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Publications of year 2006
Thesis
  1. Elvis Tombini. Amélioration du diagnostic en détection d'intrusions : étude et application d'une combinaison de méthodes de détection d'intrusions comportementale et par scénarios. PhD thesis, INSA de Rennes, septembre 2006. Note: M. Ducassé, H. Debar et L. Mé, directeurs de thèse.
    @PhDThesis{Tombini06,
    Author={Elvis Tombini},
    Title={Amélioration du diagnostic en détection d'intrusions : étude et application d'une combinaison de méthodes de détection d'intrusions comportementale et par scénarios},
    School={INSA de Rennes},
    Year={2006},
    Month={septembre},
    Note={M. Ducassé, H. Debar et L. Mé, directeurs de thèse}
    }
    


Articles in journal or book chapters
  1. Denis Bechet and Annie Foret. k-Valued Non-Associative Lambek Grammars are learnable from Generalized Functor-Argument Structures. Journal of Theoretical Computer Science, 2006. Note: Vol. 355, 2 (extended version). [PDF] Keyword(s): Grammatical inference, Categorial grammars, Non-associative Lambek calculus, Learning from positive examples, Model of Gold.
    Abstract:
    This paper is concerned with learning categorial grammars from positive examples in the model of Gold. Functor-argument structures (written FA) are usual syntactical decompositions of sentences in sub-components distinguishing the functional parts from the argument parts defined in the case of classical categorial grammars also known as AB-grammars. In the case of non-associative type-logical grammars, we propose a similar notion that we call generalized functor-argument structures and we show that these structures capture the essence of non-associative Lambek (NL) calculus without product. We show that (i) rigid and k-valued non-associative Lambek (NL without product) grammars are learnable from generalized functor-argument structured sentences. We also define subclasses of k-valued grammars in terms of arity. We first show that (ii) for each k and each bound on arity the class of FA-arity bounded k-valued NL languages of FA structures is finite and (iii) that FA-arity bounded k-valued NL grammars are learnable both from strings and from FA structures as a corollary. Result (i) is obtained from (ii); this learnability result (i) is interesting and surprising when compared to other results: in fact we also show that (iv) this class has infinite elasticity. Moreover, these classes are very close to classes like rigid associative Lambek grammars learned from natural deduction structured sentences (that are different and much richer than FA or generalized FA) or to k-valued non-associative Lambek grammars unlearnable from strings or even from bracketed strings. Thus, the class of k-valued non-associative Lambek grammars learned from generalized functor-argument sentences is at the frontier between learnable and unlearnable classes of languages.

    @article{Foret06tcs,
    author = {Denis Bechet and Annie Foret},
    title = { k-Valued Non-Associative {L}ambek Grammars are learnable from Generalized Functor-Argument Structures},
    journal = {Journal of Theoretical Computer Science},
    note = {Vol. 355, 2 (extended version)},
    year = 2006,
    pdf = { http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V1G-4J6230G-2&_user=6068168&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000016487&_version=1&_urlVersion=0&_userid=6068168&md5=1f61f9cb9faf4705a95c1494b7f68602},
    keywords={ Grammatical inference; Categorial grammars; Non-associative Lambek calculus; Learning from positive examples; Model of Gold},
    abstract={ This paper is concerned with learning categorial grammars from positive examples in the model of Gold. Functor-argument structures (written FA) are usual syntactical decompositions of sentences in sub-components distinguishing the functional parts from the argument parts defined in the case of classical categorial grammars also known as AB-grammars. In the case of non-associative type-logical grammars, we propose a similar notion that we call generalized functor-argument structures and we show that these structures capture the essence of non-associative Lambek (NL) calculus without product. 
    
    We show that (i) rigid and k-valued non-associative Lambek (NL without product) grammars are learnable from generalized functor-argument structured sentences. 
    
    We also define subclasses of k-valued grammars in terms of arity. We first show that (ii) for each k and each bound on arity the class of FA-arity bounded k-valued NL languages of FA structures is finite and (iii) that FA-arity bounded k-valued NL grammars are learnable both from strings and from FA structures as a corollary. 
    
    Result (i) is obtained from (ii); this learnability result (i) is interesting and surprising when compared to other results: in fact we also show that (iv) this class has infinite elasticity. Moreover, these classes are very close to classes like rigid associative Lambek grammars learned from natural deduction structured sentences (that are different and much richer than FA or generalized FA) or to k-valued non-associative Lambek grammars unlearnable from strings or even from bracketed strings. Thus, the class of k-valued non-associative Lambek grammars learned from generalized functor-argument sentences is at the frontier between learnable and unlearnable classes of languages. } 
    
    
    }
    


  2. Sébastien Ferré and R. D. King. Finding Motifs in Protein Secondary Structure for Use in Function Prediction. Journal of Computational Biology, 13(3):719-731, 2006. Keyword(s): functional genomics, protein secondary structure, flexible motifs, dichotomic search algorithm.
    @Article{FerKin2006,
    author = {Sébastien Ferré and R. D. King},
    title = {Finding Motifs in Protein Secondary Structure for Use in Function Prediction},
    journal = {Journal of Computational Biology},
    year = {2006},
    volume = {13},
    number = {3},
    pages = {719--731},
    keywords = {functional genomics, protein secondary structure, flexible motifs, dichotomic search algorithm},
    refperso = {200604B},
    
    }
    


  3. Benjamin Sigonneau and Olivier Ridoux. Indexation multiple et automatisée de composants logiciels. Technique et Science Informatiques, 2006. Note: À paraître. [PDF]
    Abstract:
    Software reuse requires that programmers be able to locate reusable components in software repositories. We propose that a general information retrieval framework, which is able to combine arbitrary indexing schemes and called Logical Information Systems, is applied to querying in software repositories. As an illustration, indexing of methods in a package is studied, and three indexing schemes are presented in this framework: a formal scheme, a semi-formal one, and an informal one. The formal one captures object-orientation by combining type isomorphism axioms and inheritance relations. The semi-formal scheme captures naming conventions and the informal one captures keywords in comments. Theory of the formal methods and details on the experiments are presented.
    Annotation:
    Numéro thématique AFADL'04

    @Article{tsi-indexation-composants,
    author = {Sigonneau, Benjamin and Ridoux, Olivier},
    title = {Indexation multiple et automatisée de composants logiciels},
    journal = {Technique et Science Informatiques},
    note = {À paraître},
    year = {2006},
    annote = {Numéro thématique AFADL'04},
    pdf = {http://www.irisa.fr/lande/sigonneau/publications/articles/tsi-preprint.pdf},
    abstract = "Software reuse requires that programmers be able to locate reusable components in software repositories. We propose that a general information retrieval framework, which is able to combine arbitrary indexing schemes and called Logical Information Systems, is applied to querying in software repositories. As an illustration, indexing of methods in a package is studied, and three indexing schemes are presented in this framework: a formal scheme, a semi-formal one, and an informal one. The formal one captures object-orientation by combining type isomorphism axioms and inheritance relations. The semi-formal scheme captures naming conventions and the informal one captures keywords in comments. Theory of the formal methods and details on the experiments are presented." 
    }
    


Conference articles
  1. Olivier Bedel, Sébastien Ferré, Olivier Ridoux, and Erwan Quesseveur. GEOLIS: A Logical Information System for Geographical Data. In Int. Conf. Spatial Analysis and GEOmatics - SAGEO 2006, 2006. [PDF] Keyword(s): logical information systems, geographical data, navigation, querying.
    Abstract:
    Today, the thematic layer is still the prevailling structure in geomatics for handling geographical information. However, the layer model is rigid: it implies partitionning geographical data in predefined categories and using the same description schema for all elements of a layer. Recently, Logical Information Systems (LIS) introduced a new paradigm for information management and retrieval. Using LIS, we propose a more flexible organisation of vectorial geographical data at a thiner level since it is centered on the geographical feature. LIS does not rely on a hierarchical organisation of information, and enable to tightly combine querying and navigation in a same search. In this article, we present a work in progress about the use of LIS model to handle geographical data. In particular, we detail a data model for geographical features and the corresponding querying and navigation model. These models have been implemented in the GEOLIS prototype, which has been used to lead experiments with real data.

    @Inproceedings{BFRQ2006,
    author = {Olivier Bedel and Sébastien Ferré and Olivier Ridoux and Erwan Quesseveur},
    title = {{GEOLIS}: A Logical Information System for Geographical Data},
    booktitle = {Int. Conf. Spatial Analysis and GEOmatics - SAGEO 2006},
    year = {2006},
    keywords = {logical information systems, geographical data, navigation, querying},
    isbn = {2-9526014-1-0},
    pdf = {http://www.irisa.fr/LIS/ferre/papers/sageo2006.pdf},
    abstract = {Today, the thematic layer is still the prevailling structure in geomatics for handling geographical information. However, the layer model is rigid: it implies partitionning geographical data in predefined categories and using the same description schema for all elements of a layer. Recently, Logical Information Systems (LIS) introduced a new paradigm for information management and retrieval. Using LIS, we propose a more flexible organisation of vectorial geographical data at a thiner level since it is centered on the geographical feature. LIS does not rely on a hierarchical organisation of information, and enable to tightly combine querying and navigation in a same search. In this article, we present a work in progress about the use of LIS model to handle geographical data. In particular, we detail a data model for geographical features and the corresponding querying and navigation model. These models have been implemented in the GEOLIS prototype, which has been used to lead experiments with real data.},
    
    }
    


  2. Olivier Bedel, Olivier Ridoux, and Erwan Quesseveur. Combining Logical Information System and OpenGIS Tools for Geographical Data Exploration. In Int. Conf. Free and OpenSource Sofware for Geoinformatics, september 2006. [WWW] Keyword(s): logical information system, GIS, graphical data.
    @InProceedings{BedRidQue2006,
    author = {Olivier Bedel and Olivier Ridoux and Erwan Quesseveur},
    title = {Combining Logical Information System and {OpenGIS} Tools for Geographical Data Exploration},
    month = {september},
    year = {2006},
    booktitle = {Int. Conf. Free and OpenSource Sofware for Geoinformatics},
    url = {http://www.foss4g2006.org/contributionDisplay.py?contribId=131&sessionId=51&confId=1},
    keywords = {logical information system, GIS, graphical data},
    
    }
    


  3. Peggy Cellier, Sébastien Ferré, Olivier Ridoux, and Mireille Ducassé. An Algorithm to Find Frequent Concepts of a Formal Context with Taxonomy. In S. Ben Yahia and E. Mephu Nguifo, editors, Int. Conf. Concept Lattices and Their Applications, LNAI 4932, pages 243-248, 2006. Springer. [PDF] Keyword(s): concept analysis, algorithm, taxonomy.
    Abstract:
    Formal Concept Analysis (FCA) considers attributes as a non-ordered set. This is appropriate when the data set is not structured. When an attribute taxonomy exists, existing techniques produce a completed context with all attributes deduced from the taxonomy. Usual algorithms can then be applied on the completed context for finding frequent concepts, but the results systematically contain redundant information. This article describes an algorithm which allows the frequent concepts of a formal context with taxonomy to be computed. It works on a non-completed context and uses the taxonomy information when needed. The results avoid the redundancy problem with equivalent performance.

    @InProceedings{CFRD2006,
    author = {Peggy Cellier and Sébastien Ferré and Olivier Ridoux and Mireille Ducassé},
    title = {An Algorithm to Find Frequent Concepts of a Formal Context with Taxonomy},
    booktitle = {Int. Conf. Concept Lattices and Their Applications},
    pages = {243--248},
    year = {2006},
    editor = {S. Ben~Yahia and E. Mephu~Nguifo},
    publisher = {Springer},
    series = {LNAI 4932},
    keywords = {concept analysis, algorithm, taxonomy},
    pdf = {http://www.irisa.fr/LIS/ferre/papers/cla2006.pdf},
    abstract = {Formal Concept Analysis (FCA) considers attributes as a non-ordered set. This is appropriate when the data set is not structured. 
    
    When an attribute taxonomy exists, existing techniques produce a completed context with all attributes deduced from the taxonomy. Usual algorithms can then be applied on the completed context for finding frequent concepts, but the results systematically contain redundant information. 
    
    This article describes an algorithm which allows the frequent concepts of a formal context with taxonomy to be computed. It works on a non-completed context and uses the taxonomy information when needed. The results avoid the redundancy problem with equivalent performance.},
    
    }
    


  4. Sébastien Ferré. Negation, Opposition, and Possibility in Logical Concept Analysis.. In Rokia Missaoui and Jürg Schmid, editors, Int. Conf. Formal Concept Analysis, LNCS 3874, pages 130-145, 2006. Springer. Keyword(s): logic, concept analysis, epistemic logic, all i know.
    @inproceedings{Fer2006b,
    author = {Sébastien Ferré},
    title = {Negation, Opposition, and Possibility in Logical Concept Analysis.},
    booktitle = {Int. Conf. Formal Concept Analysis},
    editor = {Rokia Missaoui and Jürg Schmid},
    series = {LNCS 3874},
    publisher = {Springer},
    year = {2006},
    pages = {130-145},
    keywords = {logic, concept analysis, epistemic logic, all i know},
    
    }
    


  5. Yoann Padioleau, Benjamin Sigonneau, and Olivier Ridoux. LISFS: a logical information system as a file system (demo). In Leon J. Osterweil, H. Dieter Rombach, and Mary Lou Soffa, editors, Int. Conf. Software Engineering, pages 803-806, 2006. ACM. Keyword(s): demo.
    @inproceedings{LISFS2006,
    author = {Yoann Padioleau and Benjamin Sigonneau and Olivier Ridoux},
    title = {{LISFS}: a logical information system as a file system (demo)},
    booktitle = {Int. Conf. Software Engineering},
    year = {2006},
    pages = {803-806},
    editor = {Leon J. Osterweil and H. Dieter Rombach and Mary Lou Soffa},
    publisher = {ACM},
    keywords = {demo},
    
    }
    


  6. Eric Poupard, Denis Bechet, and Annie Foret. Categorial Grammar Acquisition from a French Treebank. In Actes de la Conférence d'APprentissage 2006 (CAP'06), 2006. Note: (Poster).
    @InProceedings{Foret06a,
    author = {Eric Poupard and Denis Bechet and Annie Foret},
    title = {Categorial Grammar Acquisition from a French Treebank},
    booktitle = {Actes de la Conférence d'APprentissage 2006 (CAP'06)},
    year = 2006,
    note = {(Poster)} 
    }
    


  7. Benjamin Sigonneau and Olivier Ridoux. Software Engineering Applications of Logic File System -- Application to Automated Multi-Criteria Indexation of Software Components. In ICSE Work. Mining Software Repositories, 2006.
    @InProceedings{SigRid2006a,
    author = {Benjamin Sigonneau and Olivier Ridoux},
    title = {Software Engineering Applications of Logic File System -- Application to Automated Multi-Criteria Indexation of Software Components},
    booktitle = {ICSE Work. Mining Software Repositories},
    year = {2006},
    
    }
    


  8. Alexandre Vautier, Marie-Odile Cordier, Mireille Ducassé, and René Quiniou. Agrégation d'alarmes faiblement structurées. In Actes de l'atelier ``Fouille de données temporelles'' associé aux 6es Journées Francophones ``Extraction et de Gestion des Connaissances'', Janvier 2006. [WWW]
    Abstract:
    La contribution principale de ce document est une approche plaçant l'opérateur au coeur de l'analyse de journaux d'alarmes faiblement structurées en lui permettant d'utiliser ce qu'il sait, même si ses connaissances sont partielles, et sans le submerger d'informations. Des motifs temporels structurés sont extraits par agrégation d'alarmes généralisées et corrélation se basant sur la date des alarmes et sur la similarité d'attributs autres que la date. L'approche est appliquée aux alarmes produites par un concentrateur VPN (Virtual Private Network). Une étude de cas montre comment 5000 d'alarmes peuvent être regroupées en 50 motifs.

    @InProceedings{vautier06,
    Author={Alexandre Vautier and Marie-Odile Cordier and Mireille Ducassé and René Quiniou},
    Title={Agrégation d'alarmes faiblement structurées},
    BookTitle={Actes de l'atelier ``Fouille de données temporelles'' associé aux 6es Journées Francophones ``Extraction et de Gestion des Connaissances''},
    Year={2006},
    Month={Janvier},
    url = {http://www.irisa.fr/dream/Pages_Pros/Alexandre.Vautier/publis/egc_06_vpn.pdf},
    Abstract={La contribution principale de ce document est une approche plaçant l'opérateur au coeur de l'analyse de journaux d'alarmes faiblement structurées en lui permettant d'utiliser ce qu'il sait, même si ses connaissances sont partielles, et sans le submerger d'informations. Des motifs temporels structurés sont extraits par agrégation d'alarmes généralisées et corrélation se basant sur la date des alarmes et sur la similarité d'attributs autres que la date. L'approche est appliquée aux alarmes produites par un concentrateur VPN (Virtual Private Network). Une étude de cas montre comment 5000 d'alarmes peuvent être regroupées en 50 motifs.}
    }
    


Internal reports
  1. Sébastien Ferré and Olivier Ridoux. Logic Functors: A Toolbox of Components for Building Customized and Embeddable Logics. Research Report RR-5871, Irisa, March 2006. [WWW] Keyword(s): logic, components, modules and functors, theorem provers, type checking, application developpement.
    Abstract:
    Logic Functors form a framework for specifying new logics, and deriving automatically theorem provers and consistency/completeness diagnoses. Atomic functors are logics for manipulating symbols and concrete domains, while other functors are logic transformers that may add connectives or recursive structures, or may alter the semantics of a logic. The semantic structure of the framework is model theoretic as opposed to the verifunctional style often used in classical logic. This comes close to the semantics of description logics, and we show indeed that the logic~${\cal ALC}$ can be rebuilt using logic functors. This offers the immediate advantage that variants of~${\cal ALC}$ can be explored and implemented almost for free. This report comes with extensive appendices describing in detail a toolbox of logic functors (definitions, algorithms, theorems, and proofs).

    @TechReport{FerRid2006a,
    author = {Sébastien Ferré and Olivier Ridoux},
    title = {Logic Functors: A Toolbox of Components for Building Customized and Embeddable Logics},
    institution = {Irisa},
    year = {2006},
    type = {Research Report},
    number = {RR-5871},
    pages = {103 p.},
    month = mar,
    url = {http://www.inria.fr/rrrt/rr-5871.html},
    keywords = {logic, components, modules and functors, theorem provers, type checking, application developpement},
    abstract = {Logic Functors form a framework for specifying new logics, and deriving automatically theorem provers and consistency/completeness diagnoses. Atomic functors are logics for manipulating symbols and concrete domains, while other functors are logic transformers that may add connectives or recursive structures, or may alter the semantics of a logic. The semantic structure of the framework is model theoretic as opposed to the verifunctional style often used in classical logic. This comes close to the semantics of description logics, and we show indeed that the logic~${\cal ALC}$ can be rebuilt using logic functors. This offers the immediate advantage that variants of~${\cal ALC}$ can be explored and implemented almost for free. This report comes with extensive appendices describing in detail a toolbox of logic functors (definitions, algorithms, theorems, and proofs).},
    
    }
    


  2. Alexandre Vautier, Marie-Odile Cordier, Mireille Ducassé, and René Quiniou. Visualization of Internet Flow Records. Publication Interne 1828, IRISA, november 2006. Note: CURAR deliverable - CRE France Telecom R & D.
    @TechReport{creFT2006,
    Title = {Visualization of Internet Flow Records},
    Author = {Alexandre Vautier and Marie-Odile Cordier and Mireille Ducassé and René Quiniou},
    Institution={IRISA},
    Year = {2006},
    Type={Publication Interne},
    Number = {1828},
    Month={november },
    Note={CURAR deliverable - CRE France Telecom R \& D}
    }
    



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Last modified: Tue Mar 20 18:32:22 2018
Author: ferre.


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