Implementation of X-means clustering in Python

x_means.py

"""
以下の論文で提案された改良x-means法の実装

クラスター数を自動決定するk-meansアルゴリズムの拡張について
http://www.rd.dnc.ac.jp/~tunenori/doc/xmeans_euc.pdf
"""

import numpy as np
from scipy import stats
from sklearn.cluster import KMeans

class XMeans:
    """
    x-means法を行うクラス
    """

    def __init__(self, k_init = 2, **k_means_args):
        """
        k_init : The initial number of clusters applied to KMeans()
        """
        self.k_init = k_init
        self.k_means_args = k_means_args

    def fit(self, X):
        """
        x-means法を使ってデータXをクラスタリングする
        X : array-like or sparse matrix, shape=(n_samples, n_features)
        """
        self.__clusters = [] 

        clusters = self.Cluster.build(X, KMeans(self.k_init, **self.k_means_args).fit(X))
        self.__recursively_split(clusters)

        self.labels_ = np.empty(X.shape[0], dtype = np.intp)
        for i, c in enumerate(self.__clusters):
            self.labels_[c.index] = i

        self.cluster_centers_ = np.array([c.center for c in self.__clusters])
        self.cluster_log_likelihoods_ = np.array([c.log_likelihood() for c in self.__clusters])
        self.cluster_sizes_ = np.array([c.size for c in self.__clusters])

        return self

    def __recursively_split(self, clusters):
        """
        引数のclustersを再帰的に分割する
        clusters : list-like object, which contains instances of 'XMeans.Cluster'
        """
        for cluster in clusters:
            if cluster.size <= 3:
                self.__clusters.append(cluster)
                continue

            k_means = KMeans(2, **self.k_means_args).fit(cluster.data)
            c1, c2 = self.Cluster.build(cluster.data, k_means, cluster.index)
           
            beta = np.linalg.norm(c1.center - c2.center) / np.sqrt(np.linalg.det(c1.cov) + np.linalg.det(c2.cov))
            alpha = 0.5 / stats.norm.cdf(beta)
            bic = -2 * (cluster.size * np.log(alpha) + c1.log_likelihood() + c2.log_likelihood()) + 2 * cluster.df * np.log(cluster.size)

            if bic < cluster.bic():
                self.__recursively_split([c1, c2])
            else:
                self.__clusters.append(cluster)

    class Cluster:
        """
        k-means法によって生成されたクラスタに関する情報を持ち、尤度やBICの計算を行うクラス
        """

        @classmethod
        def build(cls, X, k_means, index = None):
            if index == None:
                index = np.array(range(0, X.shape[0]))
            labels = range(0, k_means.get_params()["n_clusters"])

            return tuple(cls(X, index, k_means, label) for label in labels)

        # index: Xの各行におけるサンプルが元データの何行目のものかを示すベクトル
        def __init__(self, X, index, k_means, label):
            self.data = X[k_means.labels_ == label]
            self.index = index[k_means.labels_ == label]
            self.size = self.data.shape[0]
            self.df = self.data.shape[1] * (self.data.shape[1] + 3) / 2
            self.center = k_means.cluster_centers_[label]
            self.cov = np.cov(self.data.T)

        def log_likelihood(self):
            return sum(stats.multivariate_normal.logpdf(x, self.center, self.cov) for x in self.data)

        def bic(self):
            return -2 * self.log_likelihood() + self.df * np.log(self.size)

if __name__ == "__main__":
    import matplotlib.pyplot as plt

    # データの準備
    x = np.array([np.random.normal(loc, 0.1, 20) for loc in np.repeat([1,2], 2)]).flatten()
    y = np.array([np.random.normal(loc, 0.1, 20) for loc in np.tile([1,2], 2)]).flatten()

    # クラスタリングの実行
    x_means = XMeans(random_state = 1).fit(np.c_[x,y]) 
    print(x_means.labels_)
    print(x_means.cluster_centers_)
    print(x_means.cluster_log_likelihoods_)
    print(x_means.cluster_sizes_)

    # 結果をプロット
    plt.rcParams["font.family"] = "Hiragino Kaku Gothic Pro"
    plt.scatter(x, y, c = x_means.labels_, s = 30)
    plt.scatter(x_means.cluster_centers_[:,0], x_means.cluster_centers_[:,1], c = "r", marker = "+", s = 100)
    plt.xlim(0, 3)
    plt.ylim(0, 3)
    plt.title("改良x-means法の実行結果  参考: 石岡(2000)")
    plt.show()
    # plt.savefig("clustering.png", dpi = 200)

Hi,

I get memory errors with the following array which is a little big , Can you please help ?

/home/mayed/Python/Drugs_Algo.py:116: FutureWarning: comparison to None will result in an elementwise object comparison in the future.
if index == None:
MemoryError: MemoryError()

/home/mayed/Python/Drugs_Algo.py(137)()
136 ####Fit and Predict the clusters
1-> 137 x_means = XMeans(random_state = 1,precompute_distances= False).fit(x_train)
138

ipdb> arr1.shape
(315, 13851)

Thanks
Mohamed

私の環境(Numpy 1.13.0)ですと73行目，if index == None:でValueErrorが発生してしまいました．
if index is None:
に置き換えたところ動作致しましたので，念のためご報告させて頂きます．

I want to detect number of colors in a image file. I've used K-mean but I want to set number of cluster automatically. Now I want to use x-mean for automatically detecting clusters. can you help me out how can i do that.

57行目

np.linalg.det(c1.cov) と np.linalg.det(c2.cov) がともにゼロの場合, ZeroDivisionError が起きます

下記のように対応しました。

if np.linalg.det(c1.cov) == 0 and np.linalg.det(c2.cov) == 0:
      beta = 0
else:
      beta = np.linalg.norm(c1.center - c2.center) / np.sqrt(np.linalg.det(c1.cov) + np.linalg.det(c2.cov))

could you modify your code?