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Publications of year 2006
Articles in journal or book chapters
  1. 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},
    
    }
    


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. 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.},
    
    }
    


  3. 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},
    
    }
    


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).},
    
    }
    



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Last modified: Wed Feb 8 19:16:22 2023
Author: ferre.


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