Haiku - a Scala combinator toolkit for semi-automated composition of metaheuristics

There is an emerging trend towards the automated design of metaheuristics at the software component level. In principle, metaheuristics have a relatively clean decomposition, where well-known frameworks such as ILS and EA are parametrised by variant components for acceptance, perturbation etc. Automated generation of these frameworks is not so simple in practice, since the coupling between components may be implementation specific. Compositionality is the ability to freely express a space of designs ‘bottom up’ in terms of elementary components: previous work in this area has used combinators, a modular and functional approach to componentisation arising from foundational Computer Science. In this article, we describeHaiku, a combinator tool-kit written in the Scala language, which builds upon previous work to further automate the process by automatically composing the external dependencies of components. We provide examples of use and give a case study in which a programatically-generated heuristic is applied to the Travelling Salesman Problem within an Evolutionary Strategies framework

Pathway-Based Analysis of a Melanoma Genome-Wide Association Study: Analysis of Genes Related to Tumour-Immunosuppression

Systemic immunosuppression is a risk factor for melanoma, and sunburn-induced immunosuppression is thought to be causal. Genes in immunosuppression pathways are therefore candidate melanoma-susceptibility genes. If variants within these genes individually have a small effect on disease risk, the association may be undetected in genome-wide association (GWA) studies due to low power to reach a high significance level. Pathway-based approaches have been suggested as a method of incorporating a priori knowledge into the analysis of GWA studies. In this study, the association of 1113 single nucleotide polymorphisms (SNPs) in 43 genes (39 genomic regions) related to immunosuppression have been analysed using a gene-set approach in 1539 melanoma cases and 3917 controls from the GenoMEL consortium GWA study. The association between melanoma susceptibility and the whole set of tumour-immunosuppression genes, and also predefined functional subgroups of genes, was considered. The analysis was based on a measure formed by summing the evidence from the most significant SNP in each gene, and significance was evaluated empirically by case-control label permutation. An association was found between melanoma and the complete set of genes (pemp = 0.002), as well as the subgroups related to the generation of tolerogenic dendritic cells (pemp = 0.006) and secretion of suppressive factors (pemp = 0.0004), thus providing preliminary evidence of involvement of tumour-immunosuppression gene polymorphisms in melanoma susceptibility. The analysis was repeated on a second phase of the GenoMEL study, which showed no evidence of an association. As one of the first attempts to replicate a pathway-level association, our results suggest that low power and heterogeneity may present challenges

Integrating Benders decomposition within Constraint Programming

Benders decomposition [1] is a solving strategy based on the separation of the variables of the problem. It is often introduced as a basis for models and techniques using the complementary strengths of constraint programming and optimization techniques. Hybridization schemes have appeared recently and provide

Rapid diagnosis of scabies by manual confocal reflectance microscopy

7sinonenonePerrot, JL; Cinotti, E; Labeille, B; Trau, C; Rabérin, H; Flori, P; Cambazard, FPerrot, Jl; Cinotti, Elisa; Labeille, B; Trau, C; Rabérin, H; Flori, P; Cambazard, F

Synthesizing Cyber-Physical Architectural Models with Real-Time Constraints

Abstract. We present techniques that enable designers to algorithmi-cally synthesize cyber-physical architectural models with real-time con-straints. We do this by providing a meta-architectural specification lan-guage that allows designers to specify what properties their architectural models should have, not how to achieve them. This provides designers with a qualitatively new level of abstraction that enables the exploration of design spaces at the earliest stages of design, when doing so provides the most benefit. Our key technical contribution is the development of an Integer linear programming Modulo Theories (IMT) solver along with a scheduling theory solver. Our solver was used to automatically synthe-size cyber-physical architectural models with hard real-time constraints from a large-scale industrial design.