Carnegie Mellon technique accelerates biological image analysis

But as the number of variables increase, the belief propagation algorithm can grow unwieldy and require an impractical amount of computing time to solve these problems.

The belief propagation algorithm assumes that neighbors — whether they are cells, or bits of text — have effects on each other. So the algorithm represents each piece of evidence used to make inferences as a node in an interconnected network, and exchanges messages between nodes. The Carnegie Mellon researchers found shortcuts for generating these messages, which significantly improved the speed of the entire network.

Murphy, director of the Lane Center for Computational Biology, said this technique could improve the performance of belief propagation algorithms in many applications, including text analysis, Web analysis and medical diagnosis. For this paper, the researchers applied their techniques to analysis of protein patterns within HeLa cells. They found the technique speeded analysis by several orders of magnitude.

In high-throughput screening processes used for drug discovery and other research, tens of thousands of wells — each containing tens or hundreds of cells — need to be analyzed each day, Murphy said. Automated analysis of the cellular relationships within so many wells would be impossible without the sort of speedups achieved in the new study, he added.

Chen, who graduated with his Ph.D. in biomedical engineering last year, is now a postdoctoral researcher at the Scripps Research Institute in La Jolla, Calif.

The Ray and Stephanie Lane Center for Computational Biology was established last year with a focus on bringing machine learning methods to bear on complex biological problems, especially cancer diagnosis and treatment. For more, see http://lane.compbio.cmu.edu.

About Carnegie Mellon: Carnegie Mellon is a private research university with a distinctive mix of programs in engineering, computer science, robotics, business, public policy, fine arts and the humanities. More than 10,000 undergraduate and graduate students receive an education characterized by its focus on creating and implementing solutions for real problems, interdisciplinary collaboration, and innovation. A small student-to-faculty ratio provides an opportunity for close interaction between students and professors. While technology is pervasive on its 144-acre Pittsburgh campus, Carnegie Mellon is also distinctive among leading research universities for the world-renowned programs in its College of Fine Arts. A global university, Carnegie Mellon has campuses in Silicon Valley, Calif., and Qatar, and programs in Asia, Australia and Europe. For more, see www.cmu.edu.