Efficient data structures for backtrack search SAT solvers

The implementation of efficient Propositional Satisfiability (SAT) solvers entails the utilization of highly efficient data structures, as illustrated by most of the recent state-of-the-art SAT solvers. However, it is in general hard to compare existing data structures, since different solvers are often characterized by fairly different algorithmic organizations and techniques, and by different search strategies and heuristics. This paper aims the evaluation of data structures for backtrack search SAT solvers, under a common unbiased SAT framework. In addition, advantages and drawbacks of each existing data structure are identified. Finally, new data structures are proposed, that are competitive with the most efficient data structures currently available, and that may be preferable for the next generation SAT solvers

Boosting Haplotype Inference with Local Search

Abstract. A very challenging problem in the genetics domain is to infer haplotypes from genotypes. This process is expected to identify genes affecting health, disease and response to drugs. One of the approaches to haplotype inference aims to minimise the number of different haplotypes used, and is known as haplotype inference by pure parsimony (HIPP). The HIPP problem is computationally difficult, being NP-hard. Recently, a SAT-based method (SHIPs) has been proposed to solve the HIPP problem. This method iteratively considers an increasing number of haplotypes, starting from an initial lower bound. Hence, one important aspect of SHIPs is the lower bounding procedure, which reduces the number of iterations of the basic algorithm, and also indirectly simplifies the resulting SAT model. This paper describes the use of local search to improve existing lower bounding procedures. The new lower bounding procedure is guaranteed to be as tight as the existing procedures. In practice the new procedure is in most cases considerably tighter, allowing significant improvement of performance on challenging problem instances.

Incremental Cardinality Constraints for MaxSAT

Maximum Satisfiability (MaxSAT) is an optimization variant of the Boolean Satisfiability (SAT) problem. In general, MaxSAT algorithms perform a succession of SAT solver calls to reach an optimum solution making extensive use of cardinality constraints. Many of these algorithms are non-incremental in nature, i.e. at each iteration the formula is rebuilt and no knowledge is reused from one iteration to another. In this paper, we exploit the knowledge acquired across iterations using novel schemes to use cardinality constraints in an incremental fashion. We integrate these schemes with several MaxSAT algorithms. Our experimental results show a significant performance boost for these algo- rithms as compared to their non-incremental counterparts. These results suggest that incremental cardinality constraints could be beneficial for other constraint solving domains.Comment: 18 pages, 4 figures, 1 table. Final version published in Principles and Practice of Constraint Programming (CP) 201

Efficient Haplotype Inference with Pseudo-Boolean Optimization

Abstract. Haplotype inference from genotype data is a key computational problem in bioinformatics, since retrieving directly haplotype information from DNA samples is not feasible using existing technology. One of the methods for solving this problem uses the pure parsimony criterion, an approach known as Haplotype Inference by Pure Parsimony (HIPP). Initial work in this area was based on a number of different Integer Linear Programming (ILP) models and branch and bound algorithms. Recent work has shown that the utilization of a Boolean Satisfiability (SAT) formulation and state of the art SAT solvers represents the most efficient approach for solving the HIPP problem. Motivated by the promising results obtained using SAT techniques, this paper investigates the utilization of modern Pseudo-Boolean Optimization (PBO) algorithms for solving the HIPP problem. The paper starts by applying PBO to existing ILP models. The results are promising, and motivate the development of a new PBO model (RPoly) for the HIPP problem, which has a compact representation and eliminates key symmetries. Experimental results indicate that RPoly outperforms the SAT-based approach on most problem instances, being, in general, significantly more efficient

aspcud: A Linux Package Configuration Tool Based on Answer Set Programming

We present the Linux package configuration tool aspcud based on Answer Set Programming. In particular, we detail aspcud's preprocessor turning a CUDF specification into a set of logical facts.Comment: In Proceedings LoCoCo 2011, arXiv:1108.609

(Re)configuration based on model generation

Reconfiguration is an important activity for companies selling configurable products or services which have a long life time. However, identification of a set of required changes in a legacy configuration is a hard problem, since even small changes in the requirements might imply significant modifications. In this paper we show a solution based on answer set programming, which is a logic-based knowledge representation formalism well suited for a compact description of (re)configuration problems. Its applicability is demonstrated on simple abstractions of several real-world scenarios. The evaluation of our solution on a set of benchmark instances derived from commercial (re)configuration problems shows its practical applicability.Comment: In Proceedings LoCoCo 2011, arXiv:1108.609