Welcome
The mission of our department is to be boldly innovative. Our intent is to undertake research at the frontiers of computer science which will prepare our students for important contributions in industry.

The department is increasing its number of ambitious projects in high performance computing, image/signal analysis, and bioinformatics, while maintaining a solid tradition in fundamental computer science.

A new team assumed responsibility of the Department of Computer Science in the fall semester of 2004. Marc Garbey is chair of the department, seconded by Dr. Olin Johnson, associate chair. This new team includes Dexter Hill as director of operations and industry relations and Dr. George Zouridakis, director of graduate studies. Dr. Venkat Subramaniam succeeding Dr. Robert Anderson, is now responsible for undergraduate studies.

Two new faculty members are joining the department: Dr. Rong Zeng, assistant professor, is a specialist of wireless networks, distributed systems, and performance modeling. Dr.Shishir Shah, assistant professor, is a specialist in quantitative microscopy, computational biology, and image analysis.

The department activity in fall 2004 was intense and the department is now enjoying a significant increase in research funding. Overall our faculty raised, as main program investigators, almost three million dollars in grant funding from national agencies during the fall semester.

Below is a review of some of the major department transformations and recent faculty accomplishments.

Events

The department hosted high school students from the C.I.S.D. Academy of Science and Technology in collaboration with the Department of Biology and Biochemistry. Together, we gave a number of demonstrations and exciting presentations to 44 students and sponsors to encourage our visitors to learn more about the University of Houston and the College of Natural Sciences and Mathematics. We hope this type of event will impact the quality of our enrolment and lead to more opportunities for collaborations.

In cooperation with TLCC, the department organized a special workshop entitled “New Frontiers in HPC and Computational Sciences” to honor the 60th birthday of Dr. Lennart Johnsson. This workshop covered some of the favorite topics of our department including computer systems, compilers, networking, linear algebra, and parallel computing. Twenty scientists paid tribute to the career accomplishments of our distinguished colleague, Dr. L. Johnsson.

Infrastructure

The department is instituting a major improvement of its infrastructure. Our objective is twofold: first, to provide a better environment for classes and our students’ personal work environment and second, to expose our undergraduate and graduate students to a broad variety of leading edge computer architectures and software environments. Chandler Wilkerson and Tom Cumpian are spearheading this effort.

PGH 376 has been equipped with 45 new Gateway desktops and this classroom will also be remodeled. All old desktop PC’s in the PGH 547 lab space have been replaced by the P4 desktops previously in service on the third floor. Two additional, new laser color printers are now available to our students through the UniPrint system delivered by NSM. More information on lab updates is available here.

We have also purchased an 8-way Opteron server for the department and bought, in partnership with NSM, a 10 dual Apple G5 Beowulf system equipped with a Gigabit Ethernet switch. Most of this new equipment was scheduled for installation during our winter break.

For each parallel computer, Dr. Dragan Mirkovic is currently building a friendly software environment with pedagogic notes, demos, and benchmarks. Our students will then have exposure to modern techniques in parallel computing within the latest available software environment.

Thanks to a team effort lead by Barbara Murray and Tom Cumpian, the department office space organization was reshaped to clarify the separation between student affairs (left aisle) and finances (right aisle). Additionally, a new reception area is at the disposal of our visitors and will especially appeal to those from industry.

Preprint

The department is renewing an old tradition of producing high quality preprints. Our new preprint series is now available electronically at http://www.cs.uh.edu/preprints/ and 8 preprints are available at this time. This preprint series illustrates our mission and shows the diversity of our activity in HPC, image/signal analysis, bioinformatics, and fundamental computer science.

Seminars

Thanks to Dr. J. C. Huang, the department enjoyed a very lively series of graduate seminars during the fall that covered all aspects of our research and exposed our master’s students to leading edge research.

In the spring semester the department will host a series of seminars for distinguished lecturers, with prestigious scientists such as Jack Dongarra (Univ. of Tennessee and Oakridge), William Henshaw (Livermore), David Plaisted (Univ. of North Carolina), and Milan Sonka (Univ. of Iowa) presenting.

New Research Programs and Grants

Several new programs and grants were initiated during the fall and are summarized below:

Dr. Barbara Chapman is the PI on a recently approved three-year NSF research grant entitled "Performance Toolset for Dynamic Optimization of High-End Hybrid Applications." The project, which was effective November 2004, has a total budget of $500,000. A summary of the work follows:

Current high-end applications usually exploit just a fraction of the theoretical peak performance of large platforms. Investigating and overcoming performance problems of Fortran/C/C++ applications parallelized using the hybrid MPI+OpenMP approach is challenging. Typical application development and tuning scenarios involve the manual and separate use of compilers and performance tools, and program modifications are based upon insights laboriously gleaned from their output. The goal of this project is to raise the quality of the application development and tuning process by creating an integrated environment for program optimization that reduces the manual labor and guesswork of existing approaches. The proposed environment integrates several different existing technologies to provide a new level of support for optimizing hybrid MPI+OpenMP codes. The tools and results of this project will be freely available to the HPC community. The research brings together compiler, performance tool, and application developers, enriching the research experience of graduate students in order to create a well-rounded IT workforce. Other collaborators of the project are Rick Kufrin (University of Illinois at Urbana-Champaign), Danesh Tafti (Virginia Tech), and Felix Wolf (University of Tennessee).

Dr. Yuriy Fofanov has been awarded a major grant in bioinformatics on "Tools for Ultraspecific Probe/Primer Design." The Homeland Security Advanced Research Projects Agency (HSARPA) is the sponsoring agency. The estimate award amount is $285,379 for Phase I of the project and $509,928 for Phase II of the project (based on the results of Phase I). The novel computational approach will deliver DNA probes and PCR primers that have an unprecedented low probability of false positives or confusion by environmental background, and which resist evasion by threat agent engineering. Other members of the team include Dr. George Fox, Professor in the Department of Biology and Biochemistry at the University of Houston, as well as an Adjunct Professor of Chemical Engineering, and Dr. Richard C. Willson, Professor of Chemical Engineering and Professor of Biochemical & Biophysical Sciences at the University of Houston.

Dr. Ioannis Kakadiaris was recently awarded a three-year $566,350 grant from the Division of Information and Intelligent Systems of the National Science Foundation (NSF) for research titled "Cardiovascular Informatics." In collaboration with leading cardiologists from AEHA, Dr. Kakadiaris and his research group aim to add a new dimension to non-symptomatic medicine. The goal of the project is to develop novel computational tools for the mining of information from Computed Tomography and Intravascular Ultrasound imaging as an aid to physicians in scoring their patients’ vulnerability and likelihood of a future coronary event.

Dr. Ioannis Pavlidis was awarded a $500,000 research contract from DOD for performing research on "Novel Thermal Imaging Systems and Methodologies for Next Generation Polygraphy." This highly intensive project has started December 1, 2004 and will culminate by September 1, 2005. With this new award, the total federal research funds that the Infrared Imaging Group has been awarded this year equals $1,200,000.

Dr Ricardo Vilalta received one of the prestigious NSF career awards by the program director of the Artificial Intelligence and Cognitive Science Division ($500,000 for 5 years). The project is entitled "CAREER: Advancing the Theory and Practice of Meta-Learning with Applications in Physics." This project focuses on the field of meta-learning by investigating the relation between learning mechanisms and the tasks and domains where these mechanisms are applicable. This project is multidisciplinary in nature, with a particular emphasis on physics and astronomy. The principal area of application lies in the classification of Mars landscapes from geo-morphological features. A major goal of this project is to combine research and educational strategies aimed at the establishment of a Pattern Classification and Machine Learning Laboratory at the University of Houston.

Visibility of the Department

Dr. Willis King was elected an IEEE Fellow for his career contributions in the development and refinement of curricula in Computer Science and Engineering over the past 25 years. The president of IEEE congratulated Dr. King for his contributions to the establishment of curriculum standards in the U.S. and throughout the world. These contributions have impacted every computer science program since 1978.

Dr. Pavlidis' new book Computer Vision beyond the Visible Spectrum, was released by Springer in 2004. More information about the book can be found at the Springer website.

Dr. Albert Cheng has been invited to join the editorial board of the International Journal of Embedded Systems as an Associate Editor.

Laura Miller composed a fantastic poster of our department’s team which is now displayed prominently at multiple locations in our department.

International

Dr. Marc Garbey with co-PI’s R. Keller (HLRS-Stuttgart), Y.Vassilevski (INM-Moscow), and Frank Hülsemann (Erlangen) were granted a two year award from NATO to finance their international cooperation on “Improving the Reliability of Computer Simulations to Predict Environmental Risks.”

Several new cooperation agreements are under way, including a program with the Harbin Institute of Technology, University "G. D'Annunzio" of Chiety, and the University of Stuttgart. We will also collaborate with Saint Steven’s college thanks to the existing agreement that the University of Houston’s Department of Mathematics has with this famous institution.

Industry

Dr. Pavlidis was awarded a new patent by the U.S. Patent Office: "Near-Infrared Human Detector," U.S. Patent No. 6370260. The patent solves the problem of the automated detection of a human presence using a fusion methodology in the short-wave infrared spectrum. The patent supports high-end security products currently marketed by Honeywell Inc.

Along with colleagues from UH, Dr Fofanov has submitted two patents in bioinformatics:

1. "Process and Apparatus for Using the Sets of Pseudo Random Subsequences Present in Genomes for Identification of Species." UHID 2317; Inventors: Yuriy Fofanov, Montgomery Pettitt, Tongbin Li and Serguei Tchoumakov; Filed June 30, 2004.

2. "Compositions, Processes and Algorithms for Microbial Detection." Disclosure ID 2003-048; Inventors: Fofanov, Montgomery Pettitt, George Fox, Richard Willson, III; Filed October 25, 2004.

Dr. Pavlidis and Dr. Garbey were awarded $50,000 in additional funds for their Honeywell research contract on "Thermal Facial Screening.” This corporate research grant will accommodate pattern recognition research on facial stress patterns. The total funding for this project so far stands at $301,000. The project started on August 1, 2003 and is expected to wind down by January 31, 2005.

M. Garbey, with H. Melki, associate dean for research in the College of Technology, and I.Kakadiaris, I.Pavlidis, and G.Zouridakis from COSC, have started collaboration with Microsoft. Their proposal entitled "Large-Scale Integration of Different Data Modalities for Computational Medical Sciences" was selected for one of the awards by SciData RFP. According to Dan Fay from Microsoft, “The submitted proposals were very competitive and your proposal was ranked quite high and thus was selected to receive one of the Microsoft Research SciData awards.” This award provides some equipment (Opteron’s servers with a 3Terabyte disk system), training, and software. This award signifies the beginning of a fruitful collaboration of the Department of Computer Science with the College of Technology as they embark upon a number of new, joint initiatives in research and teaching.