Bounds on Weighted CSPs Using Constraint Propagation and Super-Reparametrizations

We propose a framework for computing upper bounds on the optimal value of the (maximization version of) Weighted CSP (WCSP) using super-reparametrizations, which are changes of the weights that keep or increase the WCSP objective for every assignment. We show that it is in principle possible to employ arbitrary (under certain technical conditions) constraint propagation rules to improve the bound. For arc consistency in particular, the method reduces to the known Virtual AC (VAC) algorithm. Newly, we implemented the method for singleton arc consistency (SAC) and compared it to other strong local consistencies in WCSPs on a public benchmark. The results show that the bounds obtained from SAC are superior for many instance groups

A Logical Approach to Efficient Max-SAT solving

Weighted Max-SAT is the optimization version of SAT and many important problems can be naturally encoded as such. Solving weighted Max-SAT is an important problem from both a theoretical and a practical point of view. In recent years, there has been considerable interest in finding efficient solving techniques. Most of this work focus on the computation of good quality lower bounds to be used within a branch and bound DPLL-like algorithm. Most often, these lower bounds are described in a procedural way. Because of that, it is difficult to realize the {\em logic} that is behind. In this paper we introduce an original framework for Max-SAT that stresses the parallelism with classical SAT. Then, we extend the two basic SAT solving techniques: {\em search} and {\em inference}. We show that many algorithmic {\em tricks} used in state-of-the-art Max-SAT solvers are easily expressable in {\em logic} terms with our framework in a unified manner. Besides, we introduce an original search algorithm that performs a restricted amount of {\em weighted resolution} at each visited node. We empirically compare our algorithm with a variety of solving alternatives on several benchmarks. Our experiments, which constitute to the best of our knowledge the most comprehensive Max-sat evaluation ever reported, show that our algorithm is generally orders of magnitude faster than any competitor

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

<p>Abstract</p> <p>Background</p> <p>Radiation hybrid (RH) maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), haplotype map construction and refinement of candidate gene searches.</p> <p>Results</p> <p>A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement.</p> <p>Conclusion</p> <p>The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.</p

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

<p>Abstract</p> <p>Background</p> <p>Radiation hybrid (RH) maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), haplotype map construction and refinement of candidate gene searches.</p> <p>Results</p> <p>A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement.</p> <p>Conclusion</p> <p>The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.</p

An integer linear programming approach for genome scaffolding

This paper presents a simple and fast approach for genome scaffolding, combining constraint modeling and simple graph manipulation. We model the scaffolding problem as an optimization problem on a graph built from a paired-end reads alignment on contigs, then describe an heuristic to solve this problem with the iterative combination of local constraints solving and cycle breaking phases. We tested our approach on a benchmark of various genomes, and compared it with several usual scaffolders. The proposed method is quick, flexible, and provides results comparable to other scaffolders in terms of quality. In addition, contrarily to state of the art approaches that require dedicated servers, it can be run on a basic notebook computer even for large genomes

Cost Function Networks to Solve Large Computational Protein Design Problems

International audienc