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[Unmaintained] The Python implementation of k-medoids.

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kmedoids's Introduction

kmedoids

The Python implementation of k-medoids.

Example

from sklearn.metrics.pairwise import pairwise_distances
import numpy as np

import kmedoids

# 3 points in dataset
data = np.array([[1,1], 
                [2,2], 
                [10,10]])

# distance matrix
D = pairwise_distances(data, metric='euclidean')

# split into 2 clusters
M, C = kmedoids.kMedoids(D, 2)

print('medoids:')
for point_idx in M:
    print( data[point_idx] )

print('')
print('clustering result:')
for label in C:
    for point_idx in C[label]:
        print('label {0}:　{1}'.format(label, data[point_idx]))

Output:

medoids:
[1 1]
[10 10]

clustering result:
label 0:　[1 1]
label 0:　[2 2]
label 1:　[10 10]

License

This code is from:

Bauckhage C. Numpy/scipy Recipes for Data Science: k-Medoids Clustering[R]. Technical Report, University of Bonn, 2015.

Please cite the article if the code is used in your research.

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kmedoids's Issues

ValueError: attempt to get argmin of an empty sequence

This error only occurs sometimes.

I think when a cluster size is zero this happens. When trying to get the min of an empty array.
line 29, in kMedoids j = np.argmin(J)

Stack trace -
`F:\Programs\Anaconda3\lib\site-packages\numpy\core_methods.py:59: RuntimeWarning: Mean of empty slice.
warnings.warn("Mean of empty slice.", RuntimeWarning)
Traceback (most recent call last):

File "", line 1, in
runfile('D:/University/FYP/code/fyp_scritps/clustering/phrase_cluster.py', wdir='D:/University/FYP/code/fyp_scritps/clustering')

File "F:\Programs\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 880, in runfile
execfile(filename, namespace)

File "F:\Programs\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)

File "D:/University/FYP/code/fyp_scritps/clustering/phrase_cluster.py", line 43, in
M, C = kmedoids.kMedoids(D, 2)

File "D:\University\FYP\code\fyp_scritps\clustering\kmedoids\kmedoids.py", line 29, in kMedoids
j = np.argmin(J)

File "F:\Programs\Anaconda3\lib\site-packages\numpy\core\fromnumeric.py", line 1033, in argmin
return argmin(axis, out)

File "F:\Programs\Anaconda3\lib\site-packages\numpy\matrixlib\defmatrix.py", line 895, in argmin
return N.ndarray.argmin(self, axis, out)._align(axis)

ValueError: attempt to get argmin of an empty sequence`

TypeError: 'range' object does not support item assignment

This is the code I used.

Then I get the following output with an error message.

Anyone know a solution?
Your kind responses are highly appreciated.

Thank you.

NameError:Xrange is no defined

for t in xrange(tmax):
NameError: name 'xrange' is not defined

distance matrice

what is the tmax varaible for? and why did u set it to 100?
if i have a dataset of 800 points should i put tmax=800?

"TypeError: 'range' object does not support item assignment"

Hi, I tried to get the kMedoids function to work on the provided example but when running the following line:

# split into 2 clusters
M, C = kMedoids(D, 2)

I get the following error:

Traceback (most recent call last):
File "/usr/lib/python3.5/code.py", line 91, in runcode
exec(code, self.locals)
File "", line 1, in
File "", line 9, in kMedoids
File "mtrand.pyx", line 4832, in mtrand.RandomState.shuffle
File "mtrand.pyx", line 4835, in mtrand.RandomState.shuffle
TypeError: 'range' object does not support item assignment

Any idea what is causing this? Should it work on Python 3.5?

Thank you !