DocumentCode :
2112575
Title :
An efficient projected partition algorithm based on the order among genes
Author :
Zesheng Sun ; Yuhai Zhao ; Dengke Meng ; He Pan
Author_Institution :
Dept. of Inf. Sci. & Eng., Northeastern Univ., Shengyang, China
fYear :
2013
fDate :
23-25 July 2013
Firstpage :
700
Lastpage :
707
Abstract :
Most existing methods perform the projected partition over gene expression data based on the untrue assumption of independence among genes. To address the problem, we propose two novel projected partition algorithms, PPA and PPA+. The basic idea of PPA is to take the order among genes as the criterion of phenotype structure discovery. Specially, in PPA, no any specific data distribution assumption is needed. By transforming the expression values into sequential data, PPA employs the branch and bound paradigm to conduct an efficient depth-first traverse over the sample enumeration space, where a user-specific favorite function is developed. Further, based on the hill-climbing strategy and the devised evaluation function, two different strategies are proposed to make the results satisfy different customer-requirements. Efficient pruning and optimization strategies are also devised to further improve the performance of the algorithms. We conducted the performance comparison of PPA and some related alternatives on five real Microarray datasets. The results show that PPA is more effective and efficient. More important, PPA may provide a fire-new insight into the pathogenesis problem.
Keywords :
biology computing; data mining; genetics; optimisation; tree searching; PPA; branch and bound paradigm; depth-first traverse; expression value; gene expression data; hill-climbing strategy; optimization strategy; pathogenesis problem; phenotype structure discovery; projected partition algorithm; pruning strategy; user-specific favorite function; Algorithm design and analysis; Clustering algorithms; Correlation; Gene expression; Optimization; Partitioning algorithms; Silicon; data mining; gene order relationship; projected partition;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Fuzzy Systems and Knowledge Discovery (FSKD), 2013 10th International Conference on
Conference_Location :
Shenyang
Type :
conf
DOI :
10.1109/FSKD.2013.6816286
Filename :
6816286
Link To Document :
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