Hierarchical Clustering Using the Arithmetic-Harmonic Cut: Complexity and Experiments
Identifieur interne : 000D23 ( Main/Exploration ); précédent : 000D22; suivant : 000D24Hierarchical Clustering Using the Arithmetic-Harmonic Cut: Complexity and Experiments
Auteurs : Romeo Rizzi [Italie] ; Pritha Mahata [Australie] ; Luke Mathieson [Australie] ; Pablo Moscato [Australie]Source :
- PLoS ONE [ 1932-6203 ] ; 2010.
Descripteurs français
- KwdFr :
- Algorithmes, Analyse de profil d'expression de gènes, Analyse de regroupements, Biologie informatique (), Humains, Leucémies (métabolisme), Lignée cellulaire tumorale, Modèles statistiques, Modèles théoriques, Mélanome (métabolisme), Régulation de l'expression des gènes tumoraux, Tumeurs du côlon (métabolisme).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
Clustering, particularly hierarchical clustering, is an important method for understanding and analysing data across a wide variety of knowledge domains with notable utility in systems where the data can be classified in an evolutionary context. This paper introduces a new hierarchical clustering problem defined by a novel objective function we call the
Url:
DOI: 10.1371/journal.pone.0014067
PubMed: 21151943
PubMed Central: 2997101
Affiliations:
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id="aff1"><addr-line>Dipartimento di Matematica ed Informatica, University of Udine, Udine, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Matematica ed Informatica, University of Udine, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Mahata, Pritha" sort="Mahata, Pritha" uniqKey="Mahata P" first="Pritha" last="Mahata">Pritha Mahata</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>New South Wales Rural Doctors Network, Newcastle, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>New South Wales Rural Doctors Network, Newcastle</wicri:regionArea><wicri:noRegion>Newcastle</wicri:noRegion></affiliation></author><author><name sortKey="Mathieson, Luke" sort="Mathieson, Luke" uniqKey="Mathieson L" first="Luke" last="Mathieson">Luke Mathieson</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Centre for 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Biomarker Discovery & Information Based Medicine, The University of Newcastle, Callaghan, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery & Information Based Medicine, The University of Newcastle, Callaghan</wicri:regionArea><wicri:noRegion>Callaghan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Information Based Medicine Program, Hunter Medical Research Institute, Newcastle, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Information Based Medicine Program, Hunter Medical Research Institute, Newcastle</wicri:regionArea><wicri:noRegion>Newcastle</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Cell Line, Tumor</term><term>Cluster Analysis</term><term>Colonic Neoplasms (metabolism)</term><term>Computational Biology (methods)</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Neoplastic</term><term>Humans</term><term>Leukemia (metabolism)</term><term>Melanoma (metabolism)</term><term>Models, Statistical</term><term>Models, Theoretical</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Biologie informatique ()</term><term>Humains</term><term>Leucémies (métabolisme)</term><term>Lignée cellulaire tumorale</term><term>Modèles statistiques</term><term>Modèles théoriques</term><term>Mélanome (métabolisme)</term><term>Régulation de l'expression des gènes tumoraux</term><term>Tumeurs du côlon (métabolisme)</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Colonic Neoplasms</term><term>Leukemia</term><term>Melanoma</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Leucémies</term><term>Mélanome</term><term>Tumeurs du côlon</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Cell Line, Tumor</term><term>Cluster Analysis</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Neoplastic</term><term>Humans</term><term>Models, Statistical</term><term>Models, Theoretical</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Biologie informatique</term><term>Humains</term><term>Lignée cellulaire tumorale</term><term>Modèles statistiques</term><term>Modèles théoriques</term><term>Régulation de l'expression des gènes tumoraux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Clustering, particularly hierarchical clustering, is an important method for understanding and analysing data across a wide variety of knowledge domains with notable utility in systems where the data can be classified in an evolutionary context. This paper introduces a new hierarchical clustering problem defined by a novel objective function we call the <italic>arithmetic-harmonic cut</italic>. We show that the problem of finding such a cut is <inline-formula><inline-graphic xlink:href="pone.0014067.e001.jpg" mimetype="image"></inline-graphic></inline-formula>-hard and <inline-formula><inline-graphic xlink:href="pone.0014067.e002.jpg" mimetype="image"></inline-graphic></inline-formula>-hard but is fixed-parameter tractable, which indicates that although the problem is unlikely to have a polynomial time algorithm (even for approximation), exact parameterized and local search based techniques may produce workable algorithms. To this end, we implement a memetic algorithm for the problem and demonstrate the effectiveness of the arithmetic-harmonic cut on a number of datasets including a cancer type dataset and a corona virus dataset. We show favorable performance compared to currently used hierarchical clustering techniques such as <inline-formula><inline-graphic xlink:href="pone.0014067.e003.jpg" mimetype="image"></inline-graphic></inline-formula>-M<sc>eans</sc>, Graclus and N<sc>ormalized</sc>-C<sc>ut</sc>. The arithmetic-harmonic cut metric overcoming difficulties other hierarchal methods have in representing both intercluster differences and intracluster similarities.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Shi, J" uniqKey="Shi J">J Shi</name></author><author><name sortKey="Malik, J" uniqKey="Malik J">J Malik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wertheimer, M" uniqKey="Wertheimer M">M Wertheimer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Papadimitriou, Ch" uniqKey="Papadimitriou C">CH Papadimitriou</name></author><author><name sortKey="Yannakakis, M" uniqKey="Yannakakis M">M Yannakakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Hoon, Mj" uniqKey="De Hoon M">MJ de Hoon</name></author><author><name sortKey="Imoto, S" uniqKey="Imoto S">S Imoto</name></author><author><name sortKey="Nolan, J" 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Hansen</name></author><author><name sortKey="Mladenovi, N" uniqKey="Mladenovi N">N Mladenović</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Italie</li></country></list><tree><country name="Italie"><noRegion><name sortKey="Rizzi, Romeo" sort="Rizzi, Romeo" uniqKey="Rizzi R" first="Romeo" last="Rizzi">Romeo Rizzi</name></noRegion></country><country name="Australie"><noRegion><name sortKey="Mahata, Pritha" sort="Mahata, Pritha" uniqKey="Mahata P" first="Pritha" last="Mahata">Pritha Mahata</name></noRegion><name sortKey="Mathieson, Luke" sort="Mathieson, Luke" uniqKey="Mathieson L" first="Luke" last="Mathieson">Luke Mathieson</name><name sortKey="Mathieson, Luke" sort="Mathieson, Luke" uniqKey="Mathieson L" first="Luke" last="Mathieson">Luke Mathieson</name><name sortKey="Moscato, Pablo" sort="Moscato, Pablo" uniqKey="Moscato P" first="Pablo" last="Moscato">Pablo Moscato</name><name sortKey="Moscato, Pablo" sort="Moscato, Pablo" uniqKey="Moscato P" first="Pablo" last="Moscato">Pablo Moscato</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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