Data-Mining Algorithm May Uncover Secrets of Biological Processes

June 29, 2010

A group of researchers at Virginia Tech, New York University (NYU), and the University of Milan claim to have devised an algorithm that reveals how biological processes are coordinated.

Called GOALIE (Gene Ontology-based Algorithmic Logic and Invariant Extractor), the algorithm blends techniques from mathematical optimization, computer science data mining, and computational biology.

"It automatically mines the data in an unsupervised manner, identifying temporal relationships between groups of genes in order to gain a more unbiased and holistic understanding of time-based cellular behavior," said Layne Watson (Virginia Tech).

A key aim of the algorithm, said colleague Naren Ramakrishnan (Virginia Tech), "is to be able to computationally integrate data from distinct stress experiments even when the experiments had been conducted independently."

The algorithm is part of a broader effort that links data mining with modeling tools, according to Bud Mishra (Courant Institute of Mathematical Sciences at NYU), who is an investigator on a $10 million NSF grant to develop computational reasoning tools for complex systems.

Understanding other important phenomena, like disease progression, aging, host-pathogen interactions, stress responses, and cell-to-cell communication may be an added benefit of the algorithm, which was described online in the Proceedings of the National Academy of Sciences (June 21, 2010).

Source: Science Daily June 22, 2010; Scientific Computing