sklearn agglomerative clustering linkage matrix

Question

I\'m trying to draw a complete-link scipy.cluster.hierarchy.dendrogram, and I found that scipy.cluster.hierarchy.linkage is slower than sklearn.AgglomerativeClustering.

Answer 1

I ran into the same problem when setting n_clusters. I think the problem is that if you set n_clusters, the distances don't get evaluated. If you set n_clusters = None and set a distance_threshold, then it works with the code provided on sklearn. I understand that this will probably not help in your situation but I hope a fix is underway.