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On the border length minimization problem (BLMP) on a square array

Published: 02 August 2010 Publication History

Abstract

Protein/Peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and high-throughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having low serum titers and locate antibody signatures. Improving the yield of microarray fabrication involves solving a hard combinatorial optimization problem called the Border Length Minimization Problem (BLMP). An important question that remained open for the past seven years is if the BLMP is tractable or not. We settle this open problem by proving that the BLMP is NP-hard. We also present a hierarchical refinement algorithm which can refine any heuristic solution for the BLMP problem. We also prove that the TSP+1-threading heuristic is an O(N)-approximation.
The hierarchical refinement solver is available as an open-source code at http://launchpad.net/blm-solve.

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  • (2012)Hardness and approximation of the asynchronous border minimization problemProceedings of the 9th Annual international conference on Theory and Applications of Models of Computation10.1007/978-3-642-29952-0_20(164-176)Online publication date: 16-May-2012

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cover image ACM Conferences
BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
August 2010
705 pages
ISBN:9781450304382
DOI:10.1145/1854776
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 02 August 2010

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Author Tags

  1. appoximation algorithms
  2. border length minimization
  3. computational biology
  4. microarray optimization
  5. quadratic assignment

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  • (2012)Hardness and approximation of the asynchronous border minimization problemProceedings of the 9th Annual international conference on Theory and Applications of Models of Computation10.1007/978-3-642-29952-0_20(164-176)Online publication date: 16-May-2012

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