Stepwise iterative maximum likelihood clustering approach

Alok Sharma, Daichi Shigemizu, Keith A. Boroevich, Yosvany López, Yoichiro Kamatani, Michiaki Kubo, Tatsuhiko Tsunoda

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Background: Biological/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. Results: The 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. Conclusions: In 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/.

Original languageEnglish
Article number319
JournalBMC Bioinformatics
Volume17
Issue number1
DOIs
Publication statusPublished - 24-08-2016

Fingerprint

Clustering algorithms
Maximum likelihood
Maximum Likelihood
Cluster Analysis
Clustering
Clustering Methods
Clustering Algorithm
Microarrays
Statistical methods
Genes
Topology
Association reactions
Genome-Wide Association Study
Support Vector
K-means Algorithm
K-means Clustering
Iterative Procedure
Single Nucleotide Polymorphism
Microarray
Statistical method

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Sharma, A., Shigemizu, D., Boroevich, K. A., López, Y., Kamatani, Y., Kubo, M., & Tsunoda, T. (2016). Stepwise iterative maximum likelihood clustering approach. BMC Bioinformatics, 17(1), [319]. https://doi.org/10.1186/s12859-016-1184-5
Sharma, Alok ; Shigemizu, Daichi ; Boroevich, Keith A. ; López, Yosvany ; Kamatani, Yoichiro ; Kubo, Michiaki ; Tsunoda, Tatsuhiko. / Stepwise iterative maximum likelihood clustering approach. In: BMC Bioinformatics. 2016 ; Vol. 17, No. 1.
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Sharma, A, Shigemizu, D, Boroevich, KA, López, Y, Kamatani, Y, Kubo, M & Tsunoda, T 2016, 'Stepwise iterative maximum likelihood clustering approach', BMC Bioinformatics, vol. 17, no. 1, 319. https://doi.org/10.1186/s12859-016-1184-5

Stepwise iterative maximum likelihood clustering approach. / Sharma, Alok; Shigemizu, Daichi; Boroevich, Keith A.; López, Yosvany; Kamatani, Yoichiro; Kubo, Michiaki; Tsunoda, Tatsuhiko.

In: BMC Bioinformatics, Vol. 17, No. 1, 319, 24.08.2016.

Research output: Contribution to journalArticle

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Sharma A, Shigemizu D, Boroevich KA, López Y, Kamatani Y, Kubo M et al. Stepwise iterative maximum likelihood clustering approach. BMC Bioinformatics. 2016 Aug 24;17(1). 319. https://doi.org/10.1186/s12859-016-1184-5