Algorithms for Highly Symmetric Linear and Integer Programs

This paper deals with exploiting symmetry for solving linear and integer programming problems. Basic properties of linear representations of finite groups can be used to reduce symmetric linear programming to solving linear programs of lower dimension. Combining this approach with knowledge of the geometry of feasible integer solutions yields an algorithm for solving highly symmetric integer linear programs which only takes time which is linear in the number of constraints and quadratic in the dimension.Comment: 21 pages, 1 figure; some references and further comments added, title slightly change

Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree

Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of ‘hard selective sweeps’ vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

Branch-cut-and-propagate for the maximum k-colorable subgraph problem with symmetry

Given an undirected graph and a positive integer k, the maximum k-colorable subgraph problem consists of selecting a k-colorable induced subgraph of maximum cardinality. The natural integer programming formulation for this problem exhibits two kinds of symmetry: arbitrarily permuting the color classes and/or applying a nontrivial graph automorphism gives equivalent solutions. It is well known that such symmetries have negative effects on the performance of constraint/integer programming solvers. We investigate the integration of a branch-and-cut algorithm for solving the maximum k-colorable subgraph problem with constraint propagation techniques to handle the symmetry arising from the graph. The latter symmetry is handled by (non-linear) lexicographic ordering constraints and linearizations thereof. In experiments, we evaluate the influence of several components of our algorithm on the performance, including the different symmetry handling methods. We show that several components are crucial for an efficient algorithm; in particular, the handling of graph symmetries yields a significant performance speed-up

Villes et quartiers durables : la place des habitants

Cet ouvrage fait suite au colloque international clôturant le programme de recherche PAGODE « Participation, Animation et GOuvernance dans les Ecoquartiers » financé entre 2010 et 2014 par l'Agence Nationale de Recherche dans le cadre de l'appel à projets « Ville durable ». Si les démarches participatives sont désormais un levier incontournable pour chaque acteur engagé dans la gouvernance du projet urbain durable, les (re)mises en ordres ou en désordres qu'elles suscitent s'avèrent des processus centraux autant que complexes. Car une fois la participation posée en principe et en discours, reste le problème du passage de l'injonction de soutenabilité urbaine à la réalité d'une dynamique sociétale qui favoriserait la prise en charge collective, participative et pérenne du cadre de vie. C'est ce discours participatif, ses effets, les expérimentations et retours critiques qu'il suscite, que les 39 chercheurs et praticiens réunis dans cet ouvrage proposent de discuter. Dans une perspective pluridisciplinaire et à travers de nombreuses études de cas, les diverses contributions analysent de façon riche et souvent renouvelée les modalités d'une fabrique urbaine participative aux prises avec les injonctions du développement durable. Plusieurs thèmes sont ainsi mis en discussion, à l'instar des effets d'un gouvernement de la participation ou des éco-technologies, des opportunités d'appropriations et de « résistances » citoyennes, ou encore de la problématique des « communs »… Au final, dans un contexte de transition et de changement, l'adaptation participative de la ville ressort ici, entre contrôles et résistances, comme un produit transactionnel traduisant les constructions et les appropriations stratégiques d'un ordre négocié de la durabilité urbaine