Shyama Das

Publications (2)2.19 Total impact

• Article: Comparative advantages of novel algorithms using MSR threshold and MSR difference threshold for biclustering gene expression data.

  Shyama Das, Sumam Mary Idicula
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  ABSTRACT: The goal of biclustering in gene expression data matrix is to find a submatrix such that the genes in the submatrix show highly correlated activities across all conditions in the submatrix. A measure called mean squared residue (MSR) is used to simultaneously evaluate the coherence of rows and columns within the submatrix. MSR difference is the incremental increase in MSR when a gene or condition is added to the bicluster. In this chapter, three biclustering algorithms using MSR threshold (MSRT) and MSR difference threshold (MSRDT) are experimented and compared. All these methods use seeds generated from K-Means clustering algorithm. Then these seeds are enlarged by adding more genes and conditions. The first algorithm makes use of MSRT alone. Both the second and third algorithms make use of MSRT and the newly introduced concept of MSRDT. Highly coherent biclusters are obtained using this concept. In the third algorithm, a different method is used to calculate the MSRDT. The results obtained on bench mark datasets prove that these algorithms are better than many of the metaheuristic algorithms.
  Advances in experimental medicine and biology 01/2011; 696:123-34. · 1.09 Impact Factor
• Article: KMeans greedy search hybrid algorithm for biclustering gene expression data.

  Shyama Das, Sumam Mary Idicula
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  ABSTRACT: Microarray technology demands the development of algorithms capable of extracting novel and useful patterns like biclusters. A bicluster is a submatrix of the gene expression datamatrix such that the genes show highly correlated activities across all conditions in the submatrix. A measure called Mean Squared Residue (MSR) is used to evaluate the coherence of rows and columns within the submatrix. In this paper, the KMeans greedy search hybrid algorithm is developed for finding biclusters from the gene expression data. This algorithm has two steps. In the first step, high quality bicluster seeds are generated using KMeans clustering algorithm. In the second step, these seeds are enlarged by adding more genes and conditions using the greedy strategy. Here, the objective is to find the biclusters with maximum size and the MSR value lower than a given threshold. The biclusters obtained from this algorithm on both the bench mark datasets are of high quality. The statistical significance and biological relevance of the biclusters are verified using gene ontology database.
  Advances in experimental medicine and biology 01/2010; 680:181-8. · 1.09 Impact Factor