Analyse de données avec R - Complémentarité des méthodes d'analyse factorielle et de classification

International audienceL'objectif de cet exposé est de présenter les fonctionnalités disponibles sur R en analyse de données. R est un langage gratuit en pleine expansion et de plus en plus utilisé tant par le monde de l'entreprise, de l'enseignement et de la recherche. La spécificité de l'analyse des données à la française est présente dans ce logiciel grâce à plusieurs bibliothèques de fonctions. Dans une première partie de l'exposé, on montrera comment mettre en oeuvre, sous R, des méthodes d'analyses factorielles classiques (ACP, AFC ou ACM) et plus avancées (Analyse factorielle Multiple ou AFM Hiérarchique) à partir du package FactoMineR. Dans une seconde partie, on se focalisera sur la complémentarité des méthodes d'analyses factorielles et de classification pour visualiser des données. On s'appuiera sur plusieurs exemples et on mettra l'accent sur l'intérêt d'un tel outil dans le cadre de l'enseignement : gratuité et facilité de téléchargement du logiciel pour les étudiants en stage, mais également facilité d'accès du logiciel par des menus interactifs et performance du logiciel pour des méthodes évoluées

Apport de l'ACP probabiliste pour la gestion des données manquantes en ACP

International audienceDans cette présentation, nous nous intéressons à la gestion des données manquantes en Analyse en Composantes Principales (ACP). Une solution classique pour réaliser une ACP sur données incomplètes consiste à chercher les axes et les composantes qui minimisent l'erreur de reconstitution sur les données présentes. Pour ce faire, différents algorithmes ont été proposés dans la littérature dont une approche par moindres carrés alternés pondérés et une approche par ACP itérative. Cette dernière consiste en une imputation itérative des données au cours du processus d'estimation et s'apparente à un algorithme EM d'un modèle particulier. Nous détaillons dans un premier temps ces deux algorithmes et donnons leurs propriétés. Nous évoquons ensuite les difficultés rencontrées par ces algorithmes pour nous focaliser sur le problème de surajustement. Puis nous montrons comment la formulation probabiliste de l'ACP (Bishop et Tipping, 1997) offre un terme de régularisation adapté pour pallier au surajustement. Enfin, les performances de ces algorithmes sont évaluées à partir de simulations et d'exemples réels

Radiative effects in the scalar sector of vector leptoquark models

Gauge models with massive vector leptoquarks at the TeV scale provide a successful framework for addressing the B-physics anomalies. Among them, the 4321 model has been considered as the low-energy limit of some complete theories of flavor. In this work, we study the renormalization group evolution of this model, laying particular emphasis on the scalar sector. We find that, despite the asymptotic freedom of the gauge couplings, Landau poles can arise at relatively low scales due to the fast running of quartic couplings. Moreover, we discuss the possibility of radiative electroweak symmetry breaking and characterize the fine-tuning associated with the hierarchy between the electroweak scale and the additional TeV-scale scalars. Finally, the idea of scalar fields unification is explored, motivated by ultraviolet embeddings of the 4321 model

Flavor Non-universal Pati-Salam Unification and Neutrino Masses

We analyze the neutrino mass spectrum and discuss the extra-dimensional interpretation of a three-site Pati-Salam model which i) unifies all families of quark and leptons, ii) provides a natural description of the Standard Model Yukawa couplings, iii) could account for the recent $B$-physics anomalies. The key feature of the model is a breaking of the Pati-Salam and electroweak gauge symmetries localized on opposite sites, communicated to the other sites in an attenuated manner via nearest-neighbor interactions. We show that in this context gauge-singlet fermions localized on each site, receiving hierarchical Majorana masses, can allow the implementation of an inverse seesaw mechanism leading to light anarchic neutrino masses consistent with data. The continuum limit of this three-site setup has a natural interpretation in terms of a warped extra dimension with three defects, where the required exponential hierarchies can be achieved from $\mathcal{O}(1)$ differences in the bulk field masses.Comment: 14 pages, 2 figure

A Proof of Concept for Matchete: An Automated Tool for Matching Effective Theories

Studying the impact of new-physics models on low-energy observables necessitates matching to effective field theories at the relevant mass thresholds. We introduce the first public version of Matchete, a computer tool for matching weakly-coupled models at one-loop order. It uses functional methods to directly compute all matching contributions in a manifestly gauge-covariant manner, while simplification methods eliminate redundant operators from the output. We sketch the workings of the program and provide examples of how to match simple Standard Model extensions. The package, documentation, and example notebooks are publicly available at https://gitlab.com/matchete/matchete.Comment: 27 pages, 2 figures, The code and example notebooks are publicly available at https://gitlab.com/matchete/matchet

Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin [preprint]

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus Associated Domains (NADs) and Lamina Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, due to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery and with the nuclear lamina, and generally display characteristics of constitutive heterochromatin, including late DNA replication, enrichment of H3K9me3 and little gene expression. In contrast, Type II NADs associate with nucleoli but do not overlap with LADs. Type II NADs tend to replicate earlier, display greater gene expression, and are more often enriched in H3K27me3 than Type I NADs. The nucleolar associations of both classes of NADs were confirmed via DNA-FISH, which also detected Type I but not Type II probes enriched at the nuclear lamina. Interestingly, Type II NADs are enriched in distinct gene classes, notably factors important for differentiation and development. In keeping with this, we observed that a Type II NAD is developmentally regulated, present in MEFs but not in undifferentiated embryonic stem (ES) cells

Li/Mg systematics in scleractinian corals: Calibration of the thermometer

We show that the Li/Mg systematics of a large suite of aragonitic coral skeletons, representing a wide range of species inhabiting disparate environments, provides a robust proxy for ambient seawater temperature. The corals encompass both zooxanthellate and azooxanthellate species (Acropora sp., Porites sp., Cladocora caespitosa, Lophelia pertusa, Madrepora oculata and Flabellum impensum) collected from shallow, intermediate, and deep-water habitats, as well as specimens cultured in tanks under temperature-controlled conditions. The Li/Mg ratios observed in corals from these diverse tropical, temperate, and deep-water environments are shown to be highly correlated with temperature, giving an exponential temperature relationship of: Li/Mg (mmol/mol) = 5.41 exp (−0.049 * T) (r² = 0.975, n = 49). Based on the standard error of the Li/Mg versus temperature correlation, we obtain a typical precision of ±0.9 °C for the wide range of species analysed, similar or better than that of other less robust coral temperature proxies such as Sr/Ca ratios.The robustness and species independent character of the Li/Mg temperature proxy is shown to be the result of the normalization of Li to Mg, effectively eliminating the precipitation efficiency component such that temperature remains as the main controller of coral Li/Mg compositions. This is inferred from analysis of corresponding Li/Ca and Mg/Ca ratios with both ratios showing strong microstructure-related co-variations between the fibrous aragonite and centres of calcification, a characteristic that we attribute to varying physiological controls on growth rate. Furthermore, Li/Ca ratios show an offset between more rapidly growing zooxanthellate and azooxanthellate corals, and hence only an approximately inverse relationship to seawater temperature. Mg/Ca ratios show very strong physiological controls on growth rate but no significant dependence with temperature, except possibly for Acropora sp. and Porites sp. A strong positive correlation is nevertheless found between Li/Ca and Mg/Ca ratios at similar temperatures, indicating that both Li and Mg are subject to control by similar growth mechanisms, specifically the mass fraction of aragonite precipitated during calcification, which is shown to be consistent with a Rayleigh-based elemental fractionation model.The highly coherent array defined by Li/Mg versus temperature is thus largely independent of coral calcification mechanisms, with the strong temperature dependence reflecting the greater sensitivity of the KdLi/Ca partition coefficient relative to KdMg/Ca. Accordingly, Li/Mg ratios exhibit a highly coherent exponential correlation with temperature, thereby providing a more robust tool for reconstructing paleo-seawater temperatures

Mapping of Schistosomiasis and Soil-Transmitted Helminthiasis in the Regions of Centre, East and West Cameroon

Schistosomiasis and soil-transmitted helminthiasis (STH) are a major public health problem in Cameroon. The national control strategy of these diseases was based on historical data collected 25 years ago, which might be outdated in some situations due to several factors including control activities, improved or degraded sanitation and hygiene, socio-economic improvement and disease transmission dynamics. To help planning, improving control strategies and evaluation of control activities, there was a need to update the distribution of schistosomiasis and STH. We conducted parasitological surveys in three regions of Cameroon, i.e. Centre, East and West. Our results showed a significant decrease of STH infection prevalence and intensities in all these three regions, in comparison to previous mapping data, with an overall decline of prevalence from 81.1–93% to 10.5–46.6%. These results show the positive impact of annual deworming campaigns, and illustrate the progressive success of the national programme for the control of schistosomiasis and STH in Cameroon. Furthermore, our results showed an increase of the number of high transmission foci of schistosomiasis, and allowed identifying new health districts requiring mass treatment with praziquantel, and those where deworming should be reinforced