Commit 57883c9873c990fa6dbb023f775c4b7ea54a9db9
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5eb3a27646
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Implementation of kmeans with gaussian
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bin/cluster_kmeans_gaussianML.py
| File was created | 1 | ''' | |
| 2 | Un petit test pour faire du clustering | ||
| 3 | avec une distance de mahalanobis | ||
| 4 | From paper: | ||
| 5 | Convergence problems of Mahalanobis distance-based k-means clustering, | ||
| 6 | Itshak Lapidot | ||
| 7 | |||
| 8 | Just one thing: Column and lines are inversed in this script. | ||
| 9 | TODO: Random selection from the set | ||
| 10 | ''' | ||
| 11 | |||
| 12 | import matplotlib.pyplot as plt | ||
| 13 | import numpy as np | ||
| 14 | # from sklearn.manifold import TSNE | ||
| 15 | |||
| 16 | N = 50 # Number of individus | ||
| 17 | d = 2 # Number of dimensions | ||
| 18 | K = 3 # number of clusters | ||
| 19 | |||
| 20 | |||
| 21 | def initialize_model(X, number_clusters): | ||
| 22 | rand = np.random.choice(X.shape[0], number_clusters) | ||
| 23 | print(rand) | ||
| 24 | C = X[rand] | ||
| 25 | L = np.zeros((K, d, d)) | ||
| 26 | for k in range(K): | ||
| 27 | L[k] = np.identity(d) | ||
| 28 | return C, L | ||
| 29 | |||
| 30 | |||
| 31 | X = np.random.rand(N, d) # Features | ||
| 32 | C, L = initialize_model(X, K) | ||
| 33 | |||
| 34 | |||
| 35 | def gaussian(x, c, l): | ||
| 36 | ''' | ||
| 37 | G function | ||
| 38 | ''' | ||
| 39 | p1 = np.power(np.linalg.det(l), 0.5) / np.power((2 * np.pi), d/2) | ||
| 40 | p2 = np.exp(np.transpose(x - c).dot(1/2).dot(l).dot(x - c)) | ||
| 41 | return (p1 * p2).reshape(1) | ||
| 42 | |||
| 43 | |||
| 44 | def dist(a, b, l): | ||
| 45 | ''' | ||
| 46 | Distance euclidienne | ||
| 47 | ''' | ||
| 48 | a = np.reshape(a, (-1, 1)) | ||
| 49 | b = np.reshape(b, (-1, 1)) | ||
| 50 | return np.log(gaussian(a, b, l)) | ||
| 51 | |||
| 52 | |||
| 53 | def plot_iteration(iteration, points, clusters, centers): | ||
| 54 | fig = plt.figure() | ||
| 55 | ax = fig.add_subplot(111) | ||
| 56 | scatter = ax.scatter(points[:, 0], points[:, 1], c=clusters, s=50) | ||
| 57 | for i, j in centers: | ||
| 58 | ax.scatter(i, j, s=50, c='red', marker='+') | ||
| 59 | ax.set_xlabel('x') | ||
| 60 | ax.set_ylabel('y') | ||
| 61 | plt.colorbar(scatter) | ||
| 62 | plt.ylim(0, 1) | ||
| 63 | plt.xlim(0, 1) | ||
| 64 | plt.savefig("test_" + str(iteration) + ".pdf") | ||
| 65 | |||
| 66 | |||
| 67 | end_algo = False | ||
| 68 | i = 0 | ||
| 69 | while not end_algo: | ||
| 70 | if i == 10: | ||
| 71 | exit(1) | ||
| 72 | print("Iteration: ", i) | ||
| 73 | # -- Calcul matrix distance | ||
| 74 | distances = np.zeros((N, K)) | ||
| 75 | |||
| 76 | # -- Calcul closest cluster | ||
| 77 | for n in range(N): | ||
| 78 | for k in range(K): | ||
| 79 | distances[n][k] = dist(X[n], C[k], L[k]) | ||
| 80 | closest_cluster = np.argmin(distances, axis=1) | ||
| 81 | |||
| 82 | # -- Debug tool ---------------------- | ||
| 83 | if i % 1 == 0: | ||
| 84 | # TSNE | ||
| 85 | X_embedded = np.concatenate((X, C), axis=0) | ||
| 86 | # X_embedded = TSNE(n_components=2).fit_transform(np.concatenate((X, C), axis=0)) | ||
| 87 | # Then plot | ||
| 88 | plot_iteration( | ||
| 89 | i, | ||
| 90 | X_embedded[:X.shape[0]], | ||
| 91 | closest_cluster, | ||
| 92 | X_embedded[X.shape[0]:] | ||
| 93 | ) | ||
| 94 | # ------------------------------------ | ||
| 95 | |||
| 96 | end_algo = True | ||
| 97 | for k in range(K): | ||
| 98 | # Find subset of X with values closed to the centroid c_k. | ||
| 99 | X_sub = np.where(closest_cluster == k) | ||
| 100 | X_sub = np.take(X, X_sub[0], axis=0) | ||
| 101 | np.mean(X_sub, axis=0) | ||
| 102 | C_new = np.mean(X_sub, axis=0) | ||
| 103 | |||
| 104 | # -- COMPUTE NEW LAMBDA (here named K) -- | ||
| 105 | K_new = np.zeros((L.shape[1], L.shape[2])) | ||
| 106 | for x in X_sub: | ||
| 107 | x = np.reshape(x, (-1, 1)) | ||
| 108 | c_tmp = np.reshape(C_new, (-1, 1)) | ||
| 109 | K_new = K_new + (x - c_tmp).dot((x - c_tmp).transpose()) | ||
| 110 | K_new = K_new / X_sub.shape[0] | ||
| 111 | K_new = np.linalg.inv(K_new) | ||
| 112 | |||
| 113 | if end_algo and (not (C[k] == C_new).all()): # If the same stop | ||
| 114 | end_algo = False | ||
| 115 | C[k] = C_new | ||
| 116 | L[k] = K_new | ||
| 117 | i = i + 1 | ||
| 118 | |||
| 119 | plot_iteration( | ||
| 120 | i, | ||
| 121 | X_embedded[:X.shape[0]], | ||
| 122 | closest_cluster, | ||
| 123 | X_embedded[X.shape[0]:] | ||
| 124 | ) | ||
| 125 |