Search For:

Displaying 1-29 out of 29 total
A New Path Based Hybrid Measurefor Gene Ontology Similarity
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Sanghamitra Bandyopadhyay,Koushik Mallick
Issue Date:January 2014
pp. 116-127
Gene Ontology (GO) consists of a controlled vocabulary of terms, annotating a gene or gene product, structured in a directed acyclic graph. In the graph, semantic relations connect the terms, that represent the knowledge of functional description and cellu...
 
Reformulated Kemeny Optimal Aggregation with Application in Consensus Ranking of microRNA Targets
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Debarka Sengupta,Aroonalok Pyne,Ujjwal Maulik,Sanghamitra Bandyopadhyay
Issue Date:May 2013
pp. 742-751
MicroRNAs are very recently discovered small noncoding RNAs, responsible for negative regulation of gene expression. Members of this endogenous family of small RNA molecules have been found implicated in many genetic disorders. Each microRNA targets tens t...
 
Mining Quasi-Bicliques from HIV-1-Human Protein Interaction Network: A Multiobjective Biclustering Approach
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Ujjwal Maulik,Anirban Mukhopadhyay,Malay Bhattacharyya,Lars Kaderali,Benedikt Brors,Sanghamitra Bandyopadhyay,Roland Eils
Issue Date:March 2013
pp. 423-435
In this work, we model the problem of mining quasi-bicliques from weighted viral-host protein-protein interaction network as a biclustering problem for identifying strong interaction modules. In this regard, a multiobjective genetic algorithm-based biclust...
 
Weighted Markov Chain Based Aggregation of Biomolecule Orderings
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Debarka Sengupta,Ujjwal Maulik,Sanghamitra Bandyopadhyay
Issue Date:May 2012
pp. 924-933
The scope and effectiveness of Rank Aggregation (RA) have already been established in contemporary bioinformatics research. Rank aggregation helps in meta-analysis of putative results collected from different analytic or experimental sources. For example, ...
 
A Biologically Inspired Measure for Coexpression Analysis
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Sanghamitra Bandyopadhyay, Malay Bhattacharyya
Issue Date:July 2011
pp. 929-942
Two genes are said to be coexpressed if their expression levels have a similar spatial or temporal pattern. Ever since the profiling of gene microarrays has been in progress, computational modeling of coexpression has acquired a major focus. As a result, s...
 
A New Measure of Stability of Clustering Solutions: Application to Data Partitioning
Found in: Artificial Intelligence Systems, IEEE International Conference on
By Sriparna Saha, Sanghamitra Bandyopadhyay
Issue Date:September 2009
pp. 181-186
In this paper at first a new measure of stability of clustering solutions over different bootstrap samples of a data set is proposed. Thereafter in this paper, a multiobjective optimization based clustering technique is developed which optimizes both the m...
 
Mining the Largest Quasi-clique in Human Protein Interactome
Found in: Artificial Intelligence Systems, IEEE International Conference on
By Malay Bhattacharyya, Sanghamitra Bandyopadhyay
Issue Date:September 2009
pp. 194-199
A clique is a complete subgraph of a graph. Often, a clique is interpreted as a dense module of vertices within a graph. However, in many real-world situations, the classical problem of finding a clique is required to be relaxed. This motivates the problem...
 
Multiobjective Genetic Clustering with Ensemble Among Pareto Front Solutions: Application to MRI Brain Image Segmentation
Found in: Advances in Pattern Recognition, International Conference on
By Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay
Issue Date:February 2009
pp. 236-239
This article describes a multiobjective genetic fuzzy clustering scheme that utilizes the search capabilities of NSGA-II, a popular multiobjective genetic algorithm and optimizes a number of fuzzy cluster validity measures. Real-coded encoding of the clust...
 
A Validity Index Based on Connectivity
Found in: Advances in Pattern Recognition, International Conference on
By Sriparna Saha, Sanghamitra Bandyopadhyay
Issue Date:February 2009
pp. 91-94
In this paper we have developed a connectivity based cluster validity index. This validity index is able to detect the number of clusters automatically from data sets having well separated clusters of any shape, size or convexity. The proposed cluster vali...
 
Integration of Co-expression Networks for Gene Clustering
Found in: Advances in Pattern Recognition, International Conference on
By Malay Bhattacharyya, Sanghamitra Bandyopadhyay
Issue Date:February 2009
pp. 355-358
Simultaneous overexpression or underexpression of multiplegenes, used in various forms as probes in the highthroughput microarray experiments, facilitates the identification of their underlying functional proximity. This kind of functional associativity (o...
 
A Point Symmetry-Based Clustering Technique for Automatic Evolution of Clusters
Found in: IEEE Transactions on Knowledge and Data Engineering
By Sanghamitra Bandyopadhyay, Sriparna Saha
Issue Date:November 2008
pp. 1441-1457
In this article, a new symmetry based genetic clustering algorithm is proposed which automatically evolves the number of clusters as well as the proper partitioning from a data set. Strings comprise both real numbers and the don't care symbol in order to e...
 
Multiobjective Genetic Fuzzy Clustering of Categorical Attributes
Found in: Information Technology, International Conference on
By Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay
Issue Date:December 2007
pp. 74-79
Most of the algorithms designed for categorical data clustering optimize a single measure of the clustering good- ness. Such a single measure may not be appropriate for different kinds of data sets. Therefore, consideration of multiple, often conflicting, ...
 
A Genetic Clustering Technique Using a New Line Symmetry Based Distance Measure
Found in: Advanced Computing and Communications, International Conference on
By Sriparna Saha, Sanghamitra Bandyopadhyay
Issue Date:December 2007
pp. 365-370
is described that uses a new line symmetry based distance mea- sure. Kd-tree based nearest neighbor search is used to reduce the complexity of finding the closest symmetric point. Adaptive mutation and crossover probabilities are used. The proposed GA with...
 
Performance Assessment of Some Clustering Algorithms Based on a Fuzzy Granulation-Degranulation Criterion
Found in: Information Technology, International Conference on
By Sriparna Saha, Sanghamitra Bandyopadhyay
Issue Date:December 2007
pp. 62-67
In this paper a fuzzy quantization dequantization crite- rion is used to propose an evaluation technique to determine the appropriate clustering algorithm suitable for a partic- ular data set. In general, the goodness of a partitioning is measured by compu...
 
A New Cluster Validity Index Based on Fuzzy Granulation-degranulation Criteria
Found in: Advanced Computing and Communications, International Conference on
By Sriparna Saha, Sanghamitra Bandyopadhyay
Issue Date:December 2007
pp. 353-358
the corresponding partitioning are two important considera- tions in clustering. In this paper, a new fuzzy quantization- dequantization criterion is used to propose a cluster validity index named Fuzzy Vector Quantization based validity index, FVQ index. ...
 
New Distance Measure for Microarray Gene Expressions Using Linear Dynamic Range of Photo Multiplier Tube
Found in: International Conference on Computing: Theory and Applications
By Shubhra Sankar Ray, Sanghamitra Bandyopadhyay, Sankar K. Pal
Issue Date:March 2007
pp. 337-341
This paper deals with a new distance measure for genes using theirmicroarray expressions. The distance measure is called,
 
A Fuzzy Genetic Clustering Technique Using a New Symmetry Based Distance for Automatic Evolution of Clusters
Found in: International Conference on Computing: Theory and Applications
By Sriparna Saha, Sanghamitra Bandyopadhyay
Issue Date:March 2007
pp. 309-314
In this paper a fuzzy point symmetry based genetic clustering technique (Fuzzy-VGAPS) is proposed which can determine the number of clusters present in a data set as well as a good fuzzy partitioning of the data. A new fuzzy cluster validity index, FSym-in...
 
A Multi-objective Genetic Algorithm with Relative Distance: Method, Performance Measures and Constraint Handling
Found in: International Conference on Computing: Theory and Applications
By Praveen Kumar Tripathi, Sanghamitra Bandyopadhyay, Sankar Kumar Pal
Issue Date:March 2007
pp. 315-319
A novel Multi-Objective Evolutionary Algorithm (MOEA), called Multi-objective Genetic Algorithm with Relative Distance (MOGARD) is described. A novel relative distance parameter that ensures convergence to the Pareto optimal front and a nearest neighbour b...
 
Multiobjective Genetic Algorithm for k-way Equipartitioning of a Point Set with Application to CAD-VLSI
Found in: Information Technology, International Conference on
By Sriparna Saha, Susmita Sur-Kolay, Sanghamitra Bandyopadhyay, Parthasarathi Dasgupta
Issue Date:December 2006
pp. 281-284
Buffered clock-tree design, with cells at its leaves, are known to meet timing and skew requirements better. Clustering of flip-flops leads to reduced clock-tree wirelengths and power-efficient layouts. In this paper, the problem of clustering flip-flops i...
 
A New Symmetry Based Cluster Validity Index: Application to Satellite Image Segmentation
Found in: Information Technology, International Conference on
By Sriparna Saha, Sanghamitra Bandyopadhyay, Ujjwal Maulik
Issue Date:December 2006
pp. 121-124
An important approach for image segmentation is clustering the pixels based on their spectral properties. In this paper, a newly developed point symmetry distance is used to propose a new cluster validity index named S-index (Symmetry distance based index)...
 
Efficient Two-stage Fuzzy Clustering of Microarray Gene Expression Data
Found in: Information Technology, International Conference on
By Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay
Issue Date:December 2006
pp. 11-14
This article presents an efficient two-stage clustering method for clustering microarray gene expression time series data. The algorithm is based on the identification of genes having significant membership to multiple classes. A recently proposed variable...
 
Simulated Annealing Using a Reversible Jump Markov Chain Monte Carlo Algorithm for Fuzzy Clustering
Found in: IEEE Transactions on Knowledge and Data Engineering
By Sanghamitra Bandyopadhyay
Issue Date:April 2005
pp. 479-490
In this paper, an approach for automatically clustering a data set into a number of fuzzy partitions with a simulated annealing using a Reversible Jump Markov Chain Monte Carlo algorithm is proposed. This is in contrast to the widely used fuzzy clustering ...
 
New Operators of Genetic Algorithms for Traveling Salesman Problem
Found in: Pattern Recognition, International Conference on
By Shubhra Sankar Ray, Sanghamitra Bandyopadhyay, Sankar K. Pal
Issue Date:August 2004
pp. 497-500
This paper describes an application of genetic algorithm to the traveling salesman problem. New knowledge based multiple inversion operator and a neighborhood swapping operator are proposed. Experimental results on different benchmark data sets have been f...
 
Performance Evaluation of Some Clustering Algorithms and Validity Indices
Found in: IEEE Transactions on Pattern Analysis and Machine Intelligence
By Ujjwal Maulik, Sanghamitra Bandyopadhyay
Issue Date:December 2002
pp. 1650-1654
<p><b>Abstract</b>—In this article, we evaluate the performance of three clustering algorithms, hard K-Means, single linkage, and a simulated annealing (SA) based technique, in conjunction with four cluster validity indices, namely Davies...
 
A Survey and Comparative Study of Statistical Tests for Identifying Differential Expressionfrom Microarray Data
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Sanghamitra Bandyopadhyay,Saurav Mallik,Anirban Mukhopadhyay
Issue Date:January 2014
pp. 95-115
DNA microarray is a powerful technology that can simultaneously determine the levels of thousands of transcripts (generated, for example, from genes/miRNAs) across different experimental conditions or tissue samples. The motto of differential expression an...
 
Reformulated Kemeny Optimal Aggregation with Application in Consensus Ranking of microRNA Targets
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Aroonalok Pyne, Debarka Sengupta, Ujjwal Maulik, Sanghamitra Bandyopadhyay
Issue Date:May 2013
pp. 742-751
MicroRNAs are very recently discovered small noncoding RNAs, responsible for negative regulation of gene expression. Members of this endogenous family of small RNA molecules have been found implicated in many genetic disorders. Each microRNA targets tens t...
     
Mining Quasi-Bicliques from HIV-1-Human Protein Interaction Network: A Multiobjective Biclustering Approach
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Anirban Mukhopadhyay, Benedikt Brors, Lars Kaderali, Malay Bhattacharyya, Roland Eils, Sanghamitra Bandyopadhyay, Ujjwal Maulik
Issue Date:March 2013
pp. 423-435
In this work, we model the problem of mining quasi-bicliques from weighted viral-host protein-protein interaction network as a biclustering problem for identifying strong interaction modules. In this regard, a multiobjective genetic algorithm-based biclust...
     
De Novo Design of Potential RecA Inhibitors Using MultiObjective Optimization
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Sanghamitra Bandyopadhyay, Soumi Sengupta
Issue Date:July 2012
pp. 1139-1154
De novo ligand design involves optimization of several ligand properties such as binding affinity, ligand volume, drug likeness, etc. Therefore, optimization of these properties independently and simultaneously seems appropriate. In this paper, the ligand ...
     
A Biologically Inspired Measure for Coexpression Analysis
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Malay Bhattacharyya, Sanghamitra Bandyopadhyay
Issue Date:July 2011
pp. 929-942
Two genes are said to be coexpressed if their expression levels have a similar spatial or temporal pattern. Ever since the profiling of gene microarrays has been in progress, computational modeling of coexpression has acquired a major focus. As a result, s...
     
 1