Reliable ABC model choice via random forests

Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques. We propose a novel approach based on a machine learning tool named random forests to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with random forests and postponing the approximation of the posterior probability of the predicted MAP for a second stage also relying on random forests. Compared with earlier implementations of ABC model choice, the ABC random forest approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least fifty), and (iv) it includes an approximation of the posterior probability of the selected model. The call to random forests will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets. The proposed methodologies are implemented in the R package abcrf available on the CRAN.Comment: 39 pages, 15 figures, 6 table

A subspace fitting method based on finite elements for fast identification of damages in vibrating mechanical systems

International audienceIn this paper, a method based on subspace fitting is proposed for identification of faults in mechanical systems. The method uses the modal information from an observability matrix, provided by a stochastic subspace identification. It is used for updating a Finite Element Model through the Variable Projection algorithm. Experimental example aims to demonstrate the ability and the efficiency of the method for diagnosis of structural faults in a mechanical system

A Subspace Fitting Method based on Finite Elements for Identification and Localization of Damage in Mechanical Systems

International audienceIn this work, a subspace fitting method based on finite elements for identification of modal parameters of a mechanical system is proposed. The technique uses prior knowledge resulting from a coarse finite element model (FEM) of the structure. The proposed technique is applied to identify the parameters of several mechanical systems under deterministic and stochastic excitations. Numerical experiments highlight the relevance of the technique compared to the conventional identification techniques. Identification, localization and estimation of severity of damages are carried out

Development and assignment of bovine-specific PCR systems for the Texas nomenclature marker genes and isolation of homologous BAC probes

In 1996, Popescu et al. published the Texas standard nomenclature of the bovine karyotype in which 31 marker genes, already mapped in man, were chosen to permit unambiguous identification and numbering of each bovine chromosome. However, specific PCR systems were not available for each marker gene thus preventing the assignment of part of these markers by somatic cell hybrid analysis. In addition, some difficulties remained with the nomenclature of BTA25, BTA27 and BTA29. In this work, specific PCR systems were developed for each of the marker genes except VIL1 (see results), from either existing bovine or human sequences, and a bovine BAC library was screened to obtain the corresponding BAC clones. These PCR systems were used successfully to confirm the assignment of each marker gene (except for LDHA, see results) by analysis on the INRA hamster-bovine somatic cell hybrid panel. The difficulties observed for LDHA and VIL1 are probably due to the fact that these genes belong to large gene families and therefore suggest that they may not be the most appropriate markers for a standardisation effort. This panel of BACs is available to the scientific community and has served as a basis for the establishment of a revised standard nomenclature of bovine chromosomes

The scurs inheritance: new insights from the French Charolais breed

<p>Abstract</p> <p>Background</p> <p>Polled animals are valued in cattle industry because the absence of horns has a significant economic impact. However, some cattle are neither polled nor horned but have so-called scurs on their heads, which are corneous growths loosely attached to the skull. A better understanding of the genetic determinism of the scurs phenotype would help to fine map the polled locus. To date, only one study has attempted to map the <it>scurs </it>locus in cattle. Here, we have investigated the inheritance of the scurs phenotype in the French Charolais breed and examined whether the previously proposed localisation of the <it>scurs </it>locus on bovine chromosome 19 could be confirmed or not.</p> <p>Results</p> <p>Our results indicate that the inheritance pattern of the scurs phenotype in the French Charolais breed is autosomal recessive with complete penetrance in both sexes, which is different from what is reported for other breeds. The frequency of the <it>scurs </it>allele (<it>Sc</it>) reaches 69.9% in the French Charolais population. Eleven microsatellite markers on bovine chromosome 19 were genotyped in 267 offspring (33 half-sib and full-sib families). Both non-parametric and parametric linkage analyses suggest that in the French Charolais population the <it>scurs </it>locus may not map to the previously identified region. A new analysis of an Angus-Hereford and Hereford-Hereford pedigree published in 1978 enabled us to calculate the frequency of the <it>Sc </it>allele in the Hereford breed (89.4%) and to study the penetrance of this allele in males heterozygous for both <it>polled </it>and <it>scurs </it>loci (40%). This led us to revise the inheritance pattern of the scurs phenotype proposed for the Hereford breed and to suggest that allele <it>Sc </it>is not fully but partially dominant in double heterozygous males while it is always recessive in females. Crossbreeding involving the Charolais breed and other breeds gave results similar to those reported in the Hereford breed.</p> <p>Conclusion</p> <p>Our results suggest the existence of unknown genetics factors modifying the expression of the <it>scurs </it>locus in double heterozygous Hereford and Angus males. The specific inheritance pattern of the <it>scurs </it>locus in the French Charolais breed represents an opportunity to map this gene and to identify the molecular mechanisms regulating the growth of horns in cattle.</p

State Space Estimation Method for Robot Identification

In this paper, we study the identification of robot dynamic models. The usual technique, based on the Least-Squares method, is carefully detailed. A new procedure based on Kalman filtering and fixed interval smoothing is developed. This new technique is compared to usual one with simulated and experimental data. The obtained results show that the proposed technique is a credible alternative, especially if the system bandwidth is unknown

Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

BACKGROUND: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. METHODOLOGY/PRINCIPAL FINDINGS: This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. CONCLUSIONS/SIGNIFICANCE: Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations--the African taurine, the European taurine and zebus--may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence

Caractérisation physico-chimique et comportement hydromécanique d'une argile échangée avec l'ammonium dans le contexte des sites de stockage

International audienceEn 2007, près de 38 millions de tonnes de déchets d'origine ménagère ont été collectés par les collectivités en France (ADEME, 2009). Malgré l'essor constant du recyclage et du compostage, 31% de ces déchets municipaux traités ont été envoyé dans des installations de stockage des déchets non dangereux (ISDND) cette même année. A l'échelle européenne, ce pourcentage augmente considérablement. Dans ces sites de stockage, la percolation de l'eau à travers les déchets produit une grande quantité de lixiviats chargés en polluants de diverses natures. L'étanchéité en fond de site est notamment assurée par une couche argileuse (barrière passive). Son rôle est notamment de limiter la pollution des sols et des nappes phréatiques. Les argiles utilisées en fond de site de stockage sont principalement des smectites qui possèdent une forte capacité de rétention. Dans les analyses de lixiviats, de nombreux auteurs ont mis en évidence une très grande quantité d'ammonium susceptible de s'échanger avec le sodium ou le calcium initialement présent la barrière argileuse. Si ces dernières ont largement été décrites dans la littérature, les argiles ammoniées sont beaucoup moins connues. Le travail présenté ici s'est donc intéressé à la caractérisation complète d'une argile totalement échangée avec des cations ammonium. L'objectif de ce travail est de mieux comprendre et appréhender le comportement d'une argile ammoniée dans le contexte de la mise en décharge des déchets. En raison du poids des déchets, la barrière d'argile en fond de site subit des pressions élevées. Le deuxième objectif est de comprendre les phénomènes microscopiques et macroscopiques liées au comportement hydromécanique des matériaux argileux. Des cellules oedométriques équipées d'un système d'injection sous pression contrôlée ont été utilisés. Des différences significatives sur les capacités d'hydratation de l'argile ammoniée et sur la perméabilité de cette dernière ont été mises en évidence au cours de ce travail. L'ensemble des résultats présentés souligne l'importance du suivi des sites de stockage sur le long terme, notamment pour prévenir des pollutions des nappes phréatiques