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A Tool for Classification of Sequential Data

Giacomo Kahn, Yannick Loiseau, Olivier Raynaud
2016 European Conference on Artificial Intelligence  
Classification of sequential data (data obtained from series of actions in chronological order) has many applications in security, marketing or ergonomy. In this paper, we present a tool for classification of sequential data. We introduce a new clean dataset of web-browsing logs, and study the case of implicit authentification from web-browsing. We then detail more of the functioning of the tool and some of its parameters.
dblp:conf/ecai/KahnLR16 fatcat:xzowfbasrnhyljkscptidyhaoy

Eclipse Golo

Julien Ponge, Yannick Loiseau, Frédéric Le Mouël, Nicolas Stouls, Philippe Charrière, Daniel Petisme, Sylvain Desgrais, Franck Verrot
2016 Journal of Open Source Software  
doi:10.21105/joss.00093 fatcat:tjsykc53mnhwhh2odkbchurmj4

A closed sets based learning classifier for implicit authentication in web browsing

Diyé Dia, Giacomo Kahn, Fabien Labernia, Yannick Loiseau, Olivier Raynaud
2018 Discrete Applied Mathematics  
Faced with both identity theft and the theft of means of authentication, users of digital services are starting to look rather suspiciously at online systems. To increase access security it is necessary to introduce some new factor of implicit authentication such as user behavior analysis. A behavior is made up of a series of observable actions and taken as a whole, the most frequent of these actions amount to habit. The challenge is to detect identity theft as quickly as possible and,
more » ... lly, to validate a legitimate identity for as long as possible. To take up this challenge, we introduce in this paper a closed set-based learning classifier. This classifier is inspired by classification in concept lattices from positive and negative examples and several works on emerging patterns. We also rely on the tf-idf parameter used in the context of information retrieval. We propose three heuristics named H c tf −idf , H c sup and H c supM in to select closed patterns for each class to be described. To compute performance of our models we have followed an experimental protocol described in a previous study which had the same purpose. Then, we compared the results from our own dataset of web navigation connection logs of 3, 000 users over a six-month period with the heuristic H sup introduced in this study. Moreover, to strengthen our analysis, we have designed and set up one model based on the naive Bayes classifier to be used as a reference statistical tool.
doi:10.1016/j.dam.2018.11.016 fatcat:khs6i2o3irdbbauyd5eezdwyau

Rank-Ordering Documents According to Their Relevance in Information Retrieval Using Refinements of Ordered-Weighted Aggregations [chapter]

Mohand Boughanem, Yannick Loiseau, Henri Prade
2006 Lecture Notes in Computer Science  
Classical information retrieval methods often lose valuable information when aggregating weights, which may diminish the discriminating power between documents. To cope with this problem, the paper presents an approach for ranking documents in IR, based on a vectorbased ordering technique already considered in fuzzy logic for multicriteria analysis purpose. Moreover, the proposed approach uses a possibilistic framework for evaluating queries to a document collection, which distinguishes between
more » ... descriptors that are certainly relevant and those which are possibly relevant only. The proposal is evaluated on a standard collection that allows to compare the effectiveness of this approach with a classical one. The proposed method provides an improvement of the precision of the Mercure IR system.
doi:10.1007/11670834_4 fatcat:mp5ivid6wjf3fo2nvhf2ic7eyq

Using Closed Itemsets for Implicit User Authentication in Web Browsing

Olivier Coupelon, Diyé Dia, Fabien Labernia, Yannick Loiseau, Olivier Raynaud
2014 International Conference on Concept Lattices and their Applications  
Faced with both identity theft and the theft of means of authentication, users of digital services are starting to look rather suspiciously at online systems. The behavior is made up of a series of observable actions of an Internet user and, taken as a whole, the most frequent of these actions amount to habit. Habit and reputation oer ways of recognizing the user. The introduction of an implicit means of authentication based upon the user's behavior allows web sites and businesses to
more » ... the risks they take when authorizing access to critical functionalities. In this paper, we propose a new model for implicit authentication of web users based on extraction of closed patterns. On a data set of web navigation connection logs of 3,000 users over a six-month period we follow the experimental protocol described in [1] to compute performance of our model.
dblp:conf/cla/CoupelonDLLR14 fatcat:f2wczfumurfuli42uuhthngrxq

Improving Document Ranking in Information Retrieval Using Ordered Weighted Aggregation and Leximin Refinement

Mohand Boughanem, Yannick Loiseau, Henri Prade
2005 European Society for Fuzzy Logic and Technology  
Classical information retrieval (IR) methods often lose valuable information when aggregating weights, which may diminish the discriminating power between documents. To cope with this problem, the paper presents an approach for ranking documents in IR, based on a vector-based ordering technique already considered in fuzzy logic for multiple criteria analysis purpose. Moreover, the proposed approach uses a possibilistic framework for encoding the retrieval status values. The approach, applied to
more » ... a benchmark collection, has been shown to improve IR precision w.r.t. classical approaches.
dblp:conf/eusflat/BoughanemLP05 fatcat:uc6izdh54fgkxc2mhvqapu4loi

Microbial biotransformation of DON: molecular basis for reduced toxicity

Alix Pierron, Sabria Mimoun, Leticia S. Murate, Nicolas Loiseau, Yannick Lippi, Ana-Paula F. L. Bracarense, Gerd Schatzmayr, Jian Wei He, Ting Zhou, Wulf-Dieter Moll, Isabelle P. Oswald
2016 Scientific Reports  
Bacteria are able to de-epoxidize or epimerize deoxynivalenol (DON), a mycotoxin, to deepoxydeoxynivalenol (deepoxy-DON or DOM-1) or 3-epi-deoxynivalenol (3-epi-DON), respectively. Using different approaches, the intestinal toxicity of 3 molecules was compared and the molecular basis for the reduced toxicity investigated. In human intestinal epithelial cells, deepoxy-DON and 3-epi-DON were not cytotoxic, did not change the oxygen consumption or impair the barrier function. In intestinal
more » ... , exposure for 4 hours to 10 μM DON induced intestinal lesions not seen in explants treated with deepoxy-DON and 3-epi-DON. A pan-genomic transcriptomic analysis was performed on intestinal explants. 747 probes, representing 323 genes, were differentially expressed, between DON-treated and control explants. By contrast, no differentially expressed genes were observed between control, deepoxy-DON and 3-epi-DON treated explants. Both DON and its biotransformation products were able to fit into the pockets of the A-site of the ribosome peptidyl transferase center. DON forms three hydrogen bonds with the A site and activates MAPKinases (mitogen-activated protein kinases). By contrast deepoxy-DON and 3-epi-DON only form two hydrogen bonds and do not activate MAPKinases. Our data demonstrate that bacterial de-epoxidation or epimerization of DON altered their interaction with the ribosome, leading to an absence of MAPKinase activation and a reduced toxicity. Mycotoxins are toxic secondary metabolites produced by various molds, such as Aspergillus, Penicillium and Fusarium which may contaminate food and feed at all stages of the food/feed chain 1,2 . Despite the improvement of agricultural and manufacturing practices, mycotoxin contamination cannot be avoided and still represents a permanent health risk for both humans and animals. It is thus important to develop decontamination strategies 3 . Among mycotoxins, deoxynivalenol (DON) produced by Fusarium species, is commonly detected in cereal crops, including wheat, barley, and maize. It is the most abundant trichothecene in food with a frequent occurrence at toxicologically relevant concentrations worldwide 4,5 . DON causes acute and chronic disorders in humans and animals, with the gastrointestinal tract being an organ sensitive to its adverse effects 6 . DON affects the intestinal histomorphology, impairs barrier function and nutrient absorption 7,8 . DON also disrupts the local intestinal immune response; it triggers and potentiates intestinal inflammation 9,10 . At the cellular and subcellular level, DON binds to the ribosome, inhibits protein and nucleic acid synthesis and triggers ribotoxic stress 11-13 leading to the activation of kinases, MAPKs and their downstream signaling pathways 14 . Several strategies have been developed to limit DON toxicity 15 , among them, bacterial biotransformation which depends on the ability of microorganisms to generate DON metabolites with reduced toxicity. De-epoxidation is a reductive chemical reaction opening the 12,13-epoxy ring transforming DON into its de-epoxide metabolite de-epoxy-deoxynivalenol (deepoxy-DON or DOM-1) (Supplementary Figure S1) 16 . Several microbial strains are capable of DON de-epoxidation 15, 17 . Several in vitro studies demonstrated the reduced toxicity of deepoxy-DON. In vivo trials on farm animals receiving feed contaminated with DON have also shown a beneficial effect of the bacteria able to de-epoxidize DON, according to zootechnical parameters and immune response 18 . The hydroxyl on carbon 3 also seems to be significant for the toxic activity of DON and a detoxification strategy targeting this part of the C3-OH, leading to the formation of 3-epi-DON, was recently proposed 19 . Four bacterial strains, all isolated from soil, have been described to epimerize DON into 3-epi-DON 20,21 . Only one paper has investigated the effect of 3-epi-DON and demonstrated the lack of toxicity, both in vitro and in vivo, of this DON metabolite 22 . The aim of the current study was to assess the efficacy of microbial transformation through analysis of the intestinal toxicity of deepoxy-DON and 3-epi-DON. Using physiological, histological and transcriptomic analysis, we have observed reduced toxicity of deepoxy-DON and 3-epi-DON, both for human intestinal epithelial cells and pig intestinal explants. We have further demonstrated that these microbial metabolites of DON fit into the ribosome pocket but do not elicit ribotoxic stress or activate the MAPKinase pathway. Our paper provides the first molecular insight for the reduced toxicity of deepoxy-DON and 3-epi-DON.
doi:10.1038/srep29105 pmid:27381510 pmcid:PMC4933977 fatcat:xmca7sqpinbkjji6hbjude3pfe

Tissular Genomic Responses to Oral FB1 Exposure in Pigs

Léonie Dopavogui, Arnaud Polizzi, Anne Fougerat, Pascal Gourbeyre, Chloé Terciolo, Wendy Klement, Philippe Pinton, Joëlle Laffite, Anne-Marie Cossalter, Jean-Denis Bailly, Olivier Puel, Yannick Lippi (+4 others)
2022 Toxins  
Fumonisin B1 (FB1) is a widespread mycotoxin produced by fungal Fusarium species—mainly in maize, one of the plants most commonly used for food and feed. Pigs and horses are the animal species most susceptible to this mycotoxin. FB1 exposure can cause highly diverse clinical symptoms, including hepatotoxicity, immunotoxicity, and intestinal barrier function disturbance. Inhibition of ceramide synthetase is a well-understood ubiquitous molecular mechanism of FB1 toxicity, but other more
more » ... ecific effects remain to be elucidated. To investigate the effects of FB1 in different exposed tissues, we cross-analyzed the transcriptomes of fours organs: liver, jejunum, jejunal Peyer's patches, and spleen. During a four-week study period, pigs were fed a control diet or a FB1-contaminated diet (10 mg/kg feed). In response to oral FB1 exposure, we observed common biological processes in the four organs, including predominant and recurrent processes (extracellular matrix organization, integrin activation, granulocyte chemotaxis, neutrophil migration, and lipid and sterol homeostasis), as well as more tissue-specific processes that appeared to be related to lipid outcomes (cell cycle regulation in jejunum, and gluconeogenesis in liver).
doi:10.3390/toxins14020083 pmid:35202111 pmcid:PMC8875869 fatcat:zwsuijq455dflib56enhbsj6de

Towards a Decoupled Context-Oriented Programming Language for the Internet of Things

Baptiste Maingret, Frédéric Le Mouël, Julien Ponge, Nicolas Stouls, Jian Cao, Yannick Loiseau
2015 Proceedings of the 7th International Workshop on Context-Oriented Programming - COP'15  
Easily programming behaviors is one major issue of a large and reconfigurable deployment in the Internet of Things. Such kind of devices often requires to externalize part of their behavior such as the sensing, the data aggregation or the code offloading. Most existing context-oriented programming languages integrate in the same class or close layers the whole behavior. We propose to abstract and separate the context tracking from the decision process, and to use event-based handlers to
more » ... nect them. We keep a very easy declarative and non-layered programming model. We illustrate by defining an extension to Golo-a JVM-based dynamic language.
doi:10.1145/2786545.2786552 dblp:conf/ecoop/MaingretMPSCL15 fatcat:gkhzrwk4yzeynborba6emcy7ja

Obesity promotes Fumonisin B1 toxicity and induces hepatitis [article]

Léonie Dopavogui, Marion Régnier, Arnaud Polizzi, Quentin Ponchon, Sarra Smati, Wendy Klement, Frédéric Lasserre, Céline Lukowicz, Yannick Lippi, Anne Fougerat, Justine Bertrand-Michel, Claire Naylies (+13 others)
2022 bioRxiv   pre-print
., 2006; Loiseau et al., 2007) .  ...  Al, Canlet, C., Tremblay-Franco, M., Ellero-Simatos, S., Langin, D., Postic, C., Wahli, W., Loiseau, N., Guillou, H., Montagner, A., 2020.  ... 
doi:10.1101/2022.07.22.500801 fatcat:vvlm7nwugfbcvjfemxukggrmnm

Hepatocyte-specific deletion of Pparα promotes NASH in the context of obesity [article]

Marion Régnier, Arnaud Polizzi, Sarra Smati, Céline Lukowicz, Anne Fougerat, Yannick Lippi, Edwin Fouché, Frédéric Lasserre, Claire Naylies, Colette Bétoulières, Valentin Barquissau, Etienne Mouisel (+12 others)
2018 bioRxiv   pre-print
AbstractObjectivesPeroxisome proliferator activated receptor α (PPARα) acts as a fatty acid sensor to orchestrate the transcription of genes coding for rate-limiting enzymes required for lipid oxidation in hepatocytes. Mice only lacking Pparα in hepatocytes spontaneously develop steatosis without obesity in aging. Altough steatosis is a benign condition it can develop into non alcoholic steatohepatitis (NASH), which may progress to irreversible damage, such as fibrosis and hepatocarcinoma.
more » ... NASH appears as a major public health concern worldwide, it remains an unmet medical need. Several drugs are being tested in clinical trials, including pharmacological agonists for the different PPAR isotypes. In current study, we investigated the role of hepatocyte PPARα in a preclinical model of steatosis.Methods/ResultsWe have investigated the role of hepatocyte PPARα in a preclinical model of steatosis using High Fat Diet (HFD) feeding as a model of obesity in C57BL/6J male Wild-Type mice (WT), in whole-body (Pparα-/-) mice and in mice lacking Pparα in hepatocyte (Pparαhep-/-). We provide evidence that Pparα deletion in hepatocytes promotes NASH in mice fed an HFD. This enhanced NASH susceptibility occurs without development of glucose intolerance. Moreover, our data reveal that non-hepatocytic PPARα activity predominantly contributes to the metabolic response to HFD.ConclusionTaken together, our data support hepatocyte PPARα as being essential to the prevention of steatosis progression to NASH and that extra-hepatocyte PPARα activity contributes to whole-body lipid homeostasis.HighlightsPparα deletion in hepatocytes promotes steatosis and inflammation in HFD-induced obesityHepatocyte-specific deletion of Pparα dissociates NAFLD from glucose intolerance in HFD-induced obesity obesityExtrahepatic PPARα activity contributes to the metabolic response to HFD-induced obesity
doi:10.1101/488031 fatcat:c4pk6urs2fdtlnydwakdmppzzm

ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity [article]

Anne Fougerat, Gabriele Schoiswohl, Arnaud Polizzi, Marion Regnier, Carina Wagner, Sarra Smati, Tiffany Fougeray, Yannick Lippi, Frederic Lasserre, Valentine Melin, Blandine Tramunt, Chantal Alkhoury (+16 others)
2021 bioRxiv   pre-print
Objective: In hepatocytes, peroxisome proliferator-activated receptor alpha acts as a lipid sensor that regulates hepatic lipid catabolism during fasting and orchestrates a genomic response required for whole-body homeostasis. This includes the biosynthesis of ketone bodies and the secretion of the starvation hormone fibroblast growth factor 21 (FGF21). Several lines of evidence suggest that adipose tissue lipolysis contributes to this specific process. However, whether adipose tissue lipolysis
more » ... is a dominant signal for the extensive remodeling of liver gene expression dependent on PPARalpha has not been investigated. Methods: First, using mice lacking adipose tissue lipolysis through adipocyte-specific deletion of adipose triglyceride lipase (ATGL), we characterized the responses dependent on adipocyte ATGL during fasting. Next, we performed liver whole genome expression analysis in fasted mice upon deletion of adipocyte ATGL or hepatocyte PPARalpha. Finally, we tested the consequences of hepatocyte-specific PPARalpha deficiency during pharmacological induction of adipocyte lipolysis with a Beta3-adrenergic receptor agonist. Results: In the absence of ATGL in adipocytes, ketone body and FGF21 productions were impaired in response to starvation. Liver transcriptome analysis revealed that adipocyte ATGL is critical for regulation of hepatic gene expression during fasting and highlighted a strong enrichment in PPARalpha target genes in this condition. Genome expression analysis confirmed that a large set of fasting-induced genes are sensitive to both ATGL and PPARalpha. Adipose tissue lipolysis induced by acute activation of the Beta3-adrenergic receptor also triggered PPARalpha-dependent responses in the liver, supporting a role for adipocyte-derived fatty acids as dominant signals for hepatocyte PPARalpha activity. In addition, the absence of hepatocyte PPARalpha altered brown adipose tissue (BAT) morphology and reduced UCP1 expression upon stimulation of the Beta3-adrenergic receptor. In agreement with this finding, mice lacking hepatocyte PPARalpha showed decreased tolerance to acute cold exposure. Conclusions: These results underscore the central role of hepatocyte PPARalpha in the sensing of adipocyte-derived fatty acids and reveal that its activity is essential for full activation of BAT. Intact PPARalpha activity in hepatocytes is required for cross-talk between adipose tissues and the liver during fat mobilization during fasting and cold exposure.
doi:10.1101/2021.01.28.428684 fatcat:uqqjlrw5ebdg3okjx7g7n6h4wu

The hepatocyte insulin receptor is required to program rhythmic gene expression and the liver clock [article]

Tiffany Fougeray, Arnaud Polizzi, Marion Regnier, Anne Fougerat, Sandrine Ellero-Simatos, Yannick Lippi, Sarra Smati, Frederic Lasserre, Blandine Tramunt, Marine Huillet, Leonie Dopavogui, Lorraine Smith (+13 others)
2021 bioRxiv   pre-print
In mammalian cells, gene expression is rhythmic and sensitive to various environmental and physiological stimuli. A circadian clock system helps to anticipate and synchronize gene expression with daily stimuli including cyclic light and food intake, which control the central and peripheral clock programs, respectively. Food intake also regulates insulin secretion. How much insulin contributes to the effect of feeding on the entrainment of the clock and rhythmic gene expression remains to be
more » ... stigated. An important component of insulin action is mediated by changes in insulin receptor (IR)-dependent gene expression. In the liver, insulin at high levels controls the transcription of hundreds of genes involved in glucose homeostasis to promote energy storage while repressing the expression of gluconeogenic genes. In type 2 diabetes mellitus (T2DM), selective hepatic insulin resistance impairs the inhibition of hepatic glucose production while promoting lipid synthesis. This pathogenic process promoting hyperlipidemia as well as non-alcoholic fatty liver diseases. While several lines of evidence link such metabolic diseases to defective control of circadian homeostasis, the hypothesis that IR directly synchronizes the clock has not been studied in vivo. Here, we used conditional hepatocyte-restricted gene deletion to evaluate the role of IR in the regulation and oscillation of gene expression as well as in the programming of the circadian clock in adult mouse liver.
doi:10.1101/2021.02.05.430014 fatcat:bhe5fil6gbb5ratfnopqout32y

Identification of Signaling Pathways Targeted by the Food Contaminant FB1: Transcriptome and Kinome Analysis of Samples from Pig Liver and Intestine

Marion Régnier, Pascal Gourbeyre, Philippe Pinton, Scott Napper, Joëlle Laffite, Anne-Marie Cossalter, Jean-Denis Bailly, Yannick Lippi, Justine Bertrand-Michel, Ana Paula F.R.L. Bracarense, Hervé Guillou, Nicolas Loiseau (+1 others)
2017 Molecular Nutrition & Food Research  
F., Guillou, H., Loiseau, N. (Auteur de correspondance), Oswald, I. P. (Auteur de correspondance) (2017).  ...  F., Guillou, H., Loiseau, N. (Auteur de correspondance), Oswald, I. P. (Auteur de correspondance) (2017).  ... 
doi:10.1002/mnfr.201700433 pmid:28875582 fatcat:t3ycgidxjzcc3jci52tlli6joy

Liver PPARα is crucial for whole-body fatty acid homeostasis and is protective against NAFLD

Alexandra Montagner, Arnaud Polizzi, Edwin Fouché, Simon Ducheix, Yannick Lippi, Frédéric Lasserre, Valentin Barquissau, Marion Régnier, Céline Lukowicz, Fadila Benhamed, Alison Iroz, Justine Bertrand-Michel (+12 others)
2016 Gut  
doi:10.1136/gutjnl-2015-310798 pmid:26838599 pmcid:PMC4941147 fatcat:efcuobwxrzblhc2xwibbczscpm
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