Rough based symmetrical clustering for gene expression profile analysis
Sarkar, Anasua LU
and Maulik, Ujjwal
(2015)
In IEEE Transactions on Nanobioscience
14(4).
p.360-367
- Abstract
Identification of coexpressed genes is the central goal in microarray gene expression data analysis. Point symmetry-based clustering is an important unsupervised learning technique for recognizing symmetrical convex or non-convex shaped clusters. To enable fast automatic clustering of large microarray data, in this article, a distributed time-efficient scalable parallel rough set based hybrid approach for point symmetry-based clustering algorithm has been proposed. A natural basis for analyzing gene expression data using the symmetry-based algorithm, is to group together genes with similar symmetrical patterns of expression. Rough-set theory helps in faster convergence and initial automatic optimal classification, thereby solving the... (More)
Identification of coexpressed genes is the central goal in microarray gene expression data analysis. Point symmetry-based clustering is an important unsupervised learning technique for recognizing symmetrical convex or non-convex shaped clusters. To enable fast automatic clustering of large microarray data, in this article, a distributed time-efficient scalable parallel rough set based hybrid approach for point symmetry-based clustering algorithm has been proposed. A natural basis for analyzing gene expression data using the symmetry-based algorithm, is to group together genes with similar symmetrical patterns of expression. Rough-set theory helps in faster convergence and initial automatic optimal classification, thereby solving the problem of unknown knowledge of number of clusters in microarray data. This new parallel implementation with K-means algorithm also satisfies the linear speedup in timing on large microarray datasets. This proposed algorithm is compared with another parallel symmetry-based K-means and parallel version of existing K-means over four artificial and benchmark microarray datasets. We also have experimented over three skewed cancer gene expression datasets. The statistical analysis are also performed to establish the significance of this new implementation. The biological relevance of the clustering solutions are also analyzed.
(Less)
- author
- Sarkar, Anasua
LU
and Maulik, Ujjwal
- publishing date
- 2015-06-01
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Automatic clustering algorithm, K-means algorithm, microarray gene expression data, point-symmetry based distance, rough set decision rules
- in
- IEEE Transactions on Nanobioscience
- volume
- 14
- issue
- 4
- article number
- 7097734
- pages
- 8 pages
- publisher
- IEEE - Institute of Electrical and Electronics Engineers Inc.
- external identifiers
-
- scopus:84930933394
- ISSN
- 1536-1241
- DOI
- 10.1109/TNB.2015.2421323
- language
- English
- LU publication?
- no
- id
- 20911c99-e668-4de3-a565-3e613435af9c
- date added to LUP
- 2018-09-13 10:16:30
- date last changed
- 2022-01-31 05:15:38
@article{20911c99-e668-4de3-a565-3e613435af9c,
abstract = {{<p>Identification of coexpressed genes is the central goal in microarray gene expression data analysis. Point symmetry-based clustering is an important unsupervised learning technique for recognizing symmetrical convex or non-convex shaped clusters. To enable fast automatic clustering of large microarray data, in this article, a distributed time-efficient scalable parallel rough set based hybrid approach for point symmetry-based clustering algorithm has been proposed. A natural basis for analyzing gene expression data using the symmetry-based algorithm, is to group together genes with similar symmetrical patterns of expression. Rough-set theory helps in faster convergence and initial automatic optimal classification, thereby solving the problem of unknown knowledge of number of clusters in microarray data. This new parallel implementation with K-means algorithm also satisfies the linear speedup in timing on large microarray datasets. This proposed algorithm is compared with another parallel symmetry-based K-means and parallel version of existing K-means over four artificial and benchmark microarray datasets. We also have experimented over three skewed cancer gene expression datasets. The statistical analysis are also performed to establish the significance of this new implementation. The biological relevance of the clustering solutions are also analyzed.</p>}},
author = {{Sarkar, Anasua and Maulik, Ujjwal}},
issn = {{1536-1241}},
keywords = {{Automatic clustering algorithm; K-means algorithm; microarray gene expression data; point-symmetry based distance; rough set decision rules}},
language = {{eng}},
month = {{06}},
number = {{4}},
pages = {{360--367}},
publisher = {{IEEE - Institute of Electrical and Electronics Engineers Inc.}},
series = {{IEEE Transactions on Nanobioscience}},
title = {{Rough based symmetrical clustering for gene expression profile analysis}},
url = {{http://dx.doi.org/10.1109/TNB.2015.2421323}},
doi = {{10.1109/TNB.2015.2421323}},
volume = {{14}},
year = {{2015}},
}