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I've been working on SOMs and how to get the best clustering results. One approach could be to try many runs and choose the clustering with the lowest within sum of squared errors.

However, I do not only want to initialize random values and have several tries, but also want to choose good parameters. I have read in "Influence of Learning Rates and Neighboring Functions on Self-Organizing Maps" (Stefanovic 2011) that if you do not know which parameters for the neighborhood function and learning rate to choose, it is probably the best option to choose a gaussian function and a nonlinear learning rate.

My data is a time series lets say:

matrix(c(sample(seq(from = 10, to = 20, by = runif(1,min=1,max=3)), size = 5000, replace = TRUE),(sample(seq(from = 15, to = 22, by = runif(1,min=1,max=4)), size = 5000, replace = TRUE)),(sample(seq(from = 18, to = 24, by = runif(1,min=1,max=3)), size = 5000, replace = TRUE))),nrow=300,ncol=50,byrow = TRUE) -> data

which has 300 observations with 50 values each. 100 observations each tend to be more similar.

I'm working with the kohonen package.

The code:

grid<-somgrid(4,3,"hexagonal")

kohonen<-som(data,grid)

matplot(t(kohonen$codes),col=kohonen$unit.classif,type="l")

gives me clusters with values between 10 to 22, which is similar to the obersations

enter image description here

I tried the "som" package, too, which offers a gaussian neighborhood function and a inverse-time learning rate.

som<-som(data,4,3,init="random",alphaType="inverse",neigh="gaussian")

som$visual[,4]<-with(som$visual,interaction(som$visual[,1],som$visual[,2]))

som$visual[,4]<-as.numeric(as.factor(som$visual[,4]))

matplot(t(som$code),col=som$visual[,4],type="l")

enter image description here

Here I get clusters with values between 15 and 18, so all clusters "shrink" and get more similar. With different input series I get the same phenomena

My two questions:

  1. Why do clusters from the self-organizing map with the som package get so extraordinarily similar and shrink to a much smaller range, even though it is said that you get good clusters with gaussian neigborhood function and non linear learning rate?
  2. How can I avoid this range shrinking with a gaussian neigborhood function and a non linear learning rate in order to get appropriate clusters?
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One key difference is that kohonen uses batch learning while som uses incremental learning. This can be the cause of the differences you are seeing.

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  • $\begingroup$ Can you elaborate on this point? $\endgroup$ – gung Jan 12 '16 at 14:05
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You might truncate the low high distance nodes to winner for each iteration in that way you can devoid to shrink all clusters centers. Or there are any other neighbourhood functions you might try, like linear, bubble or such. Just Google, if you like to use other neigh function. For Gaussian window, there ought to be variance variable also. Try to set it as well. If you set it lower, you can degrade the window effect

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