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Similarity Search for Scientific Workflows
No full textInternational audienceWith the increasing popularity of scientific workflows, public repositories are gaining importance as a means to share, find, and reuse such workflows. As the sizes of these repositories grow, methods to compare the scientific workflows stored in them become a necessity, for instance, to allow duplicate detection or similarity search. Scientific workflows are complex objects, and their comparison entails a number of distinct steps from comparing atomic elements to comparison of the workflows as a whole. Various studies have implemented methods for scientific workflow comparison and came up with often contradicting conclusions upon which algorithms work best. Comparing these results is cumbersome, as the original studies mixed different approaches for different steps and used different evaluation data and metrics. We contribute to the field (i) by disecting each previous approach into an explicitly defined and comparable set of subtasks, (ii) by comparing in isolation different approaches taken at each step of scientific workflow comparison, reporting on an number of unexpected findings, (iii) by investigating how these can best be combined into aggregated measures, and (iv) by making available a gold standard of over 2000 similarity ratings contributed by 15 workflow experts on a corpus of almost 1500 workflows and re-implementations of all methods we evaluated
Probabilistic Atlas and Geometric Variability Estimation to Drive Tissue Segmentation
No full textInternational audienceComputerized anatomical atlases play an important role in medical image analysis. While an atlas usually refers to a standard or mean image also called template, that presumably represents well a given population, it is not enough to characterize the observed population in detail. A template image should be learned jointly with the geometric variability of the shapes represented in the observations. These two quantities will in the sequel form the atlas of the corresponding population. The geometric variability is modelled as deformations of the template image so that it fits the observations. In this paper, we provide a detailed analysis of a new generative statistical model based on dense deformable templates that represents several tissue types observed in medical images. Our atlas contains both an estimation of probability maps of each tissue (called class) and the deformation metric. We use a stochastic algorithm for the estimation of the probabilistic atlas given a dataset. This atlas is then used for atlas-based segmentation method to segment the new images. Experiments are shown on brain T1 MRI datasets
A new method for improving the prediction and the functional annotation of ortholog groups
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La méthode du simplexe tropical
No full textSee also arXiv: 1308.0454International audienceCet exposé présente un analogue de la méthode du simplexe pour laprogrammation linéaire tropicale, c'est à dire les problèmesd'optimisation décrits par des inégalités (max,+)-linéaires.Tropicalement, les opérations de pivotage et de calcul des coûts réduitssont purement combinatoires. Pivoter s'interprète comme une successionde graphes acycliques. Le calcul des coûts réduits s'effectue via unproblème couplage de poids maximum et un problème de plus court chemin.La séquence de bases obtenue par méthode du simplexe tropicalcorrespond exactement à la séquence de bases donnée par la méthode dusimplexe classique appliquée sur le corps des séries de Puiseux
Chirurgie du segment antérieur de l’œil assistée par laser à impulsions ultra-rapides : optimisation des paramètres laser par rapport à la transparence des tissus à viabilité cellulaire
No full textThe goal of this work was to study different microscopic and macroscopic effects that will ultimately help us to improve procedures in eye surgery assisted by ultrashort pulse lasers and most notably keratoplasty (corneal grafting), which requires laser systems which are operational in pathological and therefore strongly light scattering tissue. Previously, the Optique Photonique Santé (OPS) group at the Laboratoire d'Optique Appliquée (LOA) had identified 1650 nm as an optimum wavelength at which light scattering processes inside the pathological cornea are minimised. During the present thesis, three main tasks have been addressed.An ultrashort pulse laser system based on non-linear optical crystals has been developed, optimised with respect to the requirements of laser eye surgery, and fully char-acterised. The finished set-up is compact, robust, simple and potentially qualified for clinical use.In collaboration with a group at IESL-FORTH (Iraklion, Greece) and with the participation of a previous PhD student of the group we have studied the interaction of ultrashort pulses with water, collagen (type I) solution and porcine cornea. Data on laser-tissue-interaction is precious because the interaction dynamics is usually only documented for water; our results will help to develop a tissue-specific model for the interaction process.We have investigated the interaction of the laser pulses and the effects it causes with live cells in the corneal endothelium. The preservation of endothelial cell viability is crucial notably for specific keratoplasty routines which require incisions close to the endothelium; compromised endothelial cell viability – which is likely caused by the effects of shock waves generated by optical breakdown and bubble formation – may lead to a failure of the surgical intervention. “Safe” sets of parameters concerning pulse energy and incision geometry need to be defined. We explored the maximum permitted pulse energy values at any given distance to the endothelial cells and mini-mal distances for given pulse energies and estimated the associated shock wave amplitudes.Le but de ce travail a été d'étudier les différents effets microscopiques et macroscopiques susceptibles de nous aider à améliorer les procédures de chirurgie oculaire assistée par les lasers à impulsions ultra-courtes ; plus particulièrement en kératoplastie (greffe de cornée), qui nécessite des systèmes lasers opérationnels dans les tissus pathologiques et donc de diffusant fortement la lumière. Antérieurement, le groupe Optique Photonique Santé (OPS) du Laboratoire d'Optique Appliquée (LOA) a identifié 1650 nm comme étant une longueur d'onde optimale à laquelle les processus de diffusion de la lumière à l'intérieur de la cornée pathologique sont minimisés. Au cours de cette thèse, trois tâches principales ont été abordées.Un système laser à impulsions ultra-courtes à base de cristaux optiques non linéaires a été mis au point, optimisée par rapport aux exigences de chirurgie oculaire au laser, et entièrement caractérisé. Le montage achevé est compact, robuste, simple et potentiel-lement apte à un usage en clinique.En collaboration avec un groupe de l’IESL- FORTH (Iraklion, Grèce) et avec la parti-cipation d'un ancien doctorant du groupe, nous avons étudié l'interaction des impulsions ultra-brèves avec de l'eau, une solution de collagène (type I) et des cornées de porcs. Les données sur les interactions laser-tissu sont précieuses car la dynamique d'interaction est habituellement uniquement documentée pour l'eau; nos résultats aide-ront à élaborer un modèle spécifique de tissu pour le processus d'interaction.Nous avons étudié l'interaction entre les impulsions laser et les effets causés sur des cellules vivantes de l'endothélium cornéen. La préservation de la viabilité des cellules endothéliales est cruciale, notamment pour les routines de kératoplastie spécifiques exigeant des incisions à proximité de l'endothélium ; la viabilité des cellules endothéliales compromise – probablement causée par les effets des ondes de choc générées par claquage optique et la formation de bulles – peut conduire à un échec de l'interven-tion chirurgicale. Des jeux de paramètres « saufs » concernant l'énergie d'impulsion et de la géométrie de l'incision doivent être définis. Nous avons ainsi exploré les valeurs maximales autorisées de l'énergie de l'impulsion à une quelconque distance donnée des cellules endothéliales et les distances minimales pour les énergies d'impulsions données, et estimé les amplitudes des ondes de choc associées
On certain hyperelliptic signals that are natural controls for nonholonomic motion planning
No full textIn this paper we address the general problem of approximating, in a certain optimal way, non admissible motions of a kinematic system with nonholonomic constraints. Since this kind of problems falls into the general subriemannian geometric setting, it is natural to consider optimality in the sense of approximating by means of subriemannian geodesics. We consider sys-tems modeled by a subriemannian Goursat structure, a particular case being the well known system of a car with trailers, along with the associated parallel parking problem. Several authors approximate the successive Lie brackets by using trigonometric functions. By contrast, we show that the more natural op-timal motions are related with closed hyperelliptic plane curves with a certain number of loops
Photometry of particulate mixtures : what controls the phase curve ?
No full textInternational audienc
An interpretation of the Sigma-2 fragment of classical Analysis in System T
No full textWe show that it is possible to define a realizability interpretation for the Σ 2 -fragment of classical Analysis using Gödel's System T only. This supplements a previous result of Schwichtenberg regarding bar recursion at types 0 and 1 by showing how to avoid using bar recursion altogether. Our result is proved via a conservative extension of System T with an operator for composable continuations from the theory of programming languages due to Danvy and Filinski. The fragment of Analysis is therefore essentially con-structive, even in presence of the full Axiom of Choice schema: Weak Church's Rule holds of it in spite of the fact that it is strong enough to refute the formal arithmetical version of Church's Thesis
A Logical Basis for Quantum Evolution and Entanglement
No full textInternational audienceWe reconsider discrete quantum causal dynamics where quan-tum systems are viewed as discrete structures, namely directed acyclic graphs. In such a graph, events are considered as vertices and edges de-pict propagation between events. Evolution is described as happening between a special family of spacelike slices, which were referred to as locative slices. Such slices are not so large as to result in acausal influ-ences, but large enough to capture nonlocal correlations. In our logical interpretation, edges are assigned logical formulas in a spe-cial logical system, called BV, an instance of a deep inference system. We demonstrate that BV, with its mix of commutative and noncommutative connectives, is precisely the right logic for such analysis. We show that the commutative tensor encodes (possible) entanglement, and the non-commutative seq encodes causal precedence. With this interpretation, the locative slices are precisely the derivable strings of formulas. Several new technical results about BV are developed as part of this analysis