Declutter and Resample: Towards parameter free denoising

In many data analysis applications the following scenario is commonplace: we are given a point set that is supposed to sample a hidden ground truth $K$ in a metric space, but it got corrupted with noise so that some of the data points lie far away from $K$ creating outliers also termed as {\em ambient noise}. One of the main goals of denoising algorithms is to eliminate such noise so that the curated data lie within a bounded Hausdorff distance of $K$. Popular denoising approaches such as deconvolution and thresholding often require the user to set several parameters and/or to choose an appropriate noise model while guaranteeing only asymptotic convergence. Our goal is to lighten this burden as much as possible while ensuring theoretical guarantees in all cases. Specifically, first, we propose a simple denoising algorithm that requires only a single parameter but provides a theoretical guarantee on the quality of the output on general input points. We argue that this single parameter cannot be avoided. We next present a simple algorithm that avoids even this parameter by paying for it with a slight strengthening of the sampling condition on the input points which is not unrealistic. We also provide some preliminary empirical evidence that our algorithms are effective in practice

Topological analysis of scalar fields with outliers

Given a real-valued function $f$ defined over a manifold $M$ embedded in $\mathbb{R}^d$, we are interested in recovering structural information about $f$ from the sole information of its values on a finite sample $P$. Existing methods provide approximation to the persistence diagram of $f$ when geometric noise and functional noise are bounded. However, they fail in the presence of aberrant values, also called outliers, both in theory and practice. We propose a new algorithm that deals with outliers. We handle aberrant functional values with a method inspired from the k-nearest neighbors regression and the local median filtering, while the geometric outliers are handled using the distance to a measure. Combined with topological results on nested filtrations, our algorithm performs robust topological analysis of scalar fields in a wider range of noise models than handled by current methods. We provide theoretical guarantees and experimental results on the quality of our approximation of the sampled scalar field

Estimation indirecte de l'âge en paléodémographie : approche bayésienne

International audienceEn vue d'estimer la structure par âge des populations du passé en ne disposant que d'indicateurs biologiques, les paléodémographes ont développé un certain nombre de méthodes statistiques, utilisant une population de référence pour apprécier les probabilités conditionnelles de l'âge connaissant l'indicateur. Compte tenu du faible nombre de données disponibles et du caractère instable du problème, ces méthodes sont en général décevantes. Nous montrons comment les améliorer en introduisant une méthode bayésienne simple intégrant un maximum d'informations non réductibles aux données proprement dites

Calcite production by Coccolithophores in the South East Pacific Ocean: from desert to jungle

International audienceBIOSOPE cruise achieved an oceanographic transect from the Marquise Islands to the Peru-Chili upwelling (PCU) via the centre of the South Pacific Gyre (SPG). Water samples from 6 depths in the euphotic zone were collected at 20 stations. The concentrations of suspended calcite particles, coccolithophores cells and detached coccoliths were estimated together with size and weight using an automatic polarizing microscope, a digital camera, and a collection of softwares performing morphometry and pattern recognition. Some of these softwares are new and described here for the first time. The coccolithophores standing stocks are usually low and reach maxima west of the PCU. The coccoliths of Emiliania huxleyi, Gephyrocapsa spp. and Crenalithus spp. (Order Isochrysidales) represent 50% of all the suspended calcite particles detected in the size range 0.1–46 µm (21% of PIC in term of the calcite weight). The latter species are found to grow preferentially in the Chlorophyll maximum zone. In the SPG their maximum concentrations was found to occur between 150 and 200 m, which is very deep for these taxa. The weight and size of coccoliths and coccospheres are correlated. Large and heavy coccoliths and coccospheres are found in the regions with relative higher fertility in the Marquises Island and in the PCU. Small and light coccoliths and coccospheres are found west of the PCU. This distribution may correspond to that of the concentration of calcium and carbonate ions

Vegetation response to the "African Humid Period" termination in Central Cameroon (7° N) – new pollen insight from Lake Mbalang

A new pollen sequence from the Lake Mbalang (7°19´ N, 13°44´ E, 1110 m a.s.l.) located on the eastern Adamawa plateau, in Central Cameroon, is presented in this paper to analyze the Holocene African Humid Period (AHP) termination and related vegetation changes at 7° N in tropical Africa, completing an important transect for exploring shifts in the northern margin of the African Monsoon. This sequence, spanning the last 7000 cal yr BP, shows that the vegetation response to this transitional climatic period was marked by significant successional changes within the broad context of long-term aridification. Semi-deciduous/sub-montane forest retreat in this area is initially registered as early as ca. 6100 cal yr BP and modern savannah was definitely established at ca. 3000 cal yr BP and stabilized at ca. 2400 cal yr BP; but a slight forest regeneration episode is observed between ca. 5200 and ca. 4200 cal yr BP. In this area with modern high rainfall, increasing in the length of the dry season during the AHP termination linked to a contraction of the northern margin of the Intertropical Convergence Zone (ITCZ) from ca. 6100 cal yr BP onward, probably associated with decreasing in cloud cover and/or fog frequency, has primarily controlled vegetation dynamics and above all the disappearance of the forested environment on the Adamawa plateau. Compared to previous studies undertaken in northern tropical and Central Africa, this work clearly shows that the response of vegetation to transitional periods between climatic extremes such as the AHP termination might be different in timing, mode and amplitude according to the regional climate of the study sites, but also according to the stability of vegetation before and during these climatic transitions

Standardisation of methods for assessing mould germination: A workshop report

The first workshop on predictive mycology was held in Marseille, France, 2–4 February 2005 under the auspices of the French Microbiological Society. The purpose of the workshop was to list the different techniques and definitions used by scientists for assessing mould germination and to evaluate the influence of the different techniques on the experimental results. Recommendations were made when a large consensus was obtained. In order to facilitate the study of germination, alternative methods to microscopic examination were examined

Probing the liquid-t-gas like phase transition in a cluster via a caloric curve

IP

Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view

The proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the mitochondrial rRNAs and a few tRNAs, we performed a comparative study on the 143B cell line and on its Rho-0 counterpart, i.e., devoid of mitochondrial DNA. Quantitative differences were found, of course in the respiratory complexes subunits, but also in the mitochondrial translation apparatus, mainly mitochondrial ribosomal proteins, and in the ion and protein import system, i.e., including membrane proteins. Various mitochondrial metabolic processes were also altered, especially electron transfer proteins and some dehydrogenases, but quite often on a few proteins for each pathway. This study also showed variations in some hypothetical or poorly characterized proteins, suggesting a mitochondrial localization for these proteins. Examples include a stomatin-like protein and a protein sharing homologies with bacterial proteins implicated in tyrosine catabolism. Proteins involved in apoptosis control are also found modulated in Rho-0 mitochondria.Comment: website publisher: http://www3.interscience.wiley.com