The Complexity of Rooted Phylogeny Problems

Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary tree that satisfies the formula? If the formulas do not contain disjunctions, the problem becomes the famous rooted triple consistency problem, which can be solved in polynomial time by an algorithm of Aho, Sagiv, Szymanski, and Ullman. If the clauses in the formulas are restricted to disjunctions of negated triples, Ng, Steel, and Wormald showed that the problem remains NP-complete. We systematically study the computational complexity of the problem for all such restrictions of the clauses in the input formula. For certain restricted disjunctions of triples we present an algorithm that has sub-quadratic running time and is asymptotically as fast as the fastest known algorithm for the rooted triple consistency problem. We also show that any restriction of the general rooted phylogeny problem that does not fall into our tractable class is NP-complete, using known results about the complexity of Boolean constraint satisfaction problems. Finally, we present a pebble game argument that shows that the rooted triple consistency problem (and also all generalizations studied in this paper) cannot be solved by Datalog

The complexity of rooted phylogeny problems

ABSTRACT Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the atomic formulas are rooted triples, is there a rooted binary tree that satisfies the formula? If the formulas do not contain disjunctions and negations, the problem becomes the famous rooted triple consistency problem, which can be solved in polynomial time by an algorithm of Aho, Sagiv, Szymanski, and Ullman. If the clauses in the formulas are restricted to disjunctions of negated triples, Ng, Steel, and Wormald showed that the problem remains NP-complete. We systematically study the computational complexity of the problem for all such restrictions of the clauses in the input formula. For certain restricted disjunctions of triples we present an algorithm that has sub-quadratic running time and is asymptotically as fast as the fastest known algorithm for the rooted triple consistency problem. We also show that any restriction of the general rooted phylogeny problem that does not fall into our tractable class is NP-complete, using known results about the complexity of Boolean constraint satisfaction problems. Finally, we present a pebble game argument that shows that the rooted triple consistency problem (and also all generalizations studied in this paper) cannot be solved by Datalog

The Complexity of Surjective Homomorphism Problems -- a Survey

We survey known results about the complexity of surjective homomorphism problems, studied in the context of related problems in the literature such as list homomorphism, retraction and compaction. In comparison with these problems, surjective homomorphism problems seem to be harder to classify and we examine especially three concrete problems that have arisen from the literature, two of which remain of open complexity

Phylogenetic CSPs are Approximation Resistant

We study the approximability of a broad class of computational problems -- originally motivated in evolutionary biology and phylogenetic reconstruction -- concerning the aggregation of potentially inconsistent (local) information about $n$ items of interest, and we present optimal hardness of approximation results under the Unique Games Conjecture. The class of problems studied here can be described as Constraint Satisfaction Problems (CSPs) over infinite domains, where instead of values $\{0,1\}$ or a fixed-size domain, the variables can be mapped to any of the $n$ leaves of a phylogenetic tree. The topology of the tree then determines whether a given constraint on the variables is satisfied or not, and the resulting CSPs are called Phylogenetic CSPs. Prominent examples of Phylogenetic CSPs with a long history and applications in various disciplines include: Triplet Reconstruction, Quartet Reconstruction, Subtree Aggregation (Forbidden or Desired). For example, in Triplet Reconstruction, we are given $m$ triplets of the form $ij|k$ (indicating that ``items $i,j$ are more similar to each other than to $k$'') and we want to construct a hierarchical clustering on the $n$ items, that respects the constraints as much as possible. Despite more than four decades of research, the basic question of maximizing the number of satisfied constraints is not well-understood. The current best approximation is achieved by outputting a random tree (for triplets, this achieves a 1/3 approximation). Our main result is that every Phylogenetic CSP is approximation resistant, i.e., there is no polynomial-time algorithm that does asymptotically better than a (biased) random assignment. This is a generalization of the results in Guruswami, Hastad, Manokaran, Raghavendra, and Charikar (2011), who showed that ordering CSPs are approximation resistant (e.g., Max Acyclic Subgraph, Betweenness).Comment: 45 pages, 11 figures, Abstract shortened for arxi