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 Publications of year 2006
 Articles in journal or book chapters
1. S. 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): dichotomic search algorithm, flexible motifs, protein secondary structure, functional genomics.
@article{FerKin2006,
author = {Ferré, S. and King, R. D.},
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 = {dichotomic search algorithm, flexible motifs, protein secondary structure, functional genomics},

}


 Conference articles
1. O. Bedel, S. Ferré, O. Ridoux, and E. Quesseveur. GEOLIS: A Logical Information System for Geographical Data. In Int. Conf. Spatial Analysis and GEOmatics (SAGEO), 2006. [PDF] Keyword(s): querying, navigation, geographical data, logical information systems.
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 = {Bedel, O. and Ferré, S. and Ridoux, O. and Quesseveur, E.},
title = {{GEOLIS}: A Logical Information System for Geographical Data},
booktitle = {Int. Conf. Spatial Analysis and GEOmatics (SAGEO)},
year = {2006},
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.},
keywords = {querying, navigation, geographical data, logical information systems},

}


2. P. Cellier, S. Ferré, O. Ridoux, and M. 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, pages 243-248, 2006. Faculté des Sciences de Tunis. [PDF] Keyword(s): taxonomy, algorithm, concept analysis.
@inproceedings{CFRD2006,
author = {Cellier, P. and Ferré, S. and Ridoux, O. and Ducassé, M.},
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 = {Faculté des Sciences de Tunis},
isbn = {978-9973-61-481-0},
pdf = {http://www.irisa.fr/LIS/ferre/papers/cla2006.pdf},
keywords = {taxonomy, algorithm, concept analysis},

}


3. S. Ferré. Negation, Opposition, and Possibility in Logical Concept Analysis.. In Rokia Missaoui and J rg Schmid, editors, Int. Conf. Formal Concept Analysis, LNCS 3874, pages 130-145, 2006. Springer. [PDF] Keyword(s): all i know, epistemic logic, concept analysis, logic.
@inproceedings{Fer2006b,
author = {Ferré, S.},
title = {Negation, Opposition, and Possibility in Logical Concept Analysis.},
booktitle = {Int. Conf. Formal Concept Analysis},
editor = {Rokia Missaoui and J~rg Schmid},
series = {LNCS 3874},
publisher = {Springer},
year = {2006},
pages = {130-145},
pdf = {http://www.irisa.fr/LIS/ferre/papers/icfca2006.pdf},
keywords = {all i know, epistemic logic, concept analysis, logic},

}


 Internal reports
1. S. Ferré and O. Ridoux. Logic Functors: A Toolbox of Components for Building Customized and Embeddable Logics. Technical report, INRIA, March 2006. [WWW] Keyword(s): application developpement, type checking, theorem provers, modules and functors, components, logic.
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 = {Ferré, S. and Ridoux, O.},
title = {Logic Functors: A Toolbox of Components for Building Customized and Embeddable Logics},
institution = {INRIA},
year = {2006},
number = {},
pages = {103 p.},
month = {mar},
url = {http://www.inria.fr/rrrt/rr-5871.html},
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).},
keywords = {application developpement, type checking, theorem provers, modules and functors, components, logic},

}


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