Éditeur(s) : HAL CCSD
Résumé : International audience
The extraction of knowledge from social networks is an area that has experienced significant growth in recent years. Indeed, thanks to the improvement of storage and calculation capacities, and the heterogeneity of data that can currently be extracted, much effort has been made to go beyond traditional knowledge, by proposing new kinds of patterns that take into account the context. However, while many works were interested in designing new patterns of knowledge or in optimizing existing approaches, few studies have been focused in merging patterns and on the useful knowledge emerging from such fusions. In this work, we focus on two network clustering approaches, able to extract two distinct kinds of patterns, and we seek to understand both the intersections that can exist between them and the knowledge that emerges from their fusion. The first is the classical nodes clustering approach that consists in searching for communities into a network. The second is the search for frequent conceptual links, a new link clustering approach that aims identifying frequent links between groups of nodes sharing common attributes. We propose a set of original measures that aim to evaluate the amount of shared information between these patterns when they are extracted from a same network. These measures are applied to three datasets and demonstrate the interest in simultaneously considering several sources of knowledge.
Advances in Knowledge Discovery and Management (AKDM)

hal-01514227
https://hal.archives-ouvertes.fr/hal-01514227
DOI : 10.1007/978-3-319-45763-5_13

Éditeur(s) : HAL CCSD
Résumé : International audience
The study of complex biological processes requires to forgo simplified models for extensive ones. Yet, these models' size and complexity place them beyond understanding. Their analysis requires new methods for identifying general patterns. The Transforming Growth Factor TGF-β is a multifunctional cytokine that regulates mammalian cell development , differentiation, and homeostasis. Depending on the context, it can play the antagonistic roles of growth inhibitor or of tumor promoter. Its context-dependent pleiotropic nature is associated with complex sig-naling pathways. The most comprehensive model of TGF-β-dependent signaling is composed of 15,934 chains of reactions (trajectories) linking TGF-β to at least one of its 159 target genes. Identifying functional patterns in such a network requires new automated methods. This article presents a framework for identifying groups of similar trajec-tories composed of the same molecules using an exhaustive and without prior assumptions approach. First, the trajectories were clustered using the Relevant Set Correlation model, a shared nearest-neighbors clustering method. Five groups of trajectories were identified. Second, for each cluster the over-represented molecules were determined by scoring the frequency of each molecule implicated in trajectories. Third, Gene set enrichment analysis on the clusters of trajectories revealed some specific TGF-β-dependent biological processes, with different clusters associated to the antagonists roles of TGF-β. This confirms that our approach yields biologically-relevant results. We developed a web interface that facilitates graph visualization and analysis. Our clustering-based method is suitable for identifying families of functionally-similar trajectories in the TGF-β signaling network. It can be generalized to explore any large-scale biological pathways.
CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology
Darmstadt, France

hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249/document
https://hal.archives-ouvertes.fr/hal-01559249/file/JeanCoquet_CMSB.pdf

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Aims: A description of bacterial pathogens in shrimp ponds is necessary to understand their pathogenesis. Vibrio nigripulchritudo was shown to contain saprophytic and pathogenic strains among New Caledonian isolates. We established a method to map the development of V. nigripulchritudo in pond sediments at three different genetic levels: the species level, then at the pathogenic cluster level and finally at the plasmid level, present only in all highly pathogenic isolates. Methods and Results: PCR methods were applied to shrimp pond sediments both before and after a mortality outbreak. Using crude samples, the species V. nigripulchritudo is not detected at first (0/42 samples at day 56 post stocking) but appears frequently in the sediments after the mortality event (30/42 at day 107). The distribution of strains from the pathogenic cluster of V. nigripulchritudo also follows this pattern. In contrast, the pSFn1 virulence-associated plasmid was detected in one sample at day 56 and none at day 107. An enrichment method was developed to lower the detection limits of our assays. After enrichment, the species V. nigripulchritudo was detected in all samples at both dates. The number of samples positive for pSFn1 was 42/42 samples at day 56 and 29/42 at day 107. Conclusions: These results show that the sediments contain V. nigripulchritudo, notably pathogenic strains. Surprisingly, the virulence-associated plasmid pSFn1 found in all V. nigripulchritudo isolated from moribund shrimp appears less frequently in sediments, possibly being useless or even detrimental to its recipient bacteria in this environment. Significance and Impact of the Study: This study confirms the presence of pathogenic V. nigripulchritudo strains in shrimp pond sediment before a mortality outbreak complying with a previous hypothesis that sediments could be the infecting reservoir. After the outbreak, both total V. nigripulchritudo and pathogenic strains populations have largely increased, possibly contributing to the recurrent mortality observed in this shrimp vibriosis.
Journal Of Applied Microbiology (1364-5072) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 108 , N. 6 , P. 2003-2011

Droits : 2010 The Society for Applied Microbiology - Wiley-Blackwell
http://archimer.ifremer.fr/doc/00004/11484/8177.pdf
DOI:10.1111/j.1365-2672.2009.04601.x
http://archimer.ifremer.fr/doc/00004/11484/

Éditeur(s) : HAL CCSD
Résumé : International audience
In this article, we analyse a collaborative network to understand the underlying patterns that structure the co-writing process of scientific articles. Our goal is to identify and understand the collaboration tendencies from authors publishing activities. For this purpose, we adopt a descriptive modelling through a network approach that consists first in generating the collaborative network from data on publications. Nodes of the network are then enriched with a set of individual attributes extracted from the publishing activity of each author. Finally, we search for conceptual views, a recent link clustering approach, which allows to summarize any kind of networks by highlighting the sets of attributes found frequently linked. Results show that it exists strong tendencies that unconsciously structure the collaboration behaviours. In this paper, we present these tendencies and show how they evolve according to different extraction thresholds.
EEE/ACM International Conference on Advances in Social Networks Analysis and Mining
Sydney, Australia

hal-01637563
https://hal.archives-ouvertes.fr/hal-01637563
DOI : 10.1145/3110025.3110146

Éditeur(s) : HAL CCSD
Résumé : International audience
Numerous social network mining methods have been proposed until now for addressing social mining tasks and specially searching for communities or frequent social patterns. However, the degree of complementarity of these methods has been very little studied. In this paper, we focus on two knowledge extraction processes in social networks: a link-based clustering that may extract social communities and a recent approach that searches for frequent conceptual link involving both clustering and search for frequent social patterns. We explore how the models extracted by each method may match and which potential useful knowledge they may provide. Our objective is to evaluate the potential relationships between communities and frequent conceptual links. For this purpose, we propose a set of measures for evaluating the degree to which these patterns extracted from the same dataset are matching. Our approach is applied on two datasets and demonstrates the importance of considering simultaneously various kinds of knowledge and their complementarity.
IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining
Niagara falls, Canada

hal-00874351
https://hal.archives-ouvertes.fr/hal-00874351

Éditeur(s) : HAL CCSD Human Kinetics
Résumé : International audience
OBJECTIVE: The aim was to examine the relationship between physical activity pattern and dietary profile. Although some clustering of the variables related to these major determinants of cardiovascular risk has been demonstrated, they have not been extensively studied together. PARTICIPANTS, DESIGN, AND SETTING: Two hundred two female university students from the main Guadeloupe (French West Indies) campus participated. They self-administered a validated Food Frequency Questionnaire and the 1-yr recall Modifiable Activity Questionnaire. Principal-component analysis was performed on the scores and the variables related to the physical activity pattern and dietary profile. RESULTS: A model including 10 variables explained 84.9% of the total variance. The physical activity pattern was not associated with the dietary profile, apart from fruit intake. The physical activity level was homogeneously low (median 1.58, first and last quartile cutoffs 1.54 and 1.66, respectively). There was no correlation between the physical activity level and the Food Frequency Questionnaire score (r=-.005). CONCLUSIONS: The absence of a strong relationship between the food and physical activity profiles is interpreted as a possible reflection of a dysregulation of the quality of food intake in this population with a sedentary lifestyle.
ISSN: 1526-484X

hal-00748203
https://hal.archives-ouvertes.fr/hal-00748203
DOI : 10.1123/ijsnem.20.5.401
PUBMED : 20975108

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
he search for frequent conceptual links (FCL) is a new network clustering approach that exploits both the network structure and the node properties. While recent works have been focused on the optimisation of the FCL extraction, no study has been conducted on the matching or the intersections between the conceptual links and the classical clustering approach which consists in extracting communities. In this paper, we focus on these two approaches. Our objective is to evaluate the possible relationships existing between FCL and communities to understand how the patterns obtained by each kind of methods may match as well as the useful knowledge resulting from the intersections of these two kinds of knowledge. For this purpose, we propose a set of original measures, based on the notion of homogeneity, assessing the level of shared information between these patterns when they are extracted from the same dataset. The measures are applied on three datasets and demonstrate the importance of considering simultaneously various kinds of knowledge and their intersections.
ISSN: 1869-5450

hal-01312313
https://hal.archives-ouvertes.fr/hal-01312313
DOI : 10.1007/s13278-014-0197-1

Éditeur(s) : American Geophysical Union
Résumé : Noise with periods 3 to 10 s, ubiquitous in seismic records, is expected to be mostly generated by pairs of ocean wave trains of opposing propagation directions with half the seismic frequency. Here we present the first comprehensive numerical model of microseismic generation by random ocean waves, including ocean wave reflections. Synthetic and observed seismic spectra are well correlated (r > 0.85). On the basis of the model results, noise generation events can be clustered in three broad classes: wind waves with a broad directional spectrum (class I), sea states with a significant contribution of coastal reflections (class II), and the interaction of two independent wave systems (class III). At seismic stations close to western coasts, noise generated by class II sources generally dominates, but it is intermittently outshined by the intense class III sources, limiting the reliability of seismic data as a proxy for storm climates. The modeled seismic noise critically depends on the damping of seismic waves. At some mid-ocean island stations, low seismic damping is necessary to reproduce the observed high level and smoothness of noise time series that result from a spatial integration of sources over thousands of kilometers. In contrast, some coastal stations are only sensitive to noise within a few hundreds of kilometers. This revelation of noise source patterns worldwide provides a wealth of information for seismic studies, wave climate applications, and new constraints on the possible directional distribution of wave energy.
Journal of Geophysical Research ( JGR ) - Oceans (0148-0227) (American Geophysical Union), 2011-09 , Vol. 116 , N. C09004 , P. 21 p.

Droits : 2011 by the American Geophysical Union
http://archimer.ifremer.fr/doc/00044/15531/12926.pdf
DOI:10.1029/2011JC006952
http://archimer.ifremer.fr/doc/00044/15531/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Studies of paleomagnetic fields during polarity transitions recorded over the past few million years frequently suggest a configurational persistence consistent with long-lived mantle control over the pattern of flux emanating from Earth's fluid core. Fundamental to an understanding of the core-mantle dynamics involved is the question of the spatial-temporal nature of the physical conditions at the base of the mantle that may be responsible. Our analysis of the field during a mid-Cenozoic, reverse-to-normal (R-N) polarity change, recorded in a continuous sequence of lava flows in southeastern Queensland, Australia, provides strong evidence that the time span over which local mantle features retain such an influence is far longer than had thus far been observed. Specifically. the reversal is dominated by two sequential groupings of transitional magnetic vector directions, each associated with a clustering of virtual geomagnetic poles (VGPs) at locations common to several more youthful reversal datasets from about the globe. Our Ar-40/Ar-39 age determinations indicate that these Australian lavas erupted 25.56 +/- 0.48 Ma, strongly suggesting that the characteristic time for invariant control by the mantle over flux emerging from the outer core is at least on order of a few tens of Myr. The availability of transitional paleomagnetic data from still earlier times within the Cenozoic may further delineate this duration and, perhaps, provide a means to track changes in the pattern of long-standing concentrations of magnetic flux at the core-mantle boundary. (C) 2008 Elsevier B.V. All rights reserved.
ISSN: 0031-9201

hal-00411919
https://hal.archives-ouvertes.fr/hal-00411919
DOI : 10.1016/j.pepi.2008.07.012