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This article is part of the supplement: Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2011

Open Access Research

Application of Max-SAT-based ATPG to optimal cancer therapy design

Pey-Chang Kent Lin and Sunil P Khatri*

Author Affiliations

Department of ECE, Texas A&M University, College Station, TX 77843, USA

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BMC Genomics 2012, 13(Suppl 6):S5  doi:10.1186/1471-2164-13-S6-S5

Published: 26 October 2012

Abstract

Background

Cancer and other gene related diseases are usually caused by a failure in the signaling pathway between genes and cells. These failures can occur in different areas of the gene regulatory network, but can be abstracted as faults in the regulatory function. For effective cancer treatment, it is imperative to identify faults and select appropriate drugs to treat the faults. In this paper, we present an extensible Max-SAT based automatic test pattern generation (ATPG) algorithm for cancer therapy. This ATPG algorithm is based on Boolean Satisfiability (SAT) and utilizes the stuck-at fault model for representing signaling faults. A weighted partial Max-SAT formulation is used to enable efficient selection of the most effective drug.

Results

Several usage cases are presented for fault identification and drug selection. These cases include the identification of testable faults, optimal drug selection for single/multiple known faults, and optimal drug selection for overall fault coverage. Experimental results on growth factor (GF) signaling pathways demonstrate that our algorithm is flexible, and can yield an exact solution for each feature in much less than 1 second.