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2. An Experimental Survey on Big Data Frameworks

Author

Inoubli, Wissem, Aridhi, Sabeur, Mezni, Haithem, Maddouri, Mondher, and Nguifo, Engelbert Mephu

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

Recently, increasingly large amounts of data are generated from a variety of sources. Existing data processing technologies are not suitable to cope with the huge amounts of generated data. Yet, many research works focus on Big Data, a buzzword referring to the processing of massive volumes of (unstructured) data. Recently proposed frameworks for Big Data applications help to store, analyze and process the data. In this paper, we discuss the challenges of Big Data and we survey existing Big Data frameworks. We also present an experimental evaluation and a comparative study of the most popular Big Data frameworks. This survey is concluded with a presentation of best practices related to the use of the studied frameworks in several application domains such as machine learning, graph processing and real-world applications.

Published
2016
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4. Multiple instance learning for sequence data with across bag dependencies

Author

Zoghlami, Manel, Aridhi, Sabeur, Maddouri, Mondher, and Nguifo, Engelbert Mephu

Subjects
Computer Science - Machine Learning
Abstract

In Multiple Instance Learning (MIL) problem for sequence data, the instances inside the bags are sequences. In some real world applications such as bioinformatics, comparing a random couple of sequences makes no sense. In fact, each instance may have structural and/or functional relations with instances of other bags. Thus, the classification task should take into account this across bag relation. In this work, we present two novel MIL approaches for sequence data classification named ABClass and ABSim. ABClass extracts motifs from related instances and use them to encode sequences. A discriminative classifier is then applied to compute a partial classification result for each set of related sequences. ABSim uses a similarity measure to discriminate the related instances and to compute a scores matrix. For both approaches, an aggregation method is applied in order to generate the final classification result. We applied both approaches to solve the problem of bacterial Ionizing Radiation Resistance prediction. The experimental results of the presented approaches are satisfactory.

Published
2016
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6. A large-scale and fault-tolerant approach of subgraph mining using density-based partitioning

Author

Aridhi, Sabeur, d'Orazio, Laurent, Maddouri, Mondher, and Nguifo, Engelbert Mephu

Subjects
Computer Science - Databases, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Social and Information Networks
Abstract

Recently, graph mining approaches have become very popular, especially in domains such as bioinformatics, chemoinformatics and social networks. In this scope, one of the most challenging tasks is frequent subgraph discovery. This task has been motivated by the tremendously increasing size of existing graph databases. Since then, an important problem of designing efficient and scaling approaches for frequent subgraph discovery in large clusters, has taken place. However, failures are a norm rather than being an exception in large clusters. In this context, the MapReduce framework was designed so that node failures are automatically handled by the framework. In this paper, we propose a large-scale and fault-tolerant approach of subgraph mining by means of a density-based partitioning technique, using MapReduce. Our partitioning aims to balance computation load on a collection of machines. We experimentally show that our approach decreases significantly the execution time and scales the subgraph discovery process to large graph databases., Comment: The paper is under reviewing and we want to cancel the submission. Thank you for your understanding

Published
2012
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8. Feature extraction in protein sequences classification : a new stability measure

Author

Saidi, Rabie, Aridhi, Sabeur, Maddouri, Mondher, and Nguifo, Engelbert Mephu

Subjects
Computer Science - Learning, Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Quantitative Methods
Abstract

Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a subsequence that can be seen as a property (or attribute) characterizing the sequence. Hence, we obtain an object-property table where objects are sequences and properties are motifs extracted from sequences. This output can be used to apply standard machine learning tools to perform data mining tasks such as classification. Several previous works have described feature extraction methods for bio-sequence classification, but none of them discussed the robustness of these methods when perturbing the input data. In this work, we introduce the notion of stability of the generated motifs in order to study the robustness of motif extraction methods. We express this robustness in terms of the ability of the method to reveal any change occurring in the input data and also its ability to target the interesting motifs. We use these criteria to evaluate and experimentally compare four existing extraction methods for biological sequences., Comment: The paper has been accepted by the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB) 2012. We want to cancel the submission because of the double entries of the paper in DBLP. Thank you for your understanding

Published
2012
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14. Diversity Analysis on Boosting Nominal Concepts

Author

Meddouri, Nida, Khoufi, Héla, Maddouri, Mondher Sadok, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Tan, Pang-Ning, editor, Chawla, Sanjay, editor, Ho, Chin Kuan, editor, and Bailey, James, editor

Published
2012
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15. Adaptive Learning of Nominal Concepts for Supervised Classification

Author

Meddouri, Nida, Maddouri, Mondher, Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Pandu Rangan, C., Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Goebel, Randy, Siekmann, Jörg, Wahlster, Wolfgang, Setchi, Rossitza, editor, Jordanov, Ivan, editor, Howlett, Robert J., editor, and Jain, Lakhmi C., editor

Published
2010
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16. Boosting Formal Concepts to Discover Classification Rules

Author

Meddouri, Nida, Maddouri, Mondher, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Chien, Been-Chian, editor, Hong, Tzung-Pei, editor, Chen, Shyi-Ming, editor, and Ali, Moonis, editor

Published
2009
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18. On Semantic Properties of Interestingness Measures for Extracting Rules from Data

Author

Maddouri, Mondher, Gammoudi, Jamil, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Rangan, C. Pandu, editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Beliczynski, Bartlomiej, editor, Dzielinski, Andrzej, editor, Iwanowski, Marcin, editor, and Ribeiro, Bernardete, editor

Published
2007
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20. DFC

Author

Meddouri, Nida, primary, Khoufi, Hela, additional, and Maddouri, Mondher, additional

Published
2021
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21. Catégorisation des méthodes de classification fondées sur l’Analyse de Concepts Formels

Author

AZIBI, Hayfa, Meddouri, Nida, Maddouri, Mondher, Laboratoire d'Informatique, Programmation, Algorithmique et Heuristique (LIPAH), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Equipe CODAG - Laboratoire GREYC - UMR6072, Groupe de Recherche en Informatique, Image, Automatique et Instrumentation de Caen (GREYC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), College of Business, Khulais campus, University of Jeddah, and Sébastien Ferré

Subjects
Big data, Analyse de concepts formels, Classification supervisée, Apprentissage automatique, Fouille de données, Intelligence artificielle, Méthodes d’ensemble, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

International audience; Les deux dernières décennies ont vu le développement de plusieurs méthodes de classification basées sur l’analyse de concepts formels (ACF). Dans cet article, nous présentons trois catégories de méthodes de classification basées sur l’ACF : des approches basées sur un classifieur unique, des approches basées sur une combinaison de classifieurs générés par une méthode d’ensemble et des approches basées sur un classifieur distribué.

Published
2020

22. A Novel Scalable Clustering Method for Distributed Networks

Author

Inoubli, Wissm, Aridhi, Sabeur, Mezni, Haithem, Maddouri, Mondher, Mephu Nguifo, Engelbert, Université de Tunis El Manar (UTM), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria), Strategies for Modelling and ARtificial inTelligence Laboratory (SMART-LAB), Université de Tunis, University of Jeddah (University of Jeddah), Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and inoubli, wissem

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Structural graph clustering, Community detection, [INFO.INFO-DC] Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], Graph processing, Outliers detection, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], hubs detection, Big Graph Analysis, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

Graph clustering is one of the key techniques to understand structures that are present in networks. In addition to clusters, bridges and outliers detection is also a critical task as it plays an important role in the analysis of networks. Recently, several graph clustering methods are developed and used in multiple application domains such as biological network analysis, recommendation systems and community detection. Most of these algorithms are based on the structural clustering algorithm. Yet, this kind of algorithm is based on the structural similarity, this later requires to parse all graph ' edges in order to compute the structural similarity. However, the height needs of similarity computing make this algorithm more adequate for small graphs, without significant support to deal with large-scale networks. In this paper, we propose a novel distributed graph clustering algorithm based on structural graph clustering. The experimental results show the efficiency in terms of running time of the proposed algorithm in large networks compared to existing structural graph clustering methods.

Published
2020

23. Un algorithme distribué pour le clustering de grands graphes

Author

Inoubli, Wissem, Aridhi, Sabeur, Mezni, Haithem, Maddouri, Mondher, Nguifo, Engelbert, Laboratoire d'Informatique, Programmation, Algorithmique et Heuristique (LIPAH), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université de Jendouba (UJ), Taibah University, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Aridhi, Sabeur, Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-DC] Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

International audience; Le clustering de graphes est l'une des techniques clés qui permet de comprendre les structures présentes dans les données de graphe. La détection des clusters et l'identification des ponts et des bruit sont également des tâches critiques car elles jouent un rôle important dans l'analyse des graphes. Récem-ment, plusieurs algorithmes de clustering de graphes ont été proposés et utilisés dans de nombreux domaines d'application. La plupart de ces algorithmes sont basés sur les algorithmes de clustering structurel. Néanmoins, ces derniers ont été conçus pour le traitement des petits graphes. D'où, leur performance peut se dégrader dans le cas des graphes larges qui imposent des défis supplémentaires. Dans cet article, nous proposons DSCAN, un algorithme distribué de clustering de graphes qui est basé sur le clustering structurel. Notre algorithme est im-plimenté sur la base de framework de traitement de grands graphes BLADYG. L'évaluation expérimentale de DSCAN a montré son efficacité et sa compétiti-vité pour le traitement de grands graphes.

Published
2020

32. An experimental survey on big data frameworks (Highlight paper)

Author

Inoubli, Wissem, Aridhi, Sabeur, Mezni, Haithem, Maddouri, Mondher, Nguifo, Engelbert, Université de Tunis El Manar (UTM), Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université de Jendouba (UJ), Taibah University, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), and SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

Subjects
Spark, Samza, Big data, HDFS, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Batch/stream processing, Hadoop, Storm, MapReduce, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Flink
Abstract

International audience; Recently, increasingly large amounts of data are generated from a variety of sources. Existing data processing technologies are not suitable to cope with the huge amounts of generated data. Yet, many research works focus on Big Data, a buzzword referring to the processing of massive volumes of (unstructured) data. Recently proposed frameworks for Big Data applications help to store, analyze and process the data. In this paper, we discuss the challenges of Big Data and we survey existing Big Data frameworks. We also present an experimental evaluation and a comparative study of the most popular Big Data frameworks with several representative batch.

Published
2018

33. ABClass : Une approche d'apprentissage multi-instances pour les séquences

Author

Zoghlami, Manel, Aridhi, Sabeur, Maddouri, Mondher, Nguifo, Engelbert, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, Programmation, Algorithmique et Heuristique (LIPAH), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Jeddah, and Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)

Subjects
prédiction de la résistance aux rayonnements ionisants chez les bactéries, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], multiple instance learning, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], apprentissage multi-instances, prediction of bacterial ionizing radiation resistance, séquences protéiques, protein sequences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

National audience; In Multiple Instance Learning (MIL) problem for sequence data, the learning data consist of a set of bags where each bag contains a set of instances/sequences. In some real world applications such as bioinformatics comparing a random couple of sequences makes no sense. In fact, each instance of each bag may have structural and/or functional relationship with other instances in other bags. Thus, the classification task should take into account the relation between semantically related instances across bags. In this paper, we present ABClass, a novel MIL approach for sequence data classification. Each sequence is represented by one vector of attributes extracted from the set of related instances. For each sequence of the unknown bag, a discriminative classifier is applied in order to compute a partial classification result. Then, an aggregation method is applied in order to generate the final result. We applied ABClass to solve the problem of bacterial Ionizing Radiation Resistance (IRR) prediction. The experimental results were satisfactory.; Dans le cas du problème de l'apprentissage multi-instances (MI) pour les séquences, les données d'apprentissage consistent en un ensemble de sacs où chaque sac contient un ensemble d'instances/séquences. Dans certaines applications du monde réel, comme la bioinformatique, comparer un couple aléatoire de séquences n'a aucun sens. En fait, chaque instance de chaque sac peut avoir une relation structurelle et/ou fonctionnelle avec d'autres instances dans d'autres sacs. Ainsi, la tâche de classification doit prendre en compte la relation entre les instances sémantiquement liées à travers les sacs. Dans cet article, nous présentons ABClass, une nouvelle approche de classification MI des séquences. Chaque séquence est représentée par un vecteur d'attributs extraits à partir de l'en-semble des instances qui lui sont liées. Pour chaque séquence du sac à prédire, un classifieur discriminant est appliqué afin de calculer un résultat de classification partiel. Ensuite, une méthode d'agrégation est appliquée afin de générer le résultat final. Nous avons appliqué ABClass pour résoudre le problème de la prédiction de la résistance aux rayonnements ionisants (RRI) chez les bactéries. Les résultats expérimentaux sont satisfaisants.

Published
2018

34. An Overview of in Silico Methods for the Prediction of Ionizing Radiation Resistance in Bacteria

Author

Zoghlami, Manel, Aridhi, Sabeur, Maddouri, Mondher, Mephu Nguifo, Engelbert, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, Programmation, Algorithmique et Heuristique (LIPAH), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Taibah University, University of Jeddah, Tamar Reeve, Ecole Nationale Supérieure des Mines de St Etienne-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes ( LIMOS ), Centre National de la Recherche Scientifique ( CNRS ) -Sigma CLERMONT ( Sigma CLERMONT ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)

Subjects
bacterial ionizing radiation resistance, phenotype prediction, multiple instance learning, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [ INFO.INFO-AI ] Computer Science [cs]/Artificial Intelligence [cs.AI], ComputingMilieux_MISCELLANEOUS, [ INFO.INFO-LG ] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

International audience; Ionizing-radiation-resistant bacteria (IRRB) could be used for biore-mediation of radioactive wastes and in the therapeutic industry. Limited computational works are available for the prediction of bacterial ionizing radiation resistance (IRR). In this chapter, we present some works that study the causes of the high resistance of IRRB to ionizing radiation. Then we focus on presenting in silico approaches that use protein sequences of bacteria in order to predict if an unknown bacterium belongs to IRRB or ionizing-radiation-sensitive bacteria (IRSB). These approaches formulate the problem of predicting bacterial IRR as a multiple instance learning (MIL) problem where bacteria represent the bags and * Corresponding Author: manel.zoghlami@gmail.com. 2 Manel Zoghlami, Sabeur Aridhi, Mondher Maddouri et al. primary structure of basal DNA repair proteins of each bacterium represent the instances inside the bags. We also present a formulation of the problem of MIL in sequence data and explain how it could be used to solve the problem of IRR prediction in bacteria. A brief comparison of the presented approaches is provided.

Published
2018

35. ABClass : Une approche d'apprentissage multi-instances pour les séquences(ABClass: A multiple instance learning approach for sequence data)

Author

Zoghlami, Manel, Aridhi, Sabeur, Maddouri, Mondher, Mephu Nguifo, Engelbert, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and DOREAU, Bastien

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Published
2018

37. Protein sequences classification by means of feature extraction with substitution matrices

Author

Saidi Rabie, Maddouri Mondher, and Mephu Nguifo Engelbert

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background This paper deals with the preprocessing of protein sequences for supervised classification. Motif extraction is one way to address that task. It has been largely used to encode biological sequences into feature vectors to enable using well-known machine-learning classifiers which require this format. However, designing a suitable feature space, for a set of proteins, is not a trivial task. For this purpose, we propose a novel encoding method that uses amino-acid substitution matrices to define similarity between motifs during the extraction step. Results In order to demonstrate the efficiency of such approach, we compare several encoding methods using some machine learning classifiers. The experimental results showed that our encoding method outperforms other ones in terms of classification accuracy and number of generated attributes. We also compared the classifiers in term of accuracy. Results indicated that SVM generally outperforms the other classifiers with any encoding method. We showed that SVM, coupled with our encoding method, can be an efficient protein classification system. In addition, we studied the effect of the substitution matrices variation on the quality of our method and hence on the classification quality. We noticed that our method enables good classification accuracies with all the substitution matrices and that the variances of the obtained accuracies using various substitution matrices are slight. However, the number of generated features varies from a substitution matrix to another. Furthermore, the use of already published datasets allowed us to carry out a comparison with several related works. Conclusions The outcomes of our comparative experiments confirm the efficiency of our encoding method to represent protein sequences in classification tasks.

Published
2010
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38. DFC: A Performant Dagging Approach of Classification Based on Formal Concept

Author

Meddouri, Nida, Khoufi, Hela, and Maddouri, Mondher

Abstract

Knowledge discovery data (KDD) is a research theme evolving to exploit a large data set collected every day from various fields of computing applications. The underlying idea is to extract hidden knowledge from a data set. It includes several tasks that form a process, such as data mining. Classification and clustering are data mining techniques. Several approaches were proposed in classification such as induction of decision trees, Bayes net, support vector machine, and formal concept analysis (FCA). The choice of FCA could be explained by its ability to extract hidden knowledge. Recently, researchers have been interested in the ensemble methods (sequential/parallel) to combine a set of classifiers. The combination of classifiers is made by a vote technique. There has been little focus on FCA in the context of ensemble learning. This paper presents a new approach to building a single part of the lattice with best possible concepts. This approach is based on parallel ensemble learning. It improves the state-of-the-art methods based on FCA since it handles more voluminous data.

Published
2021
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39. A multiple instance learning approach for sequence data with across bag dependencies

Author

Zoghlami, Manel, Aridhi, Sabeur, Sghaier, Haïtham, Maddouri, Mondher, Mephu Nguifo, Engelbert, DOREAU, Bastien, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Published
2016

40. Cost models for distributed pattern mining in the cloud: application to graph patterns

Author

Aridhi, Sabeur, d'Orazio, Laurent, Maddouri, Mondher, Mephu Nguifo, Engelbert, Dorazio, Laurent, Nguifo, Engelbert Mephu, University of Trento [Trento], Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Université de Tunis El Manar (UTM), and Taibah University

Subjects
[INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO]Computer Science [cs]
Abstract

International audience; Recently, distributed pattern mining approaches have become very popular, especially in certain domains such as bioinformatics, chemoinformatics and social networks. In most cases, the distribution of the pattern mining process generates a loss of information in the output results. Reducing this loss may affect the performance of the distributed approach and thus, the monetary cost when using cloud environments. In this context, cost models are needed to help selecting the best parameters of the used approach in order to achieve a better performance especially in the cloud. In this paper, we address the multi-criteria optimization problem of tuning thresholds related to distributed frequent pattern mining in cloud computing environment while optimizing the global monetary cost of storing and querying data in the cloud. To achieve this goal, we design cost models for managing and mining graph data with large scale pattern mining framework over a cloud architecture. We define four objective functions, with respect to the needs of customers. We present an experimental validation of the proposed cost models in the case of distributed subgraph mining in the cloud.

Published
2015

43. Etude de stabilité de méthodes d'extraction de motifs à partir des séquences protéiques

Author

Saidi, Rabie, Aridhi, Sabeur, Maddouri, Mondher, Mephu Nguifo, Engelbert, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and DOREAU, Bastien

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Published
2010

45. A Hybrid Approach of Boosting Against Noisy Data

Author

Stéphane Lallich, Nicolas Nicoloyannis, Emna Bahri, and Maddouri Mondher

Subjects
Boosting (machine learning), Computer science, business.industry, media_common.quotation_subject, Word error rate, Overfitting, Machine learning, computer.software_genre, Hybrid approach, Exponential function, Voting, AdaBoost, Artificial intelligence, business, computer, Classifier (UML), media_common
Abstract

To reduce error in generalization, a great number of work is carried out on the classifiers aggregation methods in order to improve generally, by voting techniques, the performance of a single classifier. Among these methods of aggregation, we find the Boosting which is most practical thanks to the adaptive update of the distribution of the examples aiming at increasing in an exponential way the weight of the badly classified examples. However, this method is blamed because of overfitting, and the convergence speed especially with noise. In this study, we propose a new approach and modifications carried out on the algorithm of AdaBoost. We will demonstrate that it is possible to improve the performance of the Boosting, by exploiting assumptions generated with the former iterations to correct the weights of the examples. An experimental study shows the interest of this new approach, called hybrid approach.

Published
2009

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