Institut de recherche mathématique de Rennes

In this article, we present FactoMineR an R package dedicated to multivariate data analysis. The main features of this package is the possibility to take into account different types of variables (quantitative or categorical), different types of structure on the data (a partition on the variables, a hierarchy on the variables, a partition on the individuals) and finally supplementary information (supplementary individuals and variables). Moreover, the dimensions issued from the different exploratory data analyses can be automatically described by quantitative and/or categorical variables. Numerous graphics are also available with various options. Finally, a graphical user interface is implemented within the Rcmdr environment in order to propose an user friendly package.

We present the R package missMDA which performs principal component methods on incomplete data sets, aiming to obtain scores, loadings and graphical representations despite missing values. Package methods include principal component analysis for continuous variables, multiple correspondence analysis for categorical variables, factorial analysis on mixed data for both continuous and categorical variables, and multiple factor analysis for multi-table data. Furthermore, missMDA can be used to perform single imputation to complete data involving continuous, categorical and mixed variables. A multiple imputation method is also available. In the principal component analysis framework, variability across different imputations is represented by confidence areas around the row and column positions on the graphical outputs. This allows assessment of the credibility of results obtained from incomplete data sets.

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This paper presents several results concerning the vector potential which can be associated with a divergence-free function in a bounded three-dimensional domain. Different types of boundary conditions are given, for which the existence, uniqueness and regularity of the potential are studied. This is applied firstly to the finite element discretization of these potentials and secondly to a new formulation of incompressible viscous flow problems. On présente dans cet article un certain nombre de résultats concernant le potentiel vecteur associé à une fonction à divergence nulle dans un ouvert borné de dimension trois. En particulier, plusieurs types de conditions aux limites sont proposés, pour lesquels on discute l'existence, l'unicité et la régularité du potentiel vecteur. On analyse la convergence d'une discrétisation par éléments finis de ces potentiels et on indique une application concernant l'approximation de fluides visqueux incompressibles. © 1998 B. G. Teubner Stuttgart—John Wiley & Sons, Ltd.

An introduction to exploratory techniques for multivariate data analysis, this book covers the key methodology, including principal components analysis, correspondence analysis, mixed models and multiple factor analysis. The authors take a practical approach, with examples leading the discussion of the methods and lots of graphics to emphasize visualization. They present the concepts in the most intuitive way possible, keeping mathematical content to a minimum or relegating it to the appendices. The book includes examples that use real data from a range of scientific disciplines and implemented using an R package developed by the authors--Provided by publisher.

Property (T) is a rigidity property for topological groups, first formulated by D. Kazhdan in the mid 1960's with the aim of demonstrating that a large class of lattices are finitely generated. Later developments have shown that Property (T) plays an important role in an amazingly large variety of subjects, including discrete subgroups of Lie groups, ergodic theory, random walks, operator algebras, combinatorics, and theoretical computer science. This monograph offers a comprehensive introduction to the theory. It describes the two most important points of view on Property (T): the first uses a unitary group representation approach, and the second a fixed point property for affine isometric actions. Via these the authors discuss a range of important examples and applications to several domains of mathematics. A detailed appendix provides a systematic exposition of parts of the theory of group representations that are used to formulate and develop Property (T).

Abstract This book is a general introduction to the theory of schemes, followed by applications to arithmetic surfaces and to the theory of reduction of algebraic curves. The first part introduces basic objects such as schemes, morphisms, base change, local properties (normality, regularity, Zariski's Main Theorem). This is followed by the more global aspect: coherent sheaves and a finiteness theorem for their cohomology groups. Then follows a chapter on sheaves of differentials, dualizing sheaves, and Grothendieck's duality theory. The first part ends with the theorem of Riemann-Roch and its application to the study of smooth projective curves over a field. Singular curves are treated through a detailed study of the Picard group. The second part starts with blowing-ups and desingularisation (embedded or not) of fibered surfaces over a Dedekind ring that leads on to intersection theory on arithmetic surfaces. Castelnuovo's criterion is proved and also the existence of the minimal regular model. This leads to the study of reduction of algebraic curves. The case of elliptic curves is studied in detail. The book concludes with the funadmental theorem of stable reduction of Deligne-Mumford. The book is essentially self-contained, including the necessary material on commutative algebra. The prerequisites are therefore few, and the book should suit a graduate student. It contains many examples and nearly 600 exercises.

Developing embryos exhibit a robust capability to reduce phenotypic variations that occur naturally or as a result of experimental manipulation. This reduction in variation occurs by an epigenetic mechanism called canalization, a phenomenon which has resisted understanding because of a lack of necessary molecular data and of appropriate gene regulation models. In recent years, quantitative gene expression data have become available for the segment determination process in the Drosophila blastoderm, revealing a specific instance of canalization. These data show that the variation of the zygotic segmentation gene expression patterns is markedly reduced compared to earlier levels by the time gastrulation begins, and this variation is significantly lower than the variation of the maternal protein gradient Bicoid. We used a predictive dynamical model of gene regulation to study the effect of Bicoid variation on the downstream gap genes. The model correctly predicts the reduced variation of the gap gene expression patterns and allows the characterization of the canalizing mechanism. We show that the canalization is the result of specific regulatory interactions among the zygotic gap genes. We demonstrate the validity of this explanation by showing that variation is increased in embryos mutant for two gap genes, Krüppel and knirps, disproving competing proposals that canalization is due to an undiscovered morphogen, or that it does not take place at all. In an accompanying article in PLoS Computational Biology (doi:10.1371/journal.pcbi.1000303), we show that cross regulation between the gap genes causes their expression to approach dynamical attractors, reducing initial variation and providing a robust output. These results demonstrate that the Bicoid gradient is not sufficient to produce gap gene borders having the low variance observed, and instead this low variance is generated by gap gene cross regulation. More generally, we show that the complex multigenic phenomenon of canalization can be understood at a quantitative and predictive level by the application of a precise dynamical model.

The classical Łojasiewicz inequality and its extensions for partial differential equation problems (Simon) and to o-minimal structures (Kurdyka) have a considerable impact on the analysis of gradient-like methods and related problems: minimization methods, complexity theory, asymptotic analysis of dissipative partial differential equations, and tame geometry. This paper provides alternative characterizations of this type of inequality for nonsmooth lower semicontinuous functions defined on a metric or a real Hilbert space. In the framework of metric spaces, we show that a generalized form of the Łojasiewicz inequality (hereby called the Kurdyka-Łojasiewicz inequality) is related to metric regularity and to the Lipschitz continuity of the sublevel mapping, yielding applications to discrete methods (strong convergence of the proximal algorithm). In a Hilbert setting we further establish that asymptotic properties of the semiflow generated by <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="minus partial-differential f"> <mml:semantics> <mml:mrow> <mml:mo> − </mml:mo> <mml:mi mathvariant="normal"> ∂ </mml:mi> <mml:mi>f</mml:mi> </mml:mrow> <mml:annotation encoding="application/x-tex">-\partial f</mml:annotation> </mml:semantics> </mml:math> </inline-formula> are strongly linked to this inequality. This is done by introducing the notion of a piecewise subgradient curve: such curves have uniformly bounded lengths if and only if the Kurdyka-Łojasiewicz inequality is satisfied. Further characterizations in terms of <italic>talweg</italic> lines —a concept linked to the location of the less steepest points at the level sets of <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="f"> <mml:semantics> <mml:mi>f</mml:mi> <mml:annotation encoding="application/x-tex">f</mml:annotation> </mml:semantics> </mml:math> </inline-formula> — and integrability conditions are given. In the convex case these results are significantly reinforced, allowing us in particular to establish a kind of asymptotic equivalence for discrete gradient methods and continuous gradient curves. On the other hand, a counterexample of a convex <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper C squared"> <mml:semantics> <mml:msup> <mml:mi>C</mml:mi> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>2</mml:mn> </mml:mrow> </mml:msup> <mml:annotation encoding="application/x-tex">C^{2}</mml:annotation> </mml:semantics> </mml:math> </inline-formula> function in <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="double-struck upper R squared"> <mml:semantics> <mml:msup> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="double-struck">R</mml:mi> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>2</mml:mn> </mml:mrow> </mml:msup> <mml:annotation encoding="application/x-tex">\mathbb {R}^{2}</mml:annotation> </mml:semantics> </mml:math> </inline-formula> is constructed to illustrate the fact that, contrary to our intuition, and unless a specific growth condition is satisfied, convex functions may fail to fulfill the Kurdyka-Łojasiewicz inequality.

We study the spectral properties of the Ruelle–Perron–Frobenius operator associated to an Anosov map on classes of functions with high smoothness. To this end we construct anisotropic Banach spaces of distributions on which the transfer operator has a small essential spectrum. In the case, the essential spectral radius is arbitrarily small, which yields a description of the correlations with arbitrary precision. Moreover, we obtain sharp spectral stability results for deterministic and random perturbations. In particular, we obtain differentiability results for spectral data (which imply differentiability of the Sinai–Ruelle–Bowen measure, the variance for the central limit theorem, the rates of decay for smooth observable, etc.).

International audience

Cette quatrième édition, entièrement revue et augmentée, a été enrichie de thèmes nouveaux : une présentation de l'analyse factorielle sur données mixtes; la prise en compte d'une structure hiérarchique sur les variables dans un tableau (individus x variables) ; une présentation de l'analyse factorielle multiple hiérarchique, prolongement naturel de l'analyse factorielle multiple.

We consider the wave equation damped with a boundary nonlinear velocity feedback p(u'). Under some geometrical conditions, we prove that the energy of the system decays to zero with an explicit decay rate estimate even if the function ρ has not a polynomial behavior in zero. This work extends some results of Nakao, Haraux, Zuazua and Komornik, who studied the case where the feedback has a polynomial behavior in zero and completes a result of Lasiecka and Tataru. The proof is based on the construction of a special weight function (that depends on the behavior of the function ρ in zero), and on a new nonlinear integral inequality.

The variation in the expression patterns of the gap genes in the blastoderm of the fruit fly Drosophila melanogaster reduces over time as a result of cross regulation between these genes, a fact that we have demonstrated in an accompanying article in PLoS Biology (see Manu et al., doi:10.1371/journal.pbio.1000049). This biologically essential process is an example of the phenomenon known as canalization. It has been suggested that the developmental trajectory of a wild-type organism is inherently stable, and that canalization is a manifestation of this property. Although the role of gap genes in the canalization process was established by correctly predicting the response of the system to particular perturbations, the stability of the developmental trajectory remains to be investigated. For many years, it has been speculated that stability against perturbations during development can be described by dynamical systems having attracting sets that drive reductions of volume in phase space. In this paper, we show that both the reduction in variability of gap gene expression as well as shifts in the position of posterior gap gene domains are the result of the actions of attractors in the gap gene dynamical system. Two biologically distinct dynamical regions exist in the early embryo, separated by a bifurcation at 53% egg length. In the anterior region, reduction in variation occurs because of stability induced by point attractors, while in the posterior, the stability of the developmental trajectory arises from a one-dimensional attracting manifold. This manifold also controls a previously characterized anterior shift of posterior region gap domains. Our analysis shows that the complex phenomena of canalization and pattern formation in the Drosophila blastoderm can be understood in terms of the qualitative features of the dynamical system. The result confirms the idea that attractors are important for developmental stability and shows a richer variety of dynamical attractors in developmental systems than has been previously recognized.

The Poisson boundary of a group G with a probability measure µ is the space of ergodic components of the time shift in the path space of the associated random walk. Via a generalization of the classical Poisson formula it gives an integral representation of bounded µ-harmonic functions on G. In this paper we develop a new method of identifying the Poisson boundary based on entropy estimates for conditional random walks. It leads to simple purely geometric criteria of boundary maximality which bear hyperbolic nature and allow us to identify the Poisson boundary with natural topological boundaries for several classes of groups: word hyperbolic groups and discontinuous groups of isometries of Gromov hyperbolic spaces, groups with infinitely many ends, cocompact lattices in Cartan-Hadamard manifolds, discrete subgroups of semisimple Lie groups. The classical Poisson integral representation formula for the harmonic

The Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission will carry into space the Ocean Color Instrument (OCI), a spectrometer measuring at 5nm spectral resolution in the ultraviolet (UV) to near infrared (NIR) with additional spectral bands in the shortwave infrared (SWIR), and two multi-angle polarimeters that will overlap the OCI spectral range and spatial coverage, i. e., the Spectrometer for Planetary Exploration (SPEXone) and the Hyper-Angular Rainbow Polarimeter (HARP2). These instruments, especially when used in synergy, have great potential for improving estimates of water reflectance in the post Earth Observing System (EOS) era. Extending the top-of-atmosphere (TOA) observations to the UV, where aerosol absorption is effective, adding spectral bands in the SWIR, where even the most turbid waters are black and sensitivity to the aerosol coarse mode is higher than at shorter wavelengths, and measuring in the oxygen A-band to estimate aerosol altitude will enable greater accuracy in atmospheric correction for ocean color science. The multi-angular and polarized measurements, sensitive to aerosol properties (e.g., size distribution, index of refraction), can further help to identify or constrain the aerosol model, or to retrieve directly water reflectance. Algorithms that exploit the new capabilities are presented, and their ability to improve accuracy is discussed. They embrace a modern, adapted heritage two-step algorithm and alternative schemes (deterministic, statistical) that aim at inverting the TOA signal in a single step. These schemes, by the nature of their construction, their robustness, their generalization properties, and their ability to associate uncertainties, are expected to become the new standard in the future. A strategy for atmospheric correction is presented that ensures continuity and consistency with past and present ocean-color missions while enabling full exploitation of the new dimensions and possibilities. Despite the major improvements anticipated with the PACE instruments, gaps/issues remain to be filled/tackled. They include dealing properly with whitecaps, taking into account Earth-curvature effects, correcting for adjacency effects, accounting for the coupling between scattering and absorption, modeling accurately water reflectance, and acquiring a sufficiently representative dataset of water reflectance in the UV to SWIR. Dedicated efforts, experimental and theoretical, are in order to gather the necessary information and rectify inadequacies. Ideas and solutions are put forward to address the unresolved issues. Thanks to its design and characteristics, the PACE mission will mark the beginning of a new era of unprecedented accuracy in ocean-color radiometry from space.

Cells of Listeria monocytogenes or Salmonella enterica serovar Typhimurium taken from six characteristic stages of growth were subjected to an acidic stress (pH 3.3). As expected, the bacterial resistance increased from the end of the exponential phase to the late stationary phase. Moreover, the shapes of the survival curves gradually evolved as the physiological states of the cells changed. A new primary model, based on two mixed Weibull distributions of cell resistance, is proposed to describe the survival curves and the change in the pattern with the modifications of resistance of two assumed subpopulations. This model resulted from simplification of the first model proposed. These models were compared to the Whiting's model. The parameters of the proposed model were stable and showed consistent evolution according to the initial physiological state of the bacterial population. Compared to the Whiting's model, the proposed model allowed a better fit and more accurate estimation of the parameters. Finally, the parameters of the simplified model had biological significance, which facilitated their interpretation.

In this paper we study a fractional diffusion Boussinesq model which couples the incompressible Euler equation for the velocity and a transport equation with fractional diffusion for the temperature. We prove global well-posedness results.

We investigate the orderability properties of fundamental groups of 3-dimensional manifolds. Many 3-manifold groups support left-invariant orderings, including all compact <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mi>P</mml:mi> <mml:mn>2</mml:mn> </mml:msup> </mml:math> -irreducible manifolds with positive first Betti number. For seven of the eight geometries (excluding hyperbolic) we are able to characterize which manifolds’ groups support a left-invariant or bi-invariant ordering. We also show that manifolds modelled on these geometries have virtually bi-orderable groups. The question of virtual orderability of 3-manifold groups in general, and even hyperbolic manifolds, remains open, and is closely related to conjectures of Waldhausen and others.

The impact of dependence between individual test statistics is currently among the most discussed topics in the multiple testing of high-dimensional data literature, especially since Benjamini and Hochberg (1995) introduced the false discovery rate (FDR). Many papers have first focused on the impact of dependence on the control of the FDR. Some more recent works have investigated approaches that account for common information shared by all the variables to stabilize the distribution of the error rates. Similarly, we propose to model this sharing of information by a factor analysis structure for the conditional variance of the test statistics. It is shown that the variance of the number of false discoveries increases along with the fraction of common variance. Test statistics for general linear contrasts are deduced, taking advantage of the common factor structure to reduce the variance of the error rates. A conditional FDR estimate is proposed and the overall performance of multiple testing procedure is shown to be markedly improved, regarding the nondiscovery rate, with respect to classical procedures. The present methodology is also assessed by comparison with leading multiple testing methods.