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

Belief propagation in monoidal categories

We discuss a categorical version of the celebrated belief propagation algorithm. This provides a way to prove that some algorithms which are known or suspected to be analogous, are actually identical when formulated generically. It also highlights the computational point of view in monoidal categories.Comment: In Proceedings QPL 2014, arXiv:1412.810

Pure Nash Equilibria: Hard and Easy Games

We investigate complexity issues related to pure Nash equilibria of strategic games. We show that, even in very restrictive settings, determining whether a game has a pure Nash Equilibrium is NP-hard, while deciding whether a game has a strong Nash equilibrium is SigmaP2-complete. We then study practically relevant restrictions that lower the complexity. In particular, we are interested in quantitative and qualitative restrictions of the way each players payoff depends on moves of other players. We say that a game has small neighborhood if the utility function for each player depends only on (the actions of) a logarithmically small number of other players. The dependency structure of a game G can be expressed by a graph DG(G) or by a hypergraph H(G). By relating Nash equilibrium problems to constraint satisfaction problems (CSPs), we show that if G has small neighborhood and if H(G) has bounded hypertree width (or if DG(G) has bounded treewidth), then finding pure Nash and Pareto equilibria is feasible in polynomial time. If the game is graphical, then these problems are LOGCFL-complete and thus in the class NC2 of highly parallelizable problems

Tractable Optimization Problems through Hypergraph-Based Structural Restrictions

Several variants of the Constraint Satisfaction Problem have been proposed and investigated in the literature for modelling those scenarios where solutions are associated with some given costs. Within these frameworks computing an optimal solution is an NP-hard problem in general; yet, when restricted over classes of instances whose constraint interactions can be modelled via (nearly-)acyclic graphs, this problem is known to be solvable in polynomial time. In this paper, larger classes of tractable instances are singled out, by discussing solution approaches based on exploiting hypergraph acyclicity and, more generally, structural decomposition methods, such as (hyper)tree decompositions

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

The Complexity of Datalog on Linear Orders

We study the program complexity of datalog on both finite and infinite linear orders. Our main result states that on all linear orders with at least two elements, the nonemptiness problem for datalog is EXPTIME-complete. While containment of the nonemptiness problem in EXPTIME is known for finite linear orders and actually for arbitrary finite structures, it is not obvious for infinite linear orders. It sharply contrasts the situation on other infinite structures; for example, the datalog nonemptiness problem on an infinite successor structure is undecidable. We extend our upper bound results to infinite linear orders with constants. As an application, we show that the datalog nonemptiness problem on Allen's interval algebra is EXPTIME-complete.Comment: 21 page