'Text data clustering with python

I am currently trying to cluster a list of sequences based on their similarity using python.

ex:

DFKLKSLFD

DLFKFKDLD

LDPELDKSL
...

The way I pre process my data is by computing the pairwise distances using for example the Levenshtein distance. After calculating all the pairwise distances and creating the distance matrix, I want to use it as input for the clustering algorithm.

I have already tried using Affinity Propagation, but convergence is a bit unpredictable and I would like to go around this problem.

Does anyone have any suggestions regarding other suitable clustering algorithms for this case?

Thank you!!

Solution 1:^[1]

Try this.

import numpy as np
from sklearn.cluster import AffinityPropagation
import distance
    
words = 'XYZ,LDPELDKSL,DFKLKSLFD,ABC,DLFKFKDLD,XYZ,LDPELDKSL,DFKLKSLFD,ABC,DLFKFKDLD,XYZ,LDPELDKSL,XYZ,LDPELDKSL,DFKLKSLFD,ABC,DLFKFKDLD,XYZ,LDPELDKSL,DFKLKSLFD,ABC,DLFKFKDLD,XYZ,LDPELDKSL'.split(',') #Replace this line
words = np.asarray(words) #So that indexing with a list will work
lev_similarity = -1*np.array([[distance.levenshtein(w1,w2) for w1 in words] for w2 in words])

affprop = AffinityPropagation(affinity="precomputed", damping=0.5)
affprop.fit(lev_similarity)
for cluster_id in np.unique(affprop.labels_):
    exemplar = words[affprop.cluster_centers_indices_[cluster_id]]
    cluster = np.unique(words[np.nonzero(affprop.labels_==cluster_id)])
    cluster_str = ", ".join(cluster)
    print(" - *%s:* %s" % (exemplar, cluster_str))

Results:

 - *LDPELDKSL:* LDPELDKSL
 - *DFKLKSLFD:* DFKLKSLFD
 - *XYZ:* ABC, XYZ
 - *DLFKFKDLD:* DLFKFKDLD

Solution 2:^[2]

common_words = kmeans.cluster_centers_.argsort()[:,-1:-11:-1]
for num, centroid in enumerate(common_words):
    print(str(num) + ' : ' + ', '.join(words[word] for word in centroid))

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'Text data clustering with python

Solution 1:[1]

Solution 2:[2]

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Solution 1:^[1]

Solution 2:^[2]