from scipy.cluster.hierarchy import linkage
import pandas as pd
import random, timeit

points = 100
df = pd.DataFrame({'x': random.sample(range(0, points), points),
                   'y': random.sample(range(0, points), points)})

%timeit linkage(df[['x', 'y']], method = 'ward', metric = 'euclidean')

1.02 ms ± 133 µs/ループ（7 回の実行の平均 ± 標準偏差、各 1000 ループ）