Additive Approximation for Near-Perfect Phylogeny Construction

DOI10.1007/978-3-642-32512-0_3zbMATH Open1358.68317arXiv1206.3334OpenAlexW1875940007MaRDI QIDQ3167382FDOQ3167382

Jamie Morgenstern, Pranjal Awasthi, Avrim Blum, Or Sheffet

Publication date: 2 November 2012

Published in: Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (Search for Journal in Brave)

Abstract: We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal tree can be found in linear time if the given dataset has a perfect phylogeny, i.e. cost of the optimal phylogeny is exactly $d$. Moreover, if the data has a near-perfect phylogeny, i.e. the cost of the optimal Steiner tree is $d+q$, it is known that an exact solution can be found in running time which is polynomial in the number of species and $d$, yet exponential in $q$. In this work, we give a polynomial-time algorithm (in both $d$ and $q$) that finds a phylogenetic tree of cost $d+O(q^2)$. This provides the best guarantees known - namely, a $(1+o(1))$-approximation - for the case $log(d)llqllsqrtd$, broadening the range of settings for which near-optimal solutions can be efficiently found. We also discuss the motivation and reasoning for studying such additive approximations.

Full work available at URL: https://arxiv.org/abs/1206.3334

Mathematics Subject Classification ID

Problems related to evolution (92D15) Approximation algorithms (68W25)

Cited In (1)

• Parameterized algorithms for the Steiner arborescence problem on a hypercube

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