Clustering optimal de gènes fondé sur une mesure de similarité sémantique
Identifieur interne : 001271 ( Main/Merge ); précédent : 001270; suivant : 001272Clustering optimal de gènes fondé sur une mesure de similarité sémantique
Auteurs : Rachid Hafiane [France] ; Malika Smaïl-Tabbone [France] ; Marie-Dominique Devignes [France] ; Salvatore Tabbone [France]Source :
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Abstract
In various application domains of knowledge extraction or information retrieval, objects are not represented as feature vectors in a vector space but as a pairwise similarity matrix. In molecular biology, such a similarity measure either captures the object structure (e.g. molecules, proteins as sequences of amino acids) or the semantics of their description (genes or diseases described with ontology terms). The numerous existing similarity measures often violate metricity properties. This is the case of our IntelliGO semantic similarity defined as a generalized cosine between two vectors of Gene Ontology terms (Gene Ontology is a directed acyclic graph representing the semantic relationship between terms). Specific techniques exist for embedding pairwise data into Euclidian space for facilitating subsequent clustering of the objects. We report in this paper comparative gene clustering with and without embedding using the Intelligo measure and benchmarks. As for the clustering algorithm, we use an implementation of the C-means algorithm taking as input either a distance" matrix or a set of vectors. We evaluate the clustering quality and discuss the results.
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BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-300291" type="indirect"><org type="institution" xml:id="struct-300291" status="OLD"><orgName>Université Henri Poincaré - Nancy 1</orgName><orgName type="acronym">UHP</orgName><date type="end">2011-12-31</date><desc><address><addrLine>24-30 rue Lionnois, BP 60120, 54 003 NANCY cedex, France</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-300292" type="indirect"><org type="institution" xml:id="struct-300292" status="OLD"><orgName>Université Nancy 2</orgName><date type="end">2011-12-31</date><desc><address><addrLine>91 avenue de la Libération, BP 454, 54001 Nancy cedex</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-300293" type="indirect"><org type="institution" xml:id="struct-300293" status="OLD"><orgName>Institut National Polytechnique de Lorraine</orgName><orgName type="acronym">INPL</orgName><date type="end">2011-12-31</date><desc><address><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-2496" type="direct"><org type="laboratory" xml:id="struct-2496" status="OLD"><orgName>INRIA Lorraine</orgName><desc><address><addrLine>615 rue du Jardin Botanique 54600 Villers-lès-Nancy</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/centre-de-recherche-inria/nancy-grand-est</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université Nancy 2</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Institut national polytechnique de Lorraine</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName></affiliation></author><author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name><affiliation wicri:level="1"><hal:affiliation type="researchteam" xml:id="struct-205125" status="VALID"><idno type="RNSR">200818291B</idno><orgName>Knowledge representation, reasonning</orgName><orgName type="acronym">ORPAILLEUR</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/orpailleur</ref></desc><listRelation><relation active="#struct-129671" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-423086" type="direct"></relation><relation active="#struct-206040" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation><tutelles><tutelle active="#struct-129671" type="direct"><org type="laboratory" xml:id="struct-129671" status="VALID"><idno type="RNSR">198618246Y</idno><orgName>INRIA Nancy - 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CS 25233 - 54052 Nancy cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-lorraine.fr/</ref></desc></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université de Lorraine</orgName></affiliation></author><author><name sortKey="Tabbone, Salvatore" sort="Tabbone, Salvatore" uniqKey="Tabbone S" first="Salvatore" last="Tabbone">Salvatore Tabbone</name><affiliation wicri:level="1"><hal:affiliation type="researchteam" xml:id="struct-119680" status="OLD"><orgName>Querying Graphics through Analysis and Recognition</orgName><orgName type="acronym">QGAR</orgName><desc><address><country key="FR"></country></address><ref type="url">http://qgar.loria.fr</ref></desc><listRelation><relation active="#struct-160" type="direct"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-300291" type="indirect"></relation><relation active="#struct-300292" type="indirect"></relation><relation active="#struct-300293" type="indirect"></relation></listRelation><tutelles><tutelle active="#struct-160" type="direct"><org type="laboratory" xml:id="struct-160" status="OLD"><orgName>Laboratoire Lorrain de Recherche en Informatique et ses Applications</orgName><orgName type="acronym">LORIA</orgName><desc><address><addrLine>Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.loria.fr</ref></desc><listRelation><relation name="UMR7503" active="#struct-441569" type="direct"></relation><relation active="#struct-300009" type="direct"></relation><relation active="#struct-300291" type="direct"></relation><relation active="#struct-300292" type="direct"></relation><relation active="#struct-300293" type="direct"></relation></listRelation></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-300291" type="indirect"><org type="institution" xml:id="struct-300291" status="OLD"><orgName>Université Henri Poincaré - Nancy 1</orgName><orgName type="acronym">UHP</orgName><date type="end">2011-12-31</date><desc><address><addrLine>24-30 rue Lionnois, BP 60120, 54 003 NANCY cedex, France</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-300292" type="indirect"><org type="institution" xml:id="struct-300292" status="OLD"><orgName>Université Nancy 2</orgName><date type="end">2011-12-31</date><desc><address><addrLine>91 avenue de la Libération, BP 454, 54001 Nancy cedex</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-300293" type="indirect"><org type="institution" xml:id="struct-300293" status="OLD"><orgName>Institut National Polytechnique de Lorraine</orgName><orgName type="acronym">INPL</orgName><date type="end">2011-12-31</date><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université Nancy 2</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Institut national polytechnique de Lorraine</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName></affiliation></author></analytic></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Embedding</term><term>Fuzzy C-means</term><term>Hierarchical ascending clustering</term><term>IntelliGO similarity measure</term><term>non metric dissimilarity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In various application domains of knowledge extraction or information retrieval, objects are not represented as feature vectors in a vector space but as a pairwise similarity matrix. In molecular biology, such a similarity measure either captures the object structure (e.g. molecules, proteins as sequences of amino acids) or the semantics of their description (genes or diseases described with ontology terms). The numerous existing similarity measures often violate metricity properties. This is the case of our IntelliGO semantic similarity defined as a generalized cosine between two vectors of Gene Ontology terms (Gene Ontology is a directed acyclic graph representing the semantic relationship between terms). Specific techniques exist for embedding pairwise data into Euclidian space for facilitating subsequent clustering of the objects. We report in this paper comparative gene clustering with and without embedding using the Intelligo measure and benchmarks. As for the clustering algorithm, we use an implementation of the C-means algorithm taking as input either a distance" matrix or a set of vectors. We evaluate the clustering quality and discuss the results.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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