我正在使用sklearn.mixture
中的Gaussian Mixture Model (GMM)来执行数据集的聚类。
我可以使用函数score()
来计算模型下的对数概率。
但是,我正在寻找一种名为“纯度”的指标,该指标在this article中定义。
如何在Python中实现它?我目前的实现如下:
from sklearn.mixture import GMM
# X is a 1000 x 2 array (1000 samples of 2 coordinates).
# It is actually a 2 dimensional PCA projection of data
# extracted from the MNIST dataset, but this random array
# is equivalent as far as the code is concerned.
X = np.random.rand(1000, 2)
clusterer = GMM(3, 'diag')
clusterer.fit(X)
cluster_labels = clusterer.predict(X)
# Now I can count the labels for each cluster..
count0 = list(cluster_labels).count(0)
count1 = list(cluster_labels).count(1)
count2 = list(cluster_labels).count(2)
但我无法循环遍历每个群集以计算混淆矩阵(根据此question)
答案 0 :(得分:8)
大卫的答案有效,但这是另一种方法。
import numpy as np
from sklearn import metrics
def purity_score(y_true, y_pred):
# compute contingency matrix (also called confusion matrix)
contingency_matrix = metrics.cluster.contingency_matrix(y_true, y_pred)
# return purity
return np.sum(np.amax(contingency_matrix, axis=0)) / np.sum(contingency_matrix)
此外,如果需要计算逆纯度,只需将“ axis = 0” 替换为“ axis = 1” 。
答案 1 :(得分:4)
sklearn
未实现群集纯度指标。您有两个选择:
答案 2 :(得分:4)
非常晚的贡献。
您可以尝试像这样实现它,就像在gist
中一样def purity_score(y_true, y_pred):
"""Purity score
Args:
y_true(np.ndarray): n*1 matrix Ground truth labels
y_pred(np.ndarray): n*1 matrix Predicted clusters
Returns:
float: Purity score
"""
# matrix which will hold the majority-voted labels
y_voted_labels = np.zeros(y_true.shape)
# Ordering labels
## Labels might be missing e.g with set like 0,2 where 1 is missing
## First find the unique labels, then map the labels to an ordered set
## 0,2 should become 0,1
labels = np.unique(y_true)
ordered_labels = np.arange(labels.shape[0])
for k in range(labels.shape[0]):
y_true[y_true==labels[k]] = ordered_labels[k]
# Update unique labels
labels = np.unique(y_true)
# We set the number of bins to be n_classes+2 so that
# we count the actual occurence of classes between two consecutive bins
# the bigger being excluded [bin_i, bin_i+1[
bins = np.concatenate((labels, [np.max(labels)+1]), axis=0)
for cluster in np.unique(y_pred):
hist, _ = np.histogram(y_true[y_pred==cluster], bins=bins)
# Find the most present label in the cluster
winner = np.argmax(hist)
y_voted_labels[y_pred==cluster] = winner
return accuracy_score(y_true, y_voted_labels)
答案 3 :(得分:0)
currently top voted answer正确地实现了纯度指标,但并不是在所有情况下都是最合适的指标,因为它不能确保每个预测的簇标签仅分配给一个真实标签一次。
例如,考虑一个非常不平衡的数据集,其中一个标签有99个示例,另一个标签有1个示例。然后,任何聚类(例如:具有两个相等的大小为50的聚类)将获得至少0.99的纯度,从而使其成为无用的指标。
相反,在簇数与标签数相同的情况下,簇精度可能更合适。这具有在无监督的情况下镜像分类精度的优点。要计算聚类准确性,我们需要使用Hungarian algorithm来找到聚类标签和真实标签之间的最佳匹配。 SciPy函数linear_sum_assignment
执行此操作:
import numpy as np
from sklearn import metrics
from scipy.optimize import linear_sum_assignment
def cluster_accuracy(y_true, y_pred):
# compute contingency matrix (also called confusion matrix)
contingency_matrix = metrics.cluster.contingency_matrix(y_true, y_pred)
# Find optimal one-to-one mapping between cluster labels and true labels
row_ind, col_ind = linear_sum_assignment(-contingency_matrix)
# Return cluster accuracy
return contingency_matrix[row_ind, col_ind].sum() / np.sum(contingency_matrix)