Minimizing stochastic complexity using local search and GLA with applications to classification of bacteria.
In this paper, we compare the performance of two iterative clustering methods when applied to an extensive data set describing strains of the bacterial family Enterobacteriaceae. In both methods, the classification (i.e. the number of classes and the partitioning) is determined by minimizing stochastic complexity. The first method performs the minimization by repeated application of the generalized Lloyd algorithm (GLA). The second method uses an optimization technique known as local search (LS). The method modifies the current solution by making global changes to the class structure and it, then, performs local fine-tuning to find a local optimum. It is observed that if we fix the number of classes, the LS finds a classification with a lower stochastic complexity value than GLA. In addition, the variance of the solutions is much smaller for the LS due to its more systematic method of searching. Overall, the two algorithms produce similar classifications but they merge certain natural classes with microbiological relevance in different ways.
Fränti
P
P
Department of Computer Science, University of Joensuu, P.O. Box 111, FIN-80101, Joensuu, Finland.
Gyllenberg
H G
HG
Gyllenberg
M
M
Kivijärvi
J
J
Koski
T
T
Lund
T
T
Nevalainen
O
O
D000465:Algorithms; D001419:Bacteria / Q000145:classification*; D016000:Cluster Analysis; D004755:Enterobacteriaceae / Q000145:classification; D013269:Stochastic Processes