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Kernel Kmeans

4.3 | 7 ratings Rate this file 69 Downloads (last 30 days) File Size: 4.13 KB File ID: #26182 Version: 1.7
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Kernel Kmeans


Mo Chen (view profile)


23 Dec 2009 (Updated )

kernel kmeans algorithm

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This function performs kernel kmeans algorithm. When the linear kernel (i.e., inner product) is used, the algorithm is equivalent to standard kmeans algorithm. Several nonlinear kernel functions are also provided. Upon request, I also include a prediction function for out-of-sample inference. Please try following code for a demo:
clear; close all;
d = 2;
k = 3;
n = 500;
[X,label] = kmeansRnd(d,k,n);
init = ceil(k*rand(1,n));
[y,mse,model] = knKmeans(X,init,@knLin);
idx = 1:2:n;
Xt = X(:,idx);
t = knKmeansPred(model, Xt);
This function is now a part of the PRML toolbox (


Pattern Recognition And Machine Learning Toolbox and Kmeans Clustering inspired this file.

MATLAB release MATLAB 9.0 (R2016a)
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Comments and Ratings (20)
21 Jul 2016 Zhao Pengfei

xiaodong ,do you solve the problem you asked? i have the same question!

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14 Jun 2016 Okey Erik

28 Jul 2015 usman shahzad

can anyone send me the full code on kernel k-means in matlab?

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28 Jun 2015 Xiaodong

Can this code return the cluster centers?

10 May 2015 mohammad ghr

how to plot the original data with color?

14 Apr 2015 Jesus G Cruz-Garza

Jung, Tajana, I found the same problem in my Matlab version R2014b.
The function "unique" on line 18 changes the variable "label" from a row vector to a column vector.
This caused the error in my case.

To fix it, transpose the variable "label" after line 18.

label = label'.

Hope it helps

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01 Apr 2015 Zachery Hernandez

Jung and Tajana, I ran the sample code without any problems but I'm wondering if your data array is the right size (2 X 1000).

In either case, you might want to see if the 'any' function in your MATLAB version can compare a vector to a scalar or to another vector. If you get the same 'Matrix dimensions must agree' error then that may be the problem.

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24 Mar 2015 Tajana Schneiderman

Jung, were you able to resolve this issue? I'm also having quite a bit of trouble with this, and can't resolve the error.

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21 Aug 2014 Jung Soo Park


I get following error message when pasted 'sample code' in code description? thanks.

>> load data;
K=x'*x; % use linear kernel
Error using ~=
Matrix dimensions must

Error in knkmeans (line 26)

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21 Aug 2014 Jung Soo Park

07 Jun 2012 Ajay Singh

02 Apr 2012 Santiago

10 Jan 2012 Mo Chen

Mo Chen (view profile)

Hi, Phillip,
You computation is right, only not very efficient. Check my new code

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11 Apr 2011 Phillip

Hello I encountered the same problem as john luckily i had the book, I added the following code. The energy is the sum squared clustering cost function. I have been optimizing my kernel hyper-parameters to minimise this energy. Been working fairly well so thanks. Not an expert so could be wrong.

for i=1:1:size(K,1)
energy = trace(K)-trace(sqrt(D)*A'*K*A*sqrt(D));

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15 Nov 2010 John Melonakos

The code appears broken to me:

>> load data;
K=x'*x; % use linear kernel
??? Undefined function or variable 'val'.

Error in ==> knkmeans at 31
energy = sum(val)+trace(K);

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20 Mar 2010 Mo Chen

Mo Chen (view profile)

Hi mathieu,
As indicated in the description, this algorithm is explained in
reference: [1] Kernel Methods for Pattern Analysis
by John Shawe-Taylor, Nello Cristianini

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23 Feb 2010 Seyed Salim

Mathieu, you can refer to machine learning and pattern recognition by Bishop, 2005. Alternatively this is for free:

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23 Feb 2010 Mathieu

I see, reading the code I do not manage to understand what are the principles behind the algorithm. Do you have a reference that I could get from the web or do you advise to buy the book ?

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11 Feb 2010 Mo Chen

Mo Chen (view profile)

This happens for standard kmeans too, which is caused by the nature of the algorithm. The reason is that when you set a very big number for k, after several iterations, some clusters might become empty.

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11 Feb 2010 Mathieu

It seems that if I request N clusters, the algorithms outputs k clusters, k<=N clusters and most of the time k<<N. I was wondering if this is by construction. If yes, could provide me with an explanation ?

25 Dec 2009 1.1

add sample data and detail description

30 Sep 2010 1.2

remove empty clusters

03 Feb 2012 1.5

fix a minor bug of returning energy

03 Feb 2012 1.6


03 Feb 2012 1.7

Improve the code and fix a bug of returning energy

07 Mar 2016 1.7

fix incompatibility issue due the stupid API change of function unique()

13 Mar 2016 1.7

update description

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