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arXiv 1503.07310cs.CC
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系统发育约束满足问题的复杂性

The Complexity of Phylogeny Constraint Satisfaction Problems

Manuel Bodirsky, Peter Jonsson, Trung Van Pham

摘要:

我们系统地研究了系统发育重建中的一类计算问题的计算复杂性。这个类包含例如有根的三重一致性问题,禁止子树问题,四重一致性问题,以及生物信息学文献中研究的许多其他问题。所研究的问题可以描述为\emph{constraint satisfaction problems}的约束有一个一阶定义的根三元关系。我们证明了每一个这样的遗传问题都可以在多项式时间内求解或者是NP-完全的。在算法方面,我们推广了一个著名的多项式时间算法的Aho,Sagiv,Szymanski和Ullman的根三重一致性问题。我们的算法反复求解线性方程组,在多项式时间内构造一个解。然后,我们表明,我们的算法不能解决的每一个遗传问题是NP-完全的。我们的分类建立了一个二分法的一大类无限的结构,我们相信是独立的兴趣,在泛代数,模型论和拓扑结构。我们的主要结果的证明结合了来自各个研究领域的结果和技术:最近分类的模型完整的核心的减少同质二进制分支C-关系,勒布的拉姆齐定理有根树,和通用代数。

英文摘要:

We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet consistency problem, and many other problems studied in the bioinformatics literature. The studied problems can be described as \emph{constraint satisfaction problems} where the constraints have a first-order definition over the rooted triple relation. We show that every such phylogeny problem can be solved in polynomial time or is NP-complete. On the algorithmic side, we generalize a well-known polynomial-time algorithm of Aho, Sagiv, Szymanski, and Ullman for the rooted triple consistency problem. Our algorithm repeatedly solves linear equation systems to construct a solution in polynomial time. We then show that every phylogeny problem that cannot be solved by our algorithm is NP-complete. Our classification establishes a dichotomy for a large class of infinite structures that we believe is of independent interest in universal algebra, model theory, and topology. The proof of our main result combines results and techniques from various research areas: a recent classification of the model-complete cores of the reducts of the homogeneous binary branching C-relation, Leeb's Ramsey theorem for rooted trees, and universal algebra.

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