Stepwise iterative maximum likelihood clustering approach

BMC Bioinformatics

Research Article

Michiaki Kubo¹  Yoichiro Kamatani¹  Keith A. Boroevich¹  Alok Sharma²  Daichi Shigemizu³  Tatsuhiko Tsunoda³  Yosvany López⁴ 

[1] RIKEN Center for Integrative Medical Sciences, 230-0045, Yokohama, Japan;RIKEN Center for Integrative Medical Sciences, 230-0045, Yokohama, Japan;CREST, JST, 230-0045, Yokohama, Japan;Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia;RIKEN Center for Integrative Medical Sciences, 230-0045, Yokohama, Japan;CREST, JST, 230-0045, Yokohama, Japan;Medical Research Institute, Tokyo Medical and Dental University, 113-8510, Tokyo, Japan;RIKEN Center for Integrative Medical Sciences, 230-0045, Yokohama, Japan;Medical Research Institute, Tokyo Medical and Dental University, 113-8510, Tokyo, Japan;

关键词: Burkitt Lymphoma;    Cluster Accuracy;    Hill Climbing Algorithm;    Tuning Time;    Support Vector Cluster;   

DOI  :  10.1186/s12859-016-1184-5

 received in 2015-11-27, accepted in 2016-08-12,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundBiological/genetic data is a complex mix of various forms or topologies which makes it quite difficult to analyze. An abundance of such data in this modern era requires the development of sophisticated statistical methods to analyze it in a reasonable amount of time. In many biological/genetic analyses, such as genome-wide association study (GWAS) analysis or multi-omics data analysis, it is required to cluster the plethora of data into sub-categories to understand the subtypes of populations, cancers or any other diseases. Traditionally, the k-means clustering algorithm is a dominant clustering method. This is due to its simplicity and reasonable level of accuracy. Many other clustering methods, including support vector clustering, have been developed in the past, but do not perform well with the biological data, either due to computational reasons or failure to identify clusters.ResultsThe proposed SIML clustering algorithm has been tested on microarray datasets and SNP datasets. It has been compared with a number of clustering algorithms. On MLL datasets, SIML achieved highest clustering accuracy and rand score on 4/9 cases; similarly on SRBCT dataset, it got for 3/5 cases; on ALL subtype it got highest clustering accuracy for 5/7 cases and highest rand score for 4/7 cases. In addition, SIML overall clustering accuracy on a 3 cluster problem using SNP data were 97.3, 94.7 and 100 %, respectively, for each of the clusters.ConclusionsIn this paper, considering the nature of biological data, we proposed a maximum likelihood clustering approach using a stepwise iterative procedure. The advantage of this proposed method is that it not only uses the distance information, but also incorporate variance information for clustering. This method is able to cluster when data appeared in overlapping and complex forms. The experimental results illustrate its performance and usefulness over other clustering methods. A Matlab package of this method (SIML) is provided at the web-link http://www.riken.jp/en/research/labs/ims/med_sci_math/.

【 授权许可】

CC BY   
© The Author(s). 2016

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