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Farhan Ahmed ’05 (Utter Pradesh, India), a double major in mathematics and electrical & computer engineering, is conducting a senior honors thesis that could contribute to the shortening of an algorithm vital to DNA research.
An algorithm is a sequence of steps used to solve computational problems. The more exhaustive an algorithm is, the more accurate its result.
Ahmed is attempting to improve the Smith-Waterman algorithm, the standard on which sequence-alignment algorithms are based. Shortening the time needed to process this algorithm would enable researchers to examine the exact makeup of DNA and protein sequences. Other algorithms most commonly used in genomics, the study of the genetic makeup of living things, are not as precise as the Smith-Waterman.
“The Smith-Waterman is the original and most exhaustive algorithm,” Ahmed explains. “Unfortunately, it has a prohibitive space and time requirement. The very long sequences of DNA and protein would take years to be processed on a desktop machine. And the memory requirement of the algorithm is higher than the current technology supports on a regular 32-bit processor machine. But [the Smith-Waterman] is the most accurate.”
The complexity of DNA and protein makes running exhaustive algorithms impractical, and those used don’t explore all possible combinations of genetic makeup because of the sheer size of the task, so the results of these algorithms are probable, not exact.
The Smith-Waterman algorithm reduces the number of calculations by finding local alignments, or similarities in the sequences of the specimen. By looking at these local alignments, the algorithm shortens the calculation process through counting a mere fraction of the whole set. Finding a consistency in a sequence can provide an idea of what the structure contains.
Shortening the time it takes to run the Smith-Waterman could also provide exact genetic makeup, and knowing the makeup of a virus would enable medicines to be produced more quickly.
Ahmed proposes to reduce the length of a given sequence by removing the redundant or highly dissimilar parts so that the algorithm still finds the best solution in a shorter time period and uses less memory.
“Any improvement in the time required to run the Smith-Waterman would be valuable. [Shortening the time it takes to run] is an incremental process, and anything would be beneficial,” says Chun Wai Liew, assistant professor of computer science and one of Ahmed’s advisers.
“[Ahmed] is a real self-starter,” adds his second adviser, John Nestor, associate professor of electrical and computer engineering. “He does a lot of work independently and I am impressed by his ability to do that.”
Ahmed finds that the most exciting thing about the topic is its timeliness.
“A lot of money and effort are being put into this area and the implications of any major breakthrough are great for the medical field,” he says. “Having an adviser in both departments helps me get a broader perspective of the problem.”
His desire to do a senior honors project comes from previous research experience. He worked with Yih-Choung Yu, assistant professor of electrical and computer engineering, to perfect an outdated system that tests artificial hearts. His research helped lay the foundation to reduce animal testing, lower the cost of artificial heart testing, and provide a teaching tool for cardiovascular physiology students.
Ahmed and Yu worked together through Lafayette’s distinctive EXCEL Scholars program, in which students conduct research with faculty while earning a stipend. The program has helped to make Lafayette a national leader in undergraduate research. Many of the more than 160 students who participate each year share their work through articles in academic journals and/or conference presentations
“That got me interested in research,” says Ahmed. “Having an interest in the biomedical aspect of engineering, as well as computer science, gave me the motivation to explore a new idea.”
“Lafayette provides an environment that is very conducive for such research projects,” he adds. “Small class size and individual attention are necessary for a successful honors thesis. Lafayette provided both and much more; the resources available for use by students are excellent. I have friends at other noted schools and they don’t get the opportunities for research that I have gotten here at Lafayette.”
Ahmed is vice president of the International Students Association, associate representative of the Student Government Academic Progress Committee, and a founder of Linux Users Group. He is a Dana Scholar, a member of Pi Mu Epsilon, the national mathematics honor society, and was a member of Lafayette’s team in the Association of Computing Machinery International Collegiate Programming Contest. He has participated in the Lehigh Valley Association of Independent Colleges Math Contest, in which Lafayette has taken first place for five years, Mathematical Contest in Modeling, and Putnam Mathematical Competition.
As a national leader in undergraduate research, Lafayette sends one of the largest contingents to the National Conference on Undergraduate Research each year. Forty-two students were accepted to present their work at last year’s annual conference in April.