Asynchronous Teams for probe selection problems

Authors:
CláUdio N. Meneses;Panos M. Pardalos;Michelle Ragle
Affiliations:
Department of Industrial and Systems Engineering, University of Florida, 303 Weil Hall, Gainesville, FL 32611, USA;Department of Industrial and Systems Engineering, University of Florida, 303 Weil Hall, Gainesville, FL 32611, USA;Department of Industrial and Systems Engineering, University of Florida, 303 Weil Hall, Gainesville, FL 32611, USA
Venue:
Discrete Optimization
Year:
2008

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Abstract

The selection of probe sets for hybridization experiments directly affects the efficiency and cost of the analysis. We propose the application of the Asynchronous Team (A-Team) technique to determine near-optimal probe sets. An A-Team is comprised of several different heuristic algorithms that communicate with each other via shared memories. The A-Team method has been applied successfully to several problems including the Set Covering Problem, the Traveling Salesman Problem, and the Point-to-Point Connection Problem, and lends itself well to the Probe Selection Problem. We designed and developed a C + + program to run instances of the Minimum Cost Probe Set and Maximum Distinguishing Probe Set problems. A program description and our results are presented in the paper.