Local search is widely used to solve combinatorial optimisation problems and to model biological evolution, but the performance of local search algorithms on different kinds of fitness landscapes is poorly understood. Here we introduce a natural approach to modelling fitness landscapes using valued constraints. This allows us to investigate minimal representations (normal forms) and to consider the effects of the structure of the constraint graph on the tractability of local search. First, we show that for fitness landscapes representable by binary Boolean valued constraints there is a minimal necessary constraint graph that can be easily computed. Second, we consider landscapes as equivalent if they allow the same (improving) local search moves; we show that a minimal normal form still exists, but is NP-hard to compute. Next we consider the complexity of local search on fitness landscapes modelled by valued constraints with restricted forms of constraint graph. In the binary Boolean case, we prove that a tree-structured constraint graph gives a tight quadratic bound on the number of improving moves made by any local search; hence, any landscape that can be represented by such a model will be tractable for local search. We build two families of examples to show that both the conditions in our tractability result are essential. With domain size three, even just a path of binary constraints can model a landscape with an exponentially long sequence of improving moves. With a treewidth two constraint graph, even with a maximum degree of three, binary Boolean constraints can model a landscape with an exponentially long sequence of improving moves.

We begin a systematic study of how Graph Decomposition problems may be represented using propositional formulas, and hence solved using SAT-solver technology. By making use of symmetry breaking techniques we are able to obtain solutions to several previously unknown cases and to significantly reduce the time needed to compute decompositions. However some fairly small instances remain unsolved, and thus provide an interesting challenge to SAT-solver technology.

We study methods for transforming valued constraint satisfaction problems (VCSPs) to binary VCSPs. First, we show that the standard dual encoding preserves many aspects of the algebraic properties that capture the computational complexity of VCSPs. Second, we extend the reduction of CSPs to binary CSPs described by Bulín et al. [ Log. Methods Comput. Sci., 11 (2015)] to VCSPs. This reduction establishes that VCSPs over a fixed valued constraint language are polynomial-time equivalent to minimum-cost homomorphism problems over a fixed digraph.

Constraint programming is a natural paradigm for many combinatorial optimisation problems. The complexity of constraint satisfaction for various forms of constraints has been widely-studied, both to inform the choice of appropriate algorithms, and to understand better the boundary between polynomial-time complexity and NP-hardness. In constraint programming it is well-known that any constraint satisfaction problem can be converted to an equivalent binary problem using the so-called dual encoding. Using this standard approach any fixed collection of constraints, of arbitrary arity, can be converted to an equivalent set of constraints of arity at most two. Here we show that this transformation, although it changes the domain of the constraints, preserves all the relevant algebraic properties that determine the complexity. Moreover, we show that the dual encoding preserves many of the key algorithmic properties of the original instance. We also show that this remains true for more general valued constraint languages, where constraints may assign different cost values to different assignments. Hence, we obtain a simple proof of the fact that to classify the computational complexity of all valued constraint languages it suffices to classify only binary valued constraint languages.

Leader election in anonymous rings and complete networks is a very practical problem in distributed computing. Previous algorithms for this problem are generally designed for a classical message passing model where complex messages are exchanged. However, the need to send and receive complex messages makes such algorithms less practical for some real applications. We present some simple synchronous algorithms for distributed leader election in anonymous rings and complete networks that are inspired by the development of the neural system of the fruit fly. Our leader election algorithms all assume that only one-bit messages are broadcast by nodes in the network and processors are only able to distinguish between silence and the arrival of one or more messages. These restrictions allow implementations to use a simpler message-passing architecture. Even with these harsh restrictions our algorithms are shown to achieve good time and message complexity both analytically and experimentally.

The increasing rate of antibiotic resistance and slowing discovery of novel antibiotic treatments presents a growing threat to public health. Here, we consider a simple model of evolution in asexually reproducing populations which considers adaptation as a biased random walk on a fitness landscape. This model associates the global properties of the fitness landscape with the algebraic properties of a Markov chain transition matrix and allows us to derive general results on the non-commutativity and irreversibility of natural selection as well as antibiotic cycling strategies. Using this formalism, we analyze 15 empirical fitness landscapes of E. coli under selection by different β-lactam antibiotics and demonstrate that the emergence of resistance to a given antibiotic can be either hindered or promoted by different sequences of drug application. Specifically, we demonstrate that the majority, approximately 70%, of sequential drug treatments with 2-4 drugs promote resistance to the final antibiotic. Further, we derive optimal drug application sequences with which we can probabilistically 'steer' the population through genotype space to avoid the emergence of resistance. This suggests a new strategy in the war against antibiotic-resistant organisms: drug sequencing to shepherd evolution through genotype space to states from which resistance cannot emerge and by which to maximize the chance of successful therapy.

Maximal Independent Set selection is a fundamental problem in distributed computing. A novel probabilistic algorithm for this problem has recently been proposed by Afek et al, inspired by the study of the way that developing cells in the fly become specialised. The algorithm they propose is simple and robust, but not as efficient as previous approaches: the expected time complexity is O(log2 n). Here we first show that the approach of Afek et al cannot achieve better efficiency than this across all networks, no matter how the global probability values are chosen.

Membrane systems (P systems) are distributed computing models inspired by living cells where a collection of processors jointly achieves a computing task. The problem of maximal independent set (MIS) selection in a graph is to choose a set of nonadjacent nodes to which no further nodes can be added. In this letter, we design a class of simple neural-like P systems to solve the MIS selection problem efficiently in a distributed way. This new class of systems possesses two features that are attractive for both distributed computing and membrane computing: first, the individual processors do not need any information about the overall size of the graph; second, they communicate using only one-bit messages.

Discrete optimization problems arise in many different areas and are studied under many different names. In many such problems the quantity to be optimized can be expressed as a sum of functions of a restricted form. Here we present a unifying theory of complexity for problems of this kind. We show that the complexity of a finite-domain discrete optimization problem is determined by certain algebraic properties of the objective function, which we call weighted polymorphisms. We define a Galois connection between sets of rational-valued functions and sets of weighted polymorphisms and show how the closed sets of this Galois connection can be characterized. These results provide a new approach to studying the complexity of discrete optimization. We use this approach to identify certain maximal tractable subproblems of the general problem and hence derive a complete classification of complexity for the Boolean case.

Local consistency techniques such as k-consistency are a key component of specialised solvers for constraint satisfaction problems. In this paper we show that the power of using k-consistency techniques on a constraint satisfaction problem is precisely captured by using a particular inference rule, which we call negative-hyper-resolution, on the standard direct encoding of the problem into Boolean clauses. We also show that current clause-learning SAT-solvers will discover in expected polynomial time any inconsistency that can be deduced from a given set of clauses using negative-hyper-resolvents of a fixed size. We combine these two results to show that, without being explicitly designed to do so, current clause-learning SAT-solvers efficiently simulate k-consistency techniques, for all fixed values of k. We then give some experimental results to show that this feature allows clause-learning SAT-solvers to efficiently solve certain families of constraint problems which are challenging for conventional constraint-programming solvers.

This paper reviews structural problem decomposition methods, such as tree and path decompositions. It is argued that these notions can be applied in two distinct ways: Either to show that a problem is efficiently solvable when a width parameter is fixed, or to prove that the unrestricted (or some width-parameter free) version of a problem is tractable by using a width-notion as a mathematical tool for directly solving the problem at hand. Examples are given for both cases. As a new showcase for the latter usage, we report some recent results on the Partner Units Problem, a form of configuration problem arising in an industrial context. We use the notion of a path decomposition to identify and solve a tractable class of instances of this problem with practical relevance.

The constraint satisfaction problem (CSP) is a central generic problem in artificial intelligence. Considerable progress has been made in identifying properties which ensure tractability in such problems, such as the property of being tree-structured. In this paper we introduce the broken-triangle property, which allows us to define a hybrid tractable class for this problem which significantly generalizes the class of problems with tree structure. We show that the broken-triangle property is conservative (i.e., it is preserved under domain reduction and hence under arc consistency operations) and that there is a polynomial-time algorithm to determine an ordering of the variables for which the broken-triangle property holds (or to determine that no such ordering exists). We also present a non-conservative extension of the broken-triangle property which is also sufficient to ensure tractability and can be detected in polynomial time.

A common type of DNA variation is called a Single Nucleotide Polymorphism (SNP), where a single position within a DNA sequence is altered from one nucleotide base to another. The problem of identifying disease-associated SNPs has been the subject of extensive research by statisticians. However, less research has been done within the computing community. In this paper, we propose a novel geometrical computing model for the SNP Motif Identification Problem. The purpose of our research is to explore the properties of SNPs in a combinatorial way. We test our algorithm on two real clinical datasets, and give computational results which demonstrate the efficiency and effectiveness of our approach.

Many natural combinatorial problems can be expressed as constraint satisfaction problems. This class of problems is known to be NP-complete in general, but certain restrictions on the form of the constraints can ensure tractability. Here we show that any set of relations used to specify the allowed forms of constraints can be associated with a finite universal algebra and we explore how the computational complexity of the corresponding constraint satisfaction problem is connected to the properties of this algebra. Hence, we completely translate the problem of classifying the complexity of restricted constraint satisfaction problems into the language of universal algebra. We introduce a notion of "tractable algebra," and investigate how the tractability of an algebra relates to the tractability of the smaller algebras which may be derived from it, including its subalgebras and homomorphic images. This allows us to reduce significantly the types of algebras which need to be classified. Using our results we also show that if the decision problem associated with a given collection of constraint types can be solved efficiently, then so can the corresponding search problem. We then classify all finite strictly simple surjective algebras with respect to tractability, obtaining a dichotomy theorem which generalizes Schaefer's dichotomy for the generalized satisfiability problem. Finally, we suggest a possible general algebraic criterion for distinguishing the tractable and intractable cases of the constraint satisfaction problem.

Many researchers in artificial intelligence are beginning to explore the use of soft constraints to express a set of (possibly conflicting) problem requirements. A soft constraint is a function defined on a collection of variables which associates some measure of desirability with each possible combination of values for those variables. However, the crucial question of the computational complexity of finding the optimal solution to a collection of soft constraints has so far received very little attention. In this paper we identify a class of soft binary constraints for which the problem of finding the optimal solution is tractable. In other words, we show that for any given set of such constraints, there exists a polynomial time algorithm to determine the assignment having the best overall combined measure of desirability. This tractable class includes many commonly-occurring soft constraints, such as 'as near as possible' or 'as soon as possible after', as well as crisp constraints such as 'greater than'. Finally, we show that this tractable class is maximal, in the sense that adding any other form of soft binary constraint which is not in the class gives rise to a class of problems which is NP-hard.

We study interval-valued constraint satisfaction problems (CSPs), in which the aim is to find an assignment of intervals to a given set of variables subject to constraints on the relative positions of intervals. Many well-known problems such as INTERVAL GRAPH RECOGNITION and INTERVAL SATISFIABILITY can be considered as examples of such CSPs. One interesting question concerning such problems is to determine exactly how the complexity of an interval-valued CSP depends on the set of constraints allowed in instances. For the framework known as Allen's interval algebra this question was completely answered earlier by the authors, by giving a complete description of the tractable cases and showing that all remaining cases are NP-complete. Here we extend the qualitative framework of Allen's algebra with additional constraints on the lengths of intervals. We allow these length constraints to be expressed as Horn disjunctive linear relations, a well-known tractable and sufficiently expressive form of constraints. The class of problems we consider contains, in particular, problems that are very closely related to the previously studied UNIT INTERVAL GRAPH SANDWICH problem. We completely characterize sets of qualitative relations for which the CSP augmented with arbitrary length constraints of the above form is tractable. We also show that, again, all the remaining cases are NP-complete.

Allen's interval algebra is one of the best established formalisms for temporal reasoning. This article provides the final step in the classification of complexity for satisfiability problems over constraints expressed in this algebra. When the constraints are chosen from the full Allen's algebra, this form of satisfiability problem is known to be NP-complete. However, eighteen tractable subalgebras have previously been identified; we show here that these subalgebras include all possible tractable subsets of Allen's algebra. In other words, we show that this algebra contains exactly eighteen maximal tractable subalgebras, and reasoning in any fragment not entirely contained in one of these subalgebras is NP-complete. We obtain this dichotomy result by giving a new uniform description of the known maximal tractable subalgebras, and then systematically using a general algebraic technique for identifying maximal subalgebras with a given property.

Many combinatorial search problems can be expressed as “constraint satisfaction problems” using an appropriate “constraint language”, that is, a set of relations over some fixed finite set of values. It is well-known that there is a trade-off between the expressive power of a constraint language and the complexity of the problems it can express. In the present paper we systematically study the complexity of all maximal constraint languages, that is, languages whose expressive power is just weaker than that of the language of all constraints. Using the algebraic invariance properties of constraints, we exhibit a strong necessary condition for tractability of such a constraint language. Moreover, we show that, at least for small sets of values, this condition is also sufficient.

MOTIVATION: Automatic tools to speed up routine biological processes are very much sought after in bio-medical research. Much repetitive work in molecular biology, such as allele calling in genetic analysis, can be made semi-automatic or task specific automatic by using existing techniques from computer science and signal processing. Computerized analysis is reproducible and avoids various forms of human error. Semi-automatic techniques with an interactive check on the results speed up the analysis and reduce the error. RESULTS: We have successfully implemented an image processing software package to automatically analyze agarose gel images of polymorphic DNA markers. We have obtained up to 90% accuracy for the classification of alleles in good quality images and up to 70% accuracy in average quality images. These results are obtained within a few seconds. Even after subsequent interactive checking to increase the accuracy of allele classification to 100%, the overall speed with which the data can be processed is greatly increased, compared to manual allele classification. AVAILABILITY: The IDL source code of the software is available on request from [email protected]

Many combinatorial search problems can be expressed as 'constraint satisfaction problems'. This class of problems is known to be NP-hard in general, but a number of restricted constraint classes have been identified which ensure tractability. This paper presents the first general results on combining tractable constraint classes to obtain larger, more general, tractable classes. We give examples to show that many known examples of tractable constraint classes, from a wide variety of different contexts, can be constructed from simpler tractable classes using a general method. We also construct several new tractable classes that have not previously been identified.

Many combinatorial search problems can be expressed as “constraint satisfaction problems” and this class of problems is known to be NP-complete in general. In this paper, we investigate the subclasses that arise from restricting the possible constraint types. We first show that any set of constraints that does not give rise to an NP-complete class of problems must satisfy a certain type of algebraic closure condition. We then investigate all the different possible forms of this algebraic closure property, and establish which of these are sufficient to ensure tractability. As examples, we show that all known classes of tractable constraints over finite domains can be characterized by such an algebraic closure property. Finally, we describe a simple computational procedure that can be used to determine the closure properties of a given set of constraints. This procedure involves solving a particular constraint satisfaction problem, which we call an “indicator problem.”

The paper describes techniques for constructing statistically independent binary sequences with prescribed ratios of zeros and ones. The first construction is a general recursive construction, which forms the sequences from a class of "elementary" sequences. The second construction is a special construction which can be used when the ratio of ones to zeros is expressed in binary notation. The second construction is shown to be optimal in terms of the numbers of input sequences required to construct the desired sequence. The paper concludes with a discussion of how to generate independent "elementary" sequences using simple digital techniques.>