tsne pca 自编码器 绘图（CC2）——一定记得做无量纲化处理使用standardscaler，数据聚类更明显

tsne

数据不做预处理：

# coding: utf-8
import collections
import numpy as np
import os
import pickle
from sklearn.neighbors import NearestNeighbors
import numpy as np
from sklearn.manifold import TSNE

    # .......
    X = X+black_verify+white_verify+unknown_verify+bd_verify
    print black_verify_labels+white_verify_labels+unknown_verify_labels+bd_verify_labels
    y = y+black_verify_labels+white_verify_labels+unknown_verify_labels+bd_verify_labels
    print("ALL data check:")
    print("len of X:", len(X))
    print("len of y:", len(y))
    # print(unknown_verify)

    X_embedded = TSNE(n_components=2).fit_transform(X)

    with open("tsne_data_X.pkl", "wb") as f:
        pickle.dump([X_embedded, y], f)

import pickle
from collections import Counter
import numpy as np
import matplotlib.pyplot as Plot

def main():
    with open("tsne_data_X.pkl", "rb") as f:
        [X_embedded, y] = pickle.load(f, encoding='iso-8859-1')

    print(len(X_embedded))
    print(len(y))
    print(X_embedded[:3])
    print(y[:3])
    i = 0
    for l in y:
        if type(l) == type([]):
            raise Exception(str([i,y]))
        i+=1
    print(Counter(y))
    Y, labels = np.array(X_embedded), np.array(y)
    titles = ("white","black","black_verify_labels","white_verify_labels","unknown_verify_labels","bd_verify_labels")
    colors=['b', 'c', 'y', 'm', 'r', 'g', 'peru']
    for i in range(0, 6):
       idx_1 = [i1 for i1 in range(len(labels)) if labels[i1]==i]
       flg1=Plot.scatter(Y[idx_1,0], Y[idx_1,1], 20,color=colors[i],label=titles[i]);
    Plot.legend()
    Plot.savefig('tsne.pdf')
    Plot.show()
main()

 

数据做standard标准化处理

使用pca，不进行预处理：

使用standard scaler预处理，再做pca：

    from sklearn import preprocessing
    scaler = preprocessing.StandardScaler().fit(X)
    #scaler = preprocessing.MinMaxScaler().fit(X)
    X = scaler.transform(X)
    print("standard X sample:", X[:3])

    black_verify = scaler.transform(black_verify)
    print(black_verify)

    white_verify = scaler.transform(white_verify)
    print(white_verify)

    unknown_verify = scaler.transform(unknown_verify)
    print(unknown_verify)

    bd_verify = scaler.transform(bd_verify)
    print(bd_verify)

    #print black_verify_labels+white_verify_labels+unknown_verify_labels+bd_verify_labels

    X = np.concatenate((X,black_verify,white_verify,unknown_verify,bd_verify))
    #X = X+black_verify+white_verify+unknown_verify+bd_verify
    y = y+black_verify_labels+white_verify_labels+unknown_verify_labels+bd_verify_labels
    print("ALL data check:")
    print("len of X:", len(X))
    print("len of y:", len(y))
    # print(unknown_verify)

    X_embedded = PCA(n_components=2).fit_transform(X)

    with open("pca_data_X_scaled.pkl", "wb") as f:
        pickle.dump([X_embedded, y], f)

最后效果：

最后使用自编码器来来降维：

代码：

    X = np.concatenate((X,black_verify,white_verify,unknown_verify,bd_verify))
    y = y+black_verify_labels+white_verify_labels+unknown_verify_labels+bd_verify_labels
    print("ALL data check:")
    print("len of X:", len(X))
    print("len of y:", len(y))
    # print(unknown_verify)

    ratio_of_train = 0.8
    X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=(1 - ratio_of_train))
    # Building the encoder
    encoder = tflearn.input_data(shape=[None, 75])
    encoder = tflearn.fully_connected(encoder, 64)
    encoder = tflearn.fully_connected(encoder, 2)

    # Building the decoder
    decoder = tflearn.fully_connected(encoder, 64)
    decoder = tflearn.fully_connected(decoder, 75, activation='sigmoid')

    # Regression, with mean square error
    net = tflearn.regression(decoder, optimizer='adam', learning_rate=0.0001,
                             loss='mean_square', metric=None)

    # Training the auto encoder
    model = tflearn.DNN(net, tensorboard_verbose=0)
    model.fit(X_train, X_train, n_epoch=200, validation_set=(X_test, X_test),
              run_id="auto_encoder", batch_size=1024)

    # Encoding X[0] for test
    print("
Test encoding of X[0]:")
    # New model, re-using the same session, for weights sharing
    encoding_model = tflearn.DNN(encoder, session=model.session)
    print(encoding_model.predict([X[0]]))


    X_embedded = encoding_model.predict(X) #TSNE(n_components=2).fit_transform(X)

    with open("tflearn_auto_enc_data_X_scaled.pkl", "wb") as f:
        pickle.dump([X_embedded, y], f)

如果是迭代次数不一样，则可能有一些差别，见下图，和上面的可能有些差别：

修改64为128: