Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

Huysmans et l’affaire de l’Index (1898-1899)

International audienceEn 1898 et 1899, l'oeuvre de Huysmans fait l'objet d'une dénonciation auprès du Saint-Siège, mêlant Secrétairerie d'État, Saint-Office et Congrégation de l'Index. L'oeuvre n'a cependant pas été mise en l'Index. Le présent article s'appuie sur les archives inédites de la Congrégation pour la Doctrine de la foi pour éclairer cette affaire

Exp\'erimentation d'une ressource pour une situation de recherche et de preuve entre pairs

This paper is about an experiment with the goal of testing a primary teacher's resource. This is the next part of a research presented at EMF2009. This resource must help a teacher to practice a research and proof activity between peers with her pupils even she had never done this before. The paper presents the problems given by this project and describes the means to build the resource and the methodology of the experiment with some classmates. The results are given illustrating the complexity of the underlying process.Comment: Espace math\'ematique francophone, Gen\`eve : Suisse (2012

ICA-based sparse feature recovery from fMRI datasets

Spatial Independent Components Analysis (ICA) is increasingly used in the context of functional Magnetic Resonance Imaging (fMRI) to study cognition and brain pathologies. Salient features present in some of the extracted Independent Components (ICs) can be interpreted as brain networks, but the segmentation of the corresponding regions from ICs is still ill-controlled. Here we propose a new ICA-based procedure for extraction of sparse features from fMRI datasets. Specifically, we introduce a new thresholding procedure that controls the deviation from isotropy in the ICA mixing model. Unlike current heuristics, our procedure guarantees an exact, possibly conservative, level of specificity in feature detection. We evaluate the sensitivity and specificity of the method on synthetic and fMRI data and show that it outperforms state-of-the-art approaches

Refined masses and distance of the young binary Haro 1-14 C

We aim to refine the dynamical masses of the individual component of the low-mass pre-main sequence binary Haro 1-14 C. We combine the data of the preliminary orbit presented previously with new interferometric observations obtained with the four 8m telescopes of the Very Large Telescope Interferometer. The derived masses are M_a=0.905\pm0.043\,\Msun and M_b=0.308\pm0.011\,\Msun for the primary and secondary components, respectively. This is about five times better than the uncertainties of the preliminary orbit. Moreover, the possibility of larger masses is now securely discarded. The new dynamical distance, $d=96\pm\,9\,$pc, is smaller than the distance to the Ophiuchus core with a significance of $2.6\,\sigma$. Fitting the spectral energy distribution yields apparent diameters of \phi_a=0.13\pm0.01\mas and \phi_b=0.10\pm0.01\mas (corresponding to \Ra=1.50\,\Rsun and \Rb=1.13\,\Rsun) and a visual extinction of $A_v\approx1.75$. Although the revised orbit has a nearly edge-on geometry, the system is unlikely to be a long-period eclipsing binary. The secondary in Haro~1-14C is one of the few low-mass, pre-main sequence stars with an accurately determined dynamical mass and distance

Improving accuracy and power with transfer learning using a meta-analytic database

Typical cohorts in brain imaging studies are not large enough for systematic testing of all the information contained in the images. To build testable working hypotheses, investigators thus rely on analysis of previous work, sometimes formalized in a so-called meta-analysis. In brain imaging, this approach underlies the specification of regions of interest (ROIs) that are usually selected on the basis of the coordinates of previously detected effects. In this paper, we propose to use a database of images, rather than coordinates, and frame the problem as transfer learning: learning a discriminant model on a reference task to apply it to a different but related new task. To facilitate statistical analysis of small cohorts, we use a sparse discriminant model that selects predictive voxels on the reference task and thus provides a principled procedure to define ROIs. The benefits of our approach are twofold. First it uses the reference database for prediction, i.e. to provide potential biomarkers in a clinical setting. Second it increases statistical power on the new task. We demonstrate on a set of 18 pairs of functional MRI experimental conditions that our approach gives good prediction. In addition, on a specific transfer situation involving different scanners at different locations, we show that voxel selection based on transfer learning leads to higher detection power on small cohorts.Comment: MICCAI, Nice : France (2012

A PIONIER View on Mass-Transferring Red Giants

Symbiotic stars display absorption lines of a cool red giant together with emission lines of a nebula ionized by a hotter star, indicative of an active binary star system in which mass transfer is occurring. PIONIER at the VLT has been used to combine the light of four telescopes at a time to study in unprecedented detail how mass is transferred in symbiotic stars. The results of a mini-survey of symbiotic stars with PIONIER are summarised and some tentative general results about the role of Roche lobe overflow are presented.Comment: Report for the ESO Messenger June issu

Electrical modeling of InAs/GaSb superlattice mid-wavelength infrared pin photodiode to analyze experimental dark current characteristics

Dark current characteristics of 7 Monolayers (ML) InAs/ 4 ML GaSb SL pin photodiodes are simulated using ATLAS software. Using appropriate models and material parameters, we obtain good agreement between the simulated and the experimental dark current curves of photodiodes grown by molecular beam epitaxy. The n-type non-intentionally-doped (nid) SL samples exhibit a dependence of the lifetime with temperature following the T−12 law, signature of Shockley-Read-Hall (SRH) Generation-Recombination current. We also studied the dependence of the dark current with the absorber doping level. It appears that the absorber doping level must not exceed a value of 2 × 1015 cm−3, above this value the dark current is increasing with increased doping level. However for this doping value, a dark current as low as 5 × 10−9 A/cm2, at 50 mV reverse bias at 77 K can be obtained

The Cave of Fouvent, also called Abri Cuvier (Fouvent-le-Bas, Haute-Saône, France): Taphonomical analysis of a Late Pleistocene Hyena Den (OIS3)

Le gisement paléontologique de Fouvent (Fouvent-le-Bas, Haute-Saône, France) est une accumulation osseuse karstique connue depuis le début du XIXe siècle. Ce site est à l’origine de nombreuses avancées paléontologiques (reconnaissance de l’hyène fossile par Cuvier, première mention du glouton en France) et taphonomique (caractérisation du repaire de carnivore). Le présent article porte sur l’analyse de 14 977 restes osseux issus à la fois de la collection historique (fouilles de 1842) et des fouilles récentes (1989-1992). Une liste faunique de 19 taxons de grands mammifères a été établie : 11 carnivores (Crocuta crocuta spelaea, Panthera (Leo) spelaea, Ursus spelaeus, Canis lupus, Vulpes vulpes, cf. Alopex, Gulo gulo, Meles meles, Martes sp., Mustela eversmanii, Mustela sp.) et 8 ongulés (Mammuthus primigenius, Coelodonta antiquitatis, Megaloceros giganteus, Cervus elaphus, Rangifer tarandus, Equus germanicus, Bos primigenius et/ou Bison priscus). L’étude des hyènes des cavernes permet de préciser les caractères d’une population du stade isotopique 3 et de discuter de sa composition. Quant au spectre d’ongulés, son identification permet de préciser la diversité des proies de l’hyène (en termes d’espèces et d’âges individuels). Les interactions entre le prédateur et ses proies sont caractérisées grâce à l’étude de la distribution squelettique, de la fragmentation osseuse, des morphologies des restes consommés et des traces de dents. L’examen détaillé de l’ensemble des éléments taphonomiques de l’accumulation osseuse de Fouvent permet de discuter et de préciser la spécificité d’un repaire d’hyènes pléistocène.The palaeontological site of Fouvent (Fouvent-le-Bas, Haute-Saône, France) is a fissure-filling bone accumulation known from the beginning of the XIXth century. This assemblage is at the origin of palaeontological (description of fossil hyena by Cuvier, first record of French wolverine) and taphonomical advances (first carnivore den characterization). This paper presents the analysis of 14 977 bone remains from both the historical collection (1842) and recent excavations (between 1989 and 1992). A faunal list of 19 mammalian species has been identified: 11 carnivore species (Crocuta crocuta spelaea, Panthera (Leo) spelaea, Ursus spelaeus, Canis lupus, Vulpes vulpes, cf. Alopex, Gulo gulo, Meles meles, Martes sp., Mustela eversmanii, Mustela sp.) and 8 large ungulate species (Mammuthus primigenius, Coelodonta antiquitatis, Megaloceros giganteus, Cervus elaphus, Rangifer tarandus, Equus germanicus, Bos primigenius and/or Bison priscus). The analysis of cave hyenas from Fouvent allows us to precise characteristics of an OIS3 population and to discuss population structure. The study of ungulate populations allows us to describe prey diversity (in terms of species and individual age). Prey skeletal part distribution, bone fragmentation, consumption morphotypes and tooth marks are observed to point out predator-prey interactions. The detailed analysis of taphonomical aspects of Fouvent bone accumulation allows also to discuss and to give criteria about hyena den characterization grids