A statistical approach for array CGH data analysis

BACKGROUND: Microarray-CGH experiments are used to detect and map chromosomal imbalances, by hybridizing targets of genomic DNA from a test and a reference sample to sequences immobilized on a slide. These probes are genomic DNA sequences (BACs) that are mapped on the genome. The signal has a spatial coherence that can be handled by specific statistical tools. Segmentation methods seem to be a natural framework for this purpose. A CGH profile can be viewed as a succession of segments that represent homogeneous regions in the genome whose BACs share the same relative copy number on average. We model a CGH profile by a random Gaussian process whose distribution parameters are affected by abrupt changes at unknown coordinates. Two major problems arise : to determine which parameters are affected by the abrupt changes (the mean and the variance, or the mean only), and the selection of the number of segments in the profile. RESULTS: We demonstrate that existing methods for estimating the number of segments are not well adapted in the case of array CGH data, and we propose an adaptive criterion that detects previously mapped chromosomal aberrations. The performances of this method are discussed based on simulations and publicly available data sets. Then we discuss the choice of modeling for array CGH data and show that the model with a homogeneous variance is adapted to this context. CONCLUSIONS: Array CGH data analysis is an emerging field that needs appropriate statistical tools. Process segmentation and model selection provide a theoretical framework that allows precise biological interpretations. Adaptive methods for model selection give promising results concerning the estimation of the number of altered regions on the genome

La première analyse de discours sur l'Algérie : la thèse de Denise Maldidier (1969)

Denise Maldidier a soutenu sa thèse, intitulée Analyse linguistique du vocabulaire politique de la guerre d'Algérie d'après six quotidiens parisiens, en 1969 . Il était extrêmement hardi de sa part de s'emparer d'un tel sujet pour une thèse de doctorat : nous étions encore très près des événements et les avions vécus directement ou indirectement en tant qu'intellectuels, citoyens et militants. C'est sur la nouveauté épistémologique de ce travail que nous voudrions mettre l'accent. Le travail pionnier de Denise Maldidier a beaucoup aidé à formuler l'objet de l'analyse du discours, en particulier pour les historiens. Les auteurs des textes que les historiens, politologues, sociologues étudient savent ce qu'ils disent quand ils écrivent et trouvent les mots dans leur langue pour le dire en fonction de la conjoncture et du rapport des forces. Mais quelles sont les procédures langagières qu'ils engagent ? Comment les mots, les propositions dans lesquelles ils se meuvent opèrent-ils ? Quelles sont les reformulations auxquelles ils ont recours et qui deviennent des enjeux polémiques et politiques ? Les travaux ultérieurs de Denise Maldidier montre qu'elle n'a janais cessé de faire bouger, ce qu'ouvrait la thèse évoquée, alors inscrite en sociolinguistique, et combien nous avons encore à gagner en nous référant à ses analyses

Floating constraints in lexical choice

Lexical choice is a computationally complex task, requiring a generation system to consider a potentially large number of mappings between concepts and words. Constraints that aid in determining which word is best come from a wide variety of sources, including syntax, semantics, pragmatics, the lexicon, and the underlying domain. Furthermore, in some situations, different constraints come into play early on, while in others, they apply much later. This makes it difficult to determine a systematic ordering in which to apply constraints. In this paper, we present a general approach to lexical choice that can handle multiple, interacting constraints. We focus on the problem of floating constraints, semantic or pragmatic constraints that float, appearing at a variety of different syntactic ranks, often merged with other semantic constraints. This means that multiple content units can be realized by a single surface element, and conversely, that a single content unit can be realized by a variety of surface elements. Our approach uses the Functional Unification Formalism (FUF) to represent a generation lexicon, allowing for declarative and compositional representation of individual constraints

Accuracy of Variational Estimates for Random Graph Mixture Models

International audienceL'analyse des réseaux exerce depuis quelques années un attrait croissant. Les données qui sont sous la forme de mesures de relations entre items sont de plus en plus disponibles, et abandonnent la structure usuelle d'un jeu de données de type individus-variables pour une structure de type individus-individus. Ces données "relationnelles" sont très souvent présentées sous la forme d'un graphe, même si cette représentation a ses limites, notamment quand le nombre d'individus dépasse la centaine. La représentation graphique des données des réseaux est alors attractive, mais nécessite un modèle synthétique. Le modèle de graphe le plus ancien et le plus utilisé est le modèle de Erdös-Rényi, dont les propriétés moyennes ou asymptotiques sont connues. L'écriture littérale de la vraisemblance de ce modèle est très simple, mais son temps de calcul croit de façon exponentielle avec le nombre d'individu. Une utilisation des algorithmes d'estimation usuels comme E-M n'est pas envisageable. Une approche variationnelle a été utilisée comme alternative pour implémenter un algorithme d'estimation des paramètres du modèle, et cela pour des réseaux de très grande taille (Daudin & al 2008). Les propriétés statistiques des estimateurs produits par cette approche sont cependant mal connues. L'objectif est de mener une étude sur la qualité de ces estimateurs et d'en prouver la convergence

Towards a Generic Trace for Rule Based Constraint Reasoning

CHR is a very versatile programming language that allows programmers to declaratively specify constraint solvers. An important part of the development of such solvers is in their testing and debugging phases. Current CHR implementations support those phases by offering tracing facilities with limited information. In this report, we propose a new trace for CHR which contains enough information to analyze any aspects of \CHRv\ execution at some useful abstract level, common to several implementations. %a large family of rule based solvers. This approach is based on the idea of generic trace. Such a trace is formally defined as an extension of the $\omega_r^\lor$ semantics of CHR. We show that it can be derived form the SWI Prolog CHR trace

Classification and estimation in the Stochastic Blockmodel based on the empirical degrees

International audienceThe Stochastic Blockmodel [16] is a mixture model for heterogeneous network data. Unlike the usual statistical framework, new nodes give additional information about the previous ones in this model. Thereby the distribution of the degrees concentrates in points conditionally on the node class. We show under a mild assumption that classification, estimation and model selection can actually be achieved with no more than the empirical degree data. We provide an algorithm able to process very large networks and consistent estimators based on it. In particular, we prove a bound of the probability of misclassification of at least one node, including when the number of classes grows

The reaction centre of the photounit of Rhodospirillum rubrum is anchored to the light-harvesting complex with four-fold rotational disorder

The minimal photounit of the photosynthetic membranes of the purple non-sulphur bacterium Rhodospirillum rubrum, comprising the reaction centre and the light-harvesting complex has been purified and crystallised in two dimensions in the presence of added phospholipids, and subsequently visualised by electron microscopy after negatively-staining. The position of the reaction centres within the light-harvesting ring has been determined at low resolution by the application of a new analysis for rotationally disordered identical units (here the reaction centres) within a two-dimensional crystalline lattice comprised of perfectly aligned unit cells (here the light-harvesting complexes). The reaction centre was found to preferentially occupy one of four orientations within the light-harvesting complex. The light-harvesting complex appears to be distorted to C4 symmetry, thus assuming a squarish shape when visualised by negative staining. A tentative structural model of the reaction centre-light-harvesting complex photounit which fits the experimental data is propose

Lexical Choice in Natural Language Generation

In this paper we survey the issue of lexical choice in natural language generation. We first define lexical choice as the choice of open-class lexical items (whether phrasal patterns or individual words) appropriate to express the content units of the utterance being generated in a given situation of enunciation. We then distinguish between five major classes of constraints on lexical choice: grammatical, inter-lexical, encyclopedic, interpersonal and discursive. For each class we review how they have been represented and used in existing generators. We conclude by pointing out the common limitations of these generators with respect to lexical choice as well as some directions for future research in the field