Outlier Detection for DNA Fragment Assembly

Abstract

Given $n$ length-$\ell$ strings $S =\{s_1, ..., s_n\}$ over a constant size alphabet $\Sigma$ together with parameters $d$ and $k$, the objective in the {\em Consensus String with Outliers} problem is to find a subset $S^*$ of $S$ of size $n-k$ and a string $s$ such that $\sum_{s_i \in S^*} d(s_i, s) \leq d$. Here $d(x, y)$ denotes the Hamming distance between the two strings $x$ and $y$. We prove 1. a variant of {\em Consensus String with Outliers} where the number of outliers $k$ is fixed and the objective is to minimize the total distance $\sum_{s_i \in S^*} d(s_i, s)$ admits a simple PTAS. (ii) Under the natural assumption that the number of outliers $k$ is small, the PTAS for the distance minimization version of {\em Consensus String with Outliers} performs well. In particular, as long as $k\leq cn$ for a fixed constant $c < 1$, the algorithm provides a $(1+\epsilon)$-approximate solution in time $f(1/\epsilon)(n\ell)^{O(1)}$ and thus, is an EPTAS. 2. In order to improve the PTAS for {\em Consensus String with Outliers} to an EPTAS, the assumption that $k$ is small is necessary. Specifically, when $k$ is allowed to be arbitrary the {\em Consensus String with Outliers} problem does not admit an EPTAS unless FPT=W[1]. This hardness result holds even for binary alphabets. 3. The decision version of {\em Consensus String with Outliers} is fixed parameter tractable when parameterized by $\frac{d}{n-k}$. and thus, also when parameterized by just $d$. To the best of our knowledge, {\em Consensus String with Outliers} is the first problem that admits a PTAS, and is fixed parameter tractable when parameterized by the value of the objective function but does not admit an EPTAS under plausible complexity assumptions.