[Eeglablist] Silhouette value for IC clustering

時本真吾 tokimoto at mejiro.ac.jp
Sat Nov 25 02:12:51 PST 2017


Dear Dr. Jens Bernhardsson,

I am deeply grateful for the excellent code. I am very sorry for the late response. This is because I took some time to understand the meaning of plotted results. I am trying to cluster 323 ICs from 31 participants by dipoles. I repeated the code 10  times, and the number of clusters for which the average Silhouette value was greatest was 15 or 16. Can I understand that the best number of clusters here is 15 or 16? Thank you very much again.

******************************************
Shingo Tokimoto, Ph.D.
in Linguistics and Psychology
Department of Foreign Languages
Mejiro University
4-31-1, Naka-Ochiai, Shinjuku, Tokyo,
161-8539, Japan
tokimoto at mejiro.ac.jp
******************************************

> 2017/11/17 19:19、Bernhardsson Jens <Jens.Bernhardsson at miun.se>のメール:
> 
> Hi,
> 
> I believe that the Silhouette value found in A10: MI-clust is based on kmeans cluster of multidimensional scaled data performed on the mutual information matrix and the kmeans found in STUDY is based on a pca derived (pre clustering) array. You can run the code below after you pre cluster in STUDY to get the mean and individual Silhouette coefficients for different cluster solutions.
> 
> avgSil = []; 
> kmod = []; 
> siSil = []; 
> 
> for num_of_cluster = 2:25
>    kmod = kmeans(STUDY.etc.preclust.preclustdata,num_of_cluster, 'replicates',10,'emptyaction','drop','distance','sqEuclidean');  
>    siSil(:,num_of_cluster-1) = silhouette(STUDY.etc.preclust.preclustdata,kmod,'sqEuclidean');
>    avgSil = [avgSil; num_of_cluster mean(siSil(:,num_of_cluster-1))];
> end
> 
> figure;  
> plot( avgSil(:,1),avgSil(:,2),'r*-.');
> % ylim([0 1])
> set(gca,'XTick',1:num_of_cluster, 'XGrid', 'on');
> 
> 
> Regards,
> Jens
> 
> -----Ursprungligt meddelande-----
> Från: eeglablist [mailto:eeglablist-bounces at sccn.ucsd.edu] För ????
> Skickat: den 17 september 2017 15:43
> Till: eeglablist at sccn.ucsd.edu
> Ämne: [Eeglablist] Silhouette value for IC clustering
> 
> Dear EEGLAB users,
> 
> I understand that the determination of the number of clusters in IC clustering is one of the difficult problems in source localizations by ICs. Silhouette value is one of the criteria for the best number of clusters in IC clustering, and I have found the description of silhouette value in EEGLAB Wiki (A10: MI-clust) for a single participant. Can we get silhouette values for group data in STUDY formats? Thank you in advance.
> 
> ******************************************
> Shingo Tokimoto, Ph.D.
> in Linguistics and Psychology
> Department of Foreign Languages
> Mejiro University
> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo,
> 161-8539, Japan
> tokimoto at mejiro.ac.jp
> ******************************************
> 
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