title: Multiobjective Simulated Annealing-Based Clustering of Tissue Samples for Cancer Diagnosis.
abstract: In the field of pattern recognition, the study of the gene expression profiles of different tissue samples over different experimental conditions has become feasible with the arrival of microarray-based technology. In cancer research, classification of tissue samples is necessary for cancer diagnosis, which can be done with the help of microarray technology. In this paper, we have presented a multiobjective optimization (MOO)-based clustering technique utilizing archived multiobjective simulated annealing(AMOSA) as the underlying optimization strategy for classification of tissue samples from cancer datasets. The presented clustering technique is evaluated for three open source benchmark cancer datasets [Brain tumor dataset, Adult Malignancy, and Small Round Blood Cell Tumors (SRBCT)]. In order to evaluate the quality or goodness of produced clusters, two cluster quality measures viz, adjusted rand index and classification accuracy ( % CoA) are calculated. Comparative results of the presented clustering algorithm with ten state-of-the-art existing clustering techniques are shown for three benchmark datasets. Also, we have conducted a statistical significance test called t-test to prove the superiority of our presented MOO-based clustering technique over other clustering techniques. Moreover, significant gene markers have been identified and demonstrated visually from the clustering solutions obtained. In the field of cancer subtype prediction, this study can have important impact.
authors.forename: Sudipta
authors.initials: S
authors.lastname: Acharya
authors.forename: Sriparna
authors.initials: S
authors.lastname: Saha
authors.forename: Yamini
authors.initials: Y
authors.lastname: Thadisina
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D014408:Biomarkers, Tumor