Hello Everybody, This question seems simple, but I can't find the solution:
I use scipy.cluster.hierarchy to do a hierarchical clustering on a set of points using "cosine" similarity metric. As an example, I have: import scipy.cluster.hierarchy as hac import matplotlib.pyplot as plt Points = np.array([[ 0. , 0.23508573], [ 0.00754775 , 0.26717266], [ 0.00595464 , 0.27775905], [ 0.01220563 , 0.23622067], [ 0.00542628 , 0.14185873], [ 0.03078922 , 0.11273108], [ 0.06707743 ,-0.1061131 ], [ 0.04411757 ,-0.10775407], [ 0.01349434 , 0.00112159], [ 0.04066034 , 0.11639591], [ 0. , 0.29046682], [ 0.07338036 , 0.00609912], [ 0.01864988 , 0.0316196 ], [ 0. , 0.07270636], [ 0. , 0. ]]) z = hac.linkage(Points, metric='cosine', method='complete') labels = hac.fcluster(z, 0.1, criterion="distance") plt.scatter(Points[:, 0], Points[:, 1], c=labels.astype(np.float)) plt.show() Since I use cosine metric, in some cases the dot product of two vectors can be negative or norm of some vectors can be zero. It means z output will have some negative or infinite elements which is not valid for fcluster (as below): z = [[ 0.00000000e+00 1.00000000e+01 0.00000000e+00 2.00000000e+00] [ 1.30000000e+01 1.50000000e+01 0.00000000e+00 3.00000000e+00] [ 8.00000000e+00 1.10000000e+01 4.26658708e-13 2.00000000e+00] [ 1.00000000e+00 2.00000000e+00 2.31748880e-05 2.00000000e+00] [ 3.00000000e+00 4.00000000e+00 8.96700489e-05 2.00000000e+00] [ 1.60000000e+01 1.80000000e+01 3.98805492e-04 5.00000000e+00] [ 1.90000000e+01 2.00000000e+01 1.33225099e-03 7.00000000e+00] [ 5.00000000e+00 9.00000000e+00 2.41120340e-03 2.00000000e+00] [ 6.00000000e+00 7.00000000e+00 1.52914684e-02 2.00000000e+00] [ 1.20000000e+01 2.20000000e+01 3.52441432e-02 3.00000000e+00] [ 2.10000000e+01 2.40000000e+01 1.38662986e-01 1.00000000e+01] [ 1.70000000e+01 2.30000000e+01 6.99056531e-01 4.00000000e+00] [ 2.50000000e+01 2.60000000e+01 1.92543748e+00 1.40000000e+01] [ -1.00000000e+00 2.70000000e+01 inf 1.50000000e+01]] To solve this problem, I checked linkage() function and inside it I needed to check _hierarchy.linkage() method. I use pycharm text editor and when I asked for "linkage" source code, it opened up a python file namely "_hierarchy.py" inside the directory like the following: .PyCharm40/system/python_stubs/-1247972723/scipy/cluster/_hierarchy.py This python file doesn't have any definition for all included functions. I am wondering what is the correct source of this function to revise it and solve my problem. I would be appreciated if someone helps me to explore the correct source. Thanks and Regards Pegah -- https://mail.python.org/mailman/listinfo/python-list
