Parameterized Complexity of Asynchronous Border Minimization

Microarrays are research tools used in gene discovery as well as disease and cancer diagnostics. Two prominent but challenging problems related to microarrays are the Border Minimization Problem (BMP) and the Border Minimization Problem with given placement (P-BMP). In this paper we investigate the parameterized complexity of natural variants of BMP and P-BMP under several natural parameters. We show that BMP and P-BMP are in FPT under the following two combinations of parameters: 1) the size of the alphabet (c), the maximum length of a sequence (string) in the input (l) and the number of rows of the microarray (r); and, 2) the size of the alphabet and the size of the border length (o). Furthermore, P-BMP is in FPT when parameterized by c and l. We complement our tractability results with corresponding hardness results

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

34th Midwest Symposium on Circuits and Systems-Final Program

Organized by the Naval Postgraduate School Monterey California. Cosponsored by the IEEE Circuits and Systems Society. Symposium Organizing Committee: General Chairman-Sherif Michael, Technical Program-Roberto Cristi, Publications-Michael Soderstrand, Special Sessions- Charles W. Therrien, Publicity: Jeffrey Burl, Finance: Ralph Hippenstiel, and Local Arrangements: Barbara Cristi