Formal Concept Analysis: applications in computational genomics

Dustin Potter
MBI, The Ohio State University

(December 8, 2005 10:30 AM - 11:30 AM)

Formal Concept Analysis: applications in computational genomics

Abstract

The central ideas of Formal Concept Analysis revolve around the notion of a formal context and a formal concept. Of interest is the duality called Galois connection that arises naturally in different contexts. This duality is often observed between sets whose elements are related, such as objects and their attributes. In a Galois connection between two sets, the increase in size of one set corresponds to the decrease in size of the other set and vice versa. For example, an increase in the number of search terms used in a Google query corresponds, in general, to a decrease in the number of hits.

I will introduce the fundamentals of Formal Concept Analysis and demonstrate how we applied the ideas of the field to problems in microarray analysis. In this work we integrate biological attributes related to genes along with their expression values obtained from a microarray experiment. The integrated data is represented as a partially ordered set that respect Galois connections inherent in the data. Metrics are applied to the representations of multiple samples to discover biological similarities.