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

On the Descriptive Complexity of Temporal Constraint Satisfaction Problems

Finite-domain constraint satisfaction problems are either solvable by Datalog, or not even expressible in fixed-point logic with counting. The border between the two regimes coincides with an important dichotomy in universal algebra; in particular, the border can be described by a strong height-one Maltsev condition. For infinite-domain CSPs, the situation is more complicated even if the template structure of the CSP is model-theoretically tame. We prove that there is no Maltsev condition that characterizes Datalog already for the CSPs of first-order reducts of (Q;<); such CSPs are called temporal CSPs and are of fundamental importance in infinite-domain constraint satisfaction. Our main result is a complete classification of temporal CSPs that can be expressed in one of the following logical formalisms: Datalog, fixed-point logic (with or without counting), or fixed-point logic with the Boolean rank operator. The classification shows that many of the equivalent conditions in the finite fail to capture expressibility in Datalog or fixed-point logic already for temporal CSPs.Comment: 57 page

Complexity Classification Transfer for CSPs via Algebraic Products

We study the complexity of infinite-domain constraint satisfaction problems: our basic setting is that a complexity classification for the CSPs of first-order expansions of a structure $\mathfrak A$ can be transferred to a classification of the CSPs of first-order expansions of another structure $\mathfrak B$. We exploit a product of structures (the algebraic product) that corresponds to the product of the respective polymorphism clones and present a complete complexity classification of the CSPs for first-order expansions of the $n$-fold algebraic power of $(\mathbb{Q};<)$. This is proved by various algebraic and logical methods in combination with knowledge of the polymorphisms of the tractable first-order expansions of $(\mathbb{Q};<)$ and explicit descriptions of the expressible relations in terms of syntactically restricted first-order formulas. By combining our classification result with general classification transfer techniques, we obtain surprisingly strong new classification results for highly relevant formalisms such as Allen's Interval Algebra, the $n$-dimensional Block Algebra, and the Cardinal Direction Calculus, even if higher-arity relations are allowed. Our results confirm the infinite-domain tractability conjecture for classes of structures that have been difficult to analyse with older methods. For the special case of structures with binary signatures, the results can be substantially strengthened and tightly connected to Ord-Horn formulas; this solves several longstanding open problems from the AI literature.Comment: 61 pages, 1 figur

Schaefer's theorem for graphs

Schaefer's theorem is a complexity classification result for so-called Boolean constraint satisfaction problems: it states that every Boolean constraint satisfaction problem is either contained in one out of six classes and can be solved in polynomial time, or is NP-complete. We present an analog of this dichotomy result for the propositional logic of graphs instead of Boolean logic. In this generalization of Schaefer's result, the input consists of a set W of variables and a conjunction \Phi\ of statements ("constraints") about these variables in the language of graphs, where each statement is taken from a fixed finite set \Psi\ of allowed quantifier-free first-order formulas; the question is whether \Phi\ is satisfiable in a graph. We prove that either \Psi\ is contained in one out of 17 classes of graph formulas and the corresponding problem can be solved in polynomial time, or the problem is NP-complete. This is achieved by a universal-algebraic approach, which in turn allows us to use structural Ramsey theory. To apply the universal-algebraic approach, we formulate the computational problems under consideration as constraint satisfaction problems (CSPs) whose templates are first-order definable in the countably infinite random graph. Our method to classify the computational complexity of those CSPs is based on a Ramsey-theoretic analysis of functions acting on the random graph, and we develop general tools suitable for such an analysis which are of independent mathematical interest.Comment: 54 page

Tractable Ontology-Mediated Query Answering with Datatypes

Adding datatypes to ontology-mediated queries (OMQs) often makes query answering hard, even for lightweight languages. As a consequence, the use of datatypes in ontologies, e.g. in OWL 2 QL, has been severely restricted. We propose a new, non-uniform, way of analyzing the data-complexity of OMQ answering with datatypes. Instead of restricting the ontology language we aim at a classification of the patterns of datatype atoms in OMQs into those that can occur in non-tractable OMQs and those that only occur in tractable OMQs. To this end we establish a close link between OMQ answering with datatypes and constraint satisfaction problems (CSPs) over the datatypes. Given that query answering in this setting is undecidable in general already for very simple datatypes, we introduce, borrowing from the database literature, a property of OMQs called the Bounded Match Depth Property (BMDP). We apply the link to CSPs– using results and techniques in universal algebra and model theory–to prove PTIME/co-NP dichotomies for OMQs with the BDMP over Horn-ALCHI extended with (1) all finite datatypes, (2) rational numbers with linear order and (3) certain families of datatypes over the integers with the successor relation