Work Aims to Provide Platform for Understanding Disease Progression
Researchers from New York University’s Courant Institute of Mathematical Sciences are developing cutting-edge computer tools to model the development of pancreatic cancer. The creation of such a model will provide a platform for systematically exploring various cancer diagnostics and therapeutics.
The award, a five-year, $1.8 million grant from the National Science Foundation, is funded under the American Recovery and Reinvestment Act of 2009. It is part of a larger $10 million grant from NSF’s Expeditions in Computing initiative that also includes researchers from Carnegie Mellon University, the University of Maryland, NASA’s Jet Propulsion Laboratory, the City University of New York’s Lehman College, and the State University of New York at Stony Brook.
The NYU Courant team is comprised of: NYU Principal Investigator Bud Mishra, a professor of computer science and mathematics and head of Courant’s Bioinformatics Group; the Project Deputy Director Amir Pnueli, a professor of computer science; and Computer Science Professor Patrick Cousot.
Scientists have had difficulty finding an appropriate model for the development of pancreatic cancer, the fourth-leading cause of cancer deaths in the United States and Europe. Developing a valid computer model could prove to be crucial in discovering how this cancer develops and how it might be detected at an early, treatable stage.
“In modeling cancer, we will be replicating different types of cancer cells, how these cells communicate with each other, and how they multiply,” explained Mishra, who also has an appointment in the Department of Cell Biology at NYU’s School of Medicine. “In doing so, we will develop a model of cancer evolution that will allow other researchers to explore possible ways to treat the disease and interpret their experimental data.”
The researchers will combine Model Checking and Abstract Interpretation-two methods that have been successful in finding errors or proving their absence in computer circuitry and software-and extend them to provide insights into models of complex systems, whether they are biological or electronic. Researchers at NYU’s partner institutions are developing models to address atrial fibrillation, a common heart-rhythm problem, and to improve the operation of aircraft and automobiles.
Model Checking is the most widely used technique for detecting and diagnosing errors in complex hardware and software designs. It considers every possible state of a hardware or software design and determines if it is consistent with the designer’s specifications. It then produces counter examples when it uncovers inconsistencies.
Abstract Interpretation, by contrast, does not attempt to look individually at every possible state of a system, but considers all of them by developing a simplified over-approximation of a system that preserves the particular properties that need to be assessed. This makes it possible to analyze very large, complex systems, such as the one million lines of code in the Airbus A380’s primary flight control system.
NSF’s Expeditions in Computing initiative funds teams of researchers and educators to pursue far-reaching research agendas that promise significant advances in the computing frontier and great benefit to society.