SpectralClustering() ValueError: expected 1-d or 2-d array or matrix, got array(None, dtype=object) #21147
Description
Describe the bug
I am trying to apply spectral clustering to the given similarity matrix (see attached csv file) for 15 clusters. Instead of the result I am getting this error. It works fine for 1-14 clusters and for 16 clusters.
Steps/Code to Reproduce
import csv
from sklearn.cluster import SpectralClustering
with open('similarity_matrix.csv', newline='') as csvfile:
x = list(csv.reader(csvfile))
spectral = SpectralClustering(n_clusters=15, affinity='precomputed', random_state=0).fit(x)
result = list(spectral.labels_)
print(result)Expected Results
The labels of the data objects
Actual Results
Traceback (most recent call last):
File "C:\Users\Nikos\PycharmProjects\community_detection_python\src\test.py", line 8, in <module>
spectral = SpectralClustering(n_clusters=15, affinity='precomputed', random_state=0).fit(x)
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\sklearn\cluster\_spectral.py", line 535, in fit
self.labels_ = spectral_clustering(self.affinity_matrix_,
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\sklearn\utils\validation.py", line 63, in inner_f
return f(*args, **kwargs)
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\sklearn\cluster\_spectral.py", line 271, in spectral_clustering
maps = spectral_embedding(affinity, n_components=n_components,
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\sklearn\utils\validation.py", line 63, in inner_f
return f(*args, **kwargs)
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\sklearn\manifold\_spectral_embedding.py", line 348, in spectral_embedding
_, diffusion_map = lobpcg(laplacian, X, tol=1e-15,
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\scipy\sparse\linalg\eigen\lobpcg\lobpcg.py", line 493, in lobpcg
activeBlockVectorAR = A(activeBlockVectorR)
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\scipy\sparse\linalg\interface.py", line 390, in __call__
return self*x
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\scipy\sparse\linalg\interface.py", line 393, in __mul__
return self.dot(x)
File "C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\scipy\sparse\linalg\interface.py", line 422, in dot
raise ValueError('expected 1-d or 2-d array or matrix, got %r'
ValueError: expected 1-d or 2-d array or matrix, got array(None, dtype=object)Versions
C:\Users\Nikos\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\distutils_patch.py:25: UserWarning: Distutils was imported before Setuptools. This usage is discouraged and may exhibit undesirable behaviors or errors. Please use Setuptools' objects directly or at least import Setuptools first.
warnings.warn(
System:
python: 3.9.2 (tags/v3.9.2:1a79785, Feb 19 2021, 13:44:55) [MSC v.1928 64 bit (AMD64)]
executable: C:\Users\Nikos\AppData\Local\Programs\Python\Python39\python.exe
machine: Windows-10-10.0.19041-SP0
Python dependencies:
pip: 21.2.4
setuptools: 49.2.1
sklearn: 0.24.1
numpy: 1.20.2
scipy: 1.6.2
Cython: None
pandas: 1.2.3
matplotlib: 3.4.0
joblib: 1.0.1
threadpoolctl: 2.1.0
Built with OpenMP: True