scikit-learn/scikit-learn

Agglomerative clustering training error for seuclidean/mahalanobis affinity and single linkage

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#26,961 opened on 2023/08/01

 (7 件のコメント) (0 件のリアクション) (0 人の担当者)Python (27,020 件のフォーク)batch import
Bughelp wanted

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説明

Describe the bug

When trying Agglomerative clustering model training with the affinity as 'seuclidean' or 'mahalanobis' and the linkage as 'single' the training fails. The same affinity values along with other linkage such as 'average' options executes for model training. There's no specification given for this issue. Also, in the code I can see the handling for the single linkage is different and there is some cython code which is not accessible.

Steps/Code to Reproduce


from sklearn.cluster import AgglomerativeClustering
from sklearn.datasets import load_iris
model = AgglomerativeClustering(affinity='mahalanobis', linkage='average')
data = load_iris(as_frame=True)['data']
model.fit(data)

Expected Results

No error should be thrown sig

Actual Results

image

Versions

System:
    python: 3.8.17 (default, Jul  5 2023, 21:04:15)  [GCC 11.2.0]
executable: /home/albint/miniconda3/envs/myenv/bin/python
   machine: Linux-5.15.0-78-generic-x86_64-with-glibc2.17

Python dependencies:
      sklearn: 1.3.0
          pip: 23.1.2
   setuptools: 67.8.0
        numpy: 1.24.4
        scipy: 1.10.1
       Cython: 3.0.0
       pandas: 2.0.3
   matplotlib: 3.7.2
       joblib: 1.3.1
threadpoolctl: 3.2.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
    num_threads: 8
         prefix: libopenblas
       filepath: /home/albint/miniconda3/envs/myenv/lib/python3.8/site-packages/numpy.libs/libopenblas64_p-r0-15028c96.3.21.so
        version: 0.3.21
threading_layer: pthreads
   architecture: Haswell

       user_api: blas
   internal_api: openblas
    num_threads: 8
         prefix: libopenblas
       filepath: /home/albint/miniconda3/envs/myenv/lib/python3.8/site-packages/scipy.libs/libopenblasp-r0-41284840.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell

       user_api: openmp
   internal_api: openmp
    num_threads: 8
         prefix: libgomp
       filepath: /home/albint/miniconda3/envs/myenv/lib/python3.8/site-packages/scikit_learn.libs/libgomp-a34b3233.so.1.0.0
        version: None

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