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arXiv · 1202.2820

On Approximating String Selection Problems with Outliers

Christina Boucher·Gad M. Landau·Avivit Levy·David Pritchard·Oren Weimann
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Abstract

Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem is, given a set S of same-length strings, and a parameter d, find a string x that maximizes the number of "non-outliers" within Hamming distance d of x. We prove this problem has no PTAS unless ZPP=NP, correcting a decade-old mistake. The Most Strings with Few Bad Columns problem is to find a maximum-size subset of input strings so that the number of non-identical positions is at most k; we show it has no PTAS unless P=NP. We also observe Closest to k Strings has no EPTAS unless W[1]=FPT. In sum, outliers help model problems associated with using biological data, but we show the problem of finding an approximate solution is computationally difficult.

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Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann. 2012-02-13. On Approximating String Selection Problems with Outliers. https://arxiv.org/abs/1202.2820

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