computer Science Department.

The project is highly interdisciplinary, involving Dr. Alex Mayer (principal investigator) of Civil & Environmental Engineering, as well as faculty in Chemical Engineering and in Forest Resources & Environmental Science. In addition, it will build upon existing educational programs at Keweenaw Bay Ojibwa Community College, several local high schools, and the Keweenaw Land Trust. Research scientists at IBM researching crowdsensing will also collaborate.

Dr. Soner Onder Awarded $153,000

Dr. Soner Onder was awarded $153,000.00 from the NSF (National Science
Foundation), division of Computer and Communication Foundations,
Software and Hardware Foundations Program in support of his research.
This research focuses on developing a framework in which compilers and
processor architectures can collaborate efficiently and effectively.

The project will support two Ph.D. students for one year. Dr. Onder
and his students will be investigating single assignment program
representations in which each variable is assigned at a single point
in the program. The direct support of these representations through
micro-architecture implementation is the key concept that can break
the barriers between the compilers and architectures. This new
approach will have a significant impact on the design of future
processors, design of compiler internal representations as well as the
back-end of the compilers. It can also change how parallelism is
exploited at various granularities and how various optimizations are
carried out.

Dr. Onder also expects that the investigated framework will help
revitalize computer architecture and compiler optimization research by
opening up unexplored paths for research in high-performance systems.
Consequently, it can affect every field of science and commerce which
relies on high-performance computation.