def KernelPCA(self, kernel, n_comps=[], sparseversion=False):
if sparseversion:
if n_comps == []: n_comps = self.numdims
self.kernelprincomp = decomp.KernelPCA(kernel,
remove_zero_eig=False)
self.kernelprincomp.fit(self.datatrain.toarray())
self.kernelprincompscores = [
self.kernelprincomp.transform(self.datatrain.toarray()),
self.kernelprincomp.transform(self.dataval.toarray()),
self.kernelprincomp.transform(self.datatest.toarray())
]
else:
if n_comps == []: n_comps = self.numdims
self.kernelprincomp = decomp.KernelPCA(kernel,
remove_zero_eig=False)
self.kernelprincomp.fit(self.datatrain)
self.kernelprincompscores = [
self.kernelprincomp.transform(self.datatrain),
self.kernelprincomp.transform(self.dataval),
self.kernelprincomp.transform(self.datatest)
]
self.kernelprincompscores[0] = np.nan_to_num(
self.kernelprincompscores[0])
self.kernelprincompscores[1] = np.nan_to_num(
self.kernelprincompscores[1])
self.kernelprincompscores[2] = np.nan_to_num(
self.kernelprincompscores[2])
def PCA(self, X, Y=None, ncomp=2, method='PCA'):
""" decompose a multivariate dataset in an orthogonal
set that explain a maximum amount of the variance
@param X: Input dataset
Keyword Arguments:
ncomp -- number or components to be kept (Default: 2)
method -- method to be used
PCA(default)/Randomized/Sparse
"""
from sklearn import decomposition
from sklearn import cross_decomposition
if method == 'Randomized':
pca = decomposition.RandomizedPCA(n_components=ncomp)
elif method == 'Sparse':
pca = decomposition.SparsePCA(n_components=ncomp)
elif method == 'rbf':
pca = decomposition.KernelPCA(n_components=ncomp,
fit_inverse_transform=True,
gamma=10,
kernel="rbf")
elif method == 'linear':
pca = decomposition.KernelPCA(n_components=ncomp, kernel="linear")
elif method == 'sigmoid':
pca = decomposition.KernelPCA(n_components=ncomp, kernel="sigmoid")
elif method == 'SVD':
pca = decomposition.TruncatedSVD(n_components=ncomp)
else:
pca = decomposition.PCA(n_components=ncomp)
method = 'PCA'
print('[ML] Using %s method' % method)
pca.fit(X)
return pca.transform(X)
def PCdata(self, n_pcs = 75):
dist, ids = self.distmatrix()
pcafunc = skdecomp.KernelPCA(n_pcs, kernel='precomputed')
kernel = np.exp(-dist**2 / dist.max()**2)
pcs = pcafunc.fit_transform(kernel)
pcsframe = pandas.DataFrame(pcs, index=ids, columns=["pc-" + str(i) for i in range(n_pcs)])
return pcsframe
def main():
# Create random data.
# https://jakevdp.github.io/PythonDataScienceHandbook/05.07-support-vector-machines.html
n = 200 # nb circles.
x, y = make_circles(n, factor=.1, noise=.1)
# Scale data to reduce weights.
# https://openclassrooms.com/fr/courses/4444646-entrainez-un-modele-predictif-lineaire/4507801-reduisez-l-amplitude-des-poids-affectes-a-vos-variables
std_scale = preprocessing.StandardScaler().fit(x)
x_scaled = std_scale.transform(x)
for i, g in enumerate([1, 10, 100]):
# Perform kernel PCA on scaled data.
kpca = decomposition.KernelPCA(n_components=1, kernel='rbf', gamma=g)
kpca.fit(x_scaled)
# Project data on principal components.
x_kpca = kpca.transform(x_scaled)
# Plot.
axis = plt.subplot(3, 2, 1 + 2 * i)
axis.scatter(x_scaled[:, 0], x_scaled[:, 1], c=x_kpca, s=50)
axis.set_title('initial space, g %03d' % g)
axis = plt.subplot(3, 2, 2 + 2 * i)
axis.scatter(x_kpca, [0] * n, c=x_kpca, s=50)
axis.set_title('redescription space, g %03d' % g)
plt.subplots_adjust(left=0.1,
bottom=0.1,
right=0.9,
top=0.9,
wspace=0.3,
hspace=0.3)
plt.suptitle('kPCA rbf')
plt.show()
def test_KPCA(*args):
x, y = args
kernels = ['linear', 'poly', 'rbf', 'sigmoid']
for k in kernels:
kpca = decomposition.KernelPCA(n_components=None, kernel=k)
kpca.fit(x, y)
print('kernel=%s-->lambdas: %s' % (k, kpca.lambdas_))
def test_pca(weight, components_num):
kpca = decomposition.KernelPCA(components_num,
degree=3,
kernel='rbf',
gamma=4)
principle_weight = kpca.fit_transform(weight)
return (principle_weight)
def plot_KPCA_poly(*data):
x, y = data
fig = plt.figure()
colors = ((1, 0, 0), (0, 1, 0), (0, 0, 1), (0.5, 0.5, 0), (0, 0.5, 0.5), (0.5, 0, 0.5), (0.4, 0.6, 0), (0.6, 0.4, 0) \
, (0, 0.6, 0.4), (0.5, 0.3, 0.2))
Params = [(3, 1, 1), (3, 10, 1), (3, 1, 10), (3, 10, 10), (10, 1, 1),
(10, 10, 1), (10, 1, 10), (10, 10, 10)]
for i, (p, gamma, r) in enumerate(Params):
kpca = decomposition.KernelPCA(n_components=2,
kernel='poly',
gamma=gamma,
degree=p,
coef0=r)
kpca.fit(x)
x_r = kpca.transform(x)
ax = fig.add_subplot(2, 4, i + 1)
for label, color in zip(np.unique(y), colors):
position = y == label # 这里的position类型为bool类型
ax.scatter(x_r[position, 0],
x_r[position, 1],
label="target=%d" % label,
color=color)
ax.set_xlabel("x[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("x[1]")
ax.legend(loc="best")
ax.set_title(r"$(%s (x \cdot z+1)+%s)^{%s}$" % (gamma, r, p))
plt.suptitle("KPCA-Poly")
plt.show()
def plot_KPCA_rbf(*data):
x, y = data
fig = plt.figure()
colors = ((1, 0, 0), (0, 1, 0), (0, 0, 1), (0.5, 0.5, 0), (0, 0.5, 0.5), (0.5, 0, 0.5), (0.4, 0.6, 0), (0.6, 0.4, 0) \
, (0, 0.6, 0.4), (0.5, 0.3, 0.2))
Gammas = [0.5, 1, 4, 10]
for i, gamma in enumerate(Gammas):
kpca = decomposition.KernelPCA(n_components=2,
kernel='rbf',
gamma=gamma)
kpca.fit(x)
x_r = kpca.transform(x)
ax = fig.add_subplot(2, 2, i + 1)
for label, color in zip(np.unique(y), colors):
position = y == label # 这里的position类型为bool类型
ax.scatter(x_r[position, 0],
x_r[position, 1],
label="target=%d" % label,
color=color)
ax.set_xlabel("x[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("x[1]")
ax.legend(loc="best")
ax.set_title(r"$\exp(-%s||x-z||^2)$" % gamma)
plt.suptitle("KPCA-rbf")
plt.show()
def plot_KPCA_rbf(*data):
'''
绘制经过 使用 rbf 核的KernelPCA 降维到二维之后的样本点
:param data: 可变参数。它是一个元组，这里要求其元素依次为：训练样本集、训练样本的标记
:return: None
'''
X,y=data
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)# 颜色集合，不同标记的样本染不同的颜色
Gammas=[0.5,1,4,10]# rbf 核的参数组成的列表。每个参数就是 gamma值
for i,gamma in enumerate(Gammas):
kpca=decomposition.KernelPCA(n_components=2,kernel='rbf',gamma=gamma)
kpca.fit(X)
X_r=kpca.transform(X)# 原始数据集转换到二维
ax=fig.add_subplot(2,2,i+1)## 两行两列，每个单元显示核函数为 rbf 的 KernelPCA 一组参数的效果图
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= %d"%label,
color=color)
ax.set_xlabel("X[0]")
ax.set_xticks([]) # 隐藏 x 轴刻度
ax.set_yticks([]) # 隐藏 y 轴刻度
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title(r"$\exp(-%s||x-z||^2)$"%gamma)
plt.suptitle("KPCA-rbf")
plt.show()
def plot_KPCA_poly(*data):
'''
绘制经过 使用 poly 核的KernelPCA 降维到二维之后的样本点
:param data: 可变参数。它是一个元组，这里要求其元素依次为：训练样本集、训练样本的标记
:return: None
'''
X,y=data
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)# 颜色集合，不同标记的样本染不同的颜色
Params=[(3,1,1),(3,10,1),(3,1,10),(3,10,10),(10,1,1),(10,10,1),(10,1,10),(10,10,10)] # poly 核的参数组成的列表。
# 每个元素是个元组，代表一组参数（依次为：p 值， gamma 值， r 值）
# p 取值为：3，10
# gamma 取值为 ：1，10
# r 取值为：1，10
# 排列组合一共 8 种组合
for i,(p,gamma,r) in enumerate(Params):
kpca=decomposition.KernelPCA(n_components=2,kernel='poly'
,gamma=gamma,degree=p,coef0=r) # poly 核，目标为2维
kpca.fit(X)
X_r=kpca.transform(X)# 原始数据集转换到二维
ax=fig.add_subplot(2,4,i+1)## 两行四列，每个单元显示核函数为 poly 的 KernelPCA 一组参数的效果图
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= %d"%label,
color=color)
ax.set_xlabel("X[0]")
ax.set_xticks([]) # 隐藏 x 轴刻度
ax.set_yticks([]) # 隐藏 y 轴刻度
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title(r"$ (%s (x \cdot z+1)+%s)^{%s}$"%(gamma,r,p))
plt.suptitle("KPCA-Poly")
plt.show()
def plot_KPCA(*data):
'''
绘制经过 KernelPCA 降维到二维之后的样本点
:param data: 可变参数。它是一个元组，这里要求其元素依次为：训练样本集、训练样本的标记
:return: None
'''
X,y=data
kernels=['linear','poly','rbf','sigmoid']
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)# 颜色集合，不同标记的样本染不同的颜色
for i,kernel in enumerate(kernels):
kpca=decomposition.KernelPCA(n_components=2,kernel=kernel)
kpca.fit(X)
X_r=kpca.transform(X)# 原始数据集转换到二维
ax=fig.add_subplot(2,2,i+1) ## 两行两列，每个单元显示一种核函数的 KernelPCA 的效果图
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= %d"%label,
color=color)
ax.set_xlabel("X[0]")
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title("kernel=%s"%kernel)
plt.suptitle("KPCA")
plt.show()
def plot_KPCA_sigmoid(*data):
'''
绘制经过 使用 sigmoid 核的KernelPCA 降维到二维之后的样本点
:param data: 可变参数。它是一个元组，这里要求其元素依次为：训练样本集、训练样本的标记
:return: None
'''
X,y=data
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)# 颜色集合，不同标记的样本染不同的颜色
Params=[(0.01,0.1),(0.01,0.2),(0.1,0.1),(0.1,0.2),(0.2,0.1),(0.2,0.2)]# sigmoid 核的参数组成的列表。
# 每个元素就是一种参数组合（依次为 gamma,coef0）
# gamma 取值为： 0.01，0.1，0.2
# coef0 取值为： 0.1,0.2
# 排列组合一共有 6 种组合
for i,(gamma,r) in enumerate(Params):
kpca=decomposition.KernelPCA(n_components=2,kernel='sigmoid',gamma=gamma,coef0=r)
kpca.fit(X)
X_r=kpca.transform(X)# 原始数据集转换到二维
ax=fig.add_subplot(3,2,i+1)## 三行两列，每个单元显示核函数为 sigmoid 的 KernelPCA 一组参数的效果图
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= %d"%label,
color=color)
ax.set_xlabel("X[0]")
ax.set_xticks([]) # 隐藏 x 轴刻度
ax.set_yticks([]) # 隐藏 y 轴刻度
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title(r"$\tanh(%s(x\cdot z)+%s)$"%(gamma,r))
plt.suptitle("KPCA-sigmoid")
plt.show()
def plot_KPCA_rbf(*data):
'''
graph with kernel of rbf
:param data: train_data, train_value
:return: None
'''
X,y=data
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)
Gammas=[0.5,1,4,10]
for i,gamma in enumerate(Gammas):
kpca=decomposition.KernelPCA(n_components=2,kernel='rbf',gamma=gamma)
kpca.fit(X)
X_r=kpca.transform(X)
ax=fig.add_subplot(2,2,i+1)
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= {0}".format(label),
color=color)
ax.set_xlabel("X[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title(r"$\exp(-{0}||x-z||^2)$".format(gamma))
plt.suptitle("KPCA-rbf")
plt.show()
def plot_KPCA_poly(*data):
'''
graph after KPCA with poly kernel
:param data: train_data, train_value
:return: None
'''
X,y=data
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)
Params=[(3,1,1),(3,10,1),(3,1,10),(3,10,10),(10,1,1),(10,10,1),(10,1,10),(10,10,10)] # parameter of poly
# p ， gamma ， r ）
# p ：3，10
# gamma ：1，10
# r ：1，10
# 8 combination
for i,(p,gamma,r) in enumerate(Params):
kpca=decomposition.KernelPCA(n_components=2,kernel='poly'
,gamma=gamma,degree=p,coef0=r)
kpca.fit(X)
X_r=kpca.transform(X)
ax=fig.add_subplot(2,4,i+1)
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= %d"%label,
color=color)
ax.set_xlabel("X[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title(r"$ ({0} (x \cdot z+1)+{1})^{{2}}$".format(gamma,r,p))
plt.suptitle("KPCA-Poly")
plt.show()
def plot_KPCA(*data):
'''
graph after KPCA
:param data: train_data, train_value
:return: None
'''
X,y=data
kernels=['linear','poly','rbf','sigmoid']
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)
for i,kernel in enumerate(kernels):
kpca=decomposition.KernelPCA(n_components=2,kernel=kernel)
kpca.fit(X)
X_r=kpca.transform(X)
ax=fig.add_subplot(2,2,i+1)
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= %d"%label,
color=color)
ax.set_xlabel("X[0]")
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title("kernel={0}".format(kernel))
plt.suptitle("KPCA")
plt.show()
def compare_KPCA():
data, target = generate_circle_data3()
pca = decomposition.PCA(n_components=2)
data1 = pca.fit_transform(data)
try:
figure1 = plt.figure(1)
ax = ax3(figure1)
ax.scatter3D(data[:, 0],
data[:, 1],
data[:, 2],
c=[color[i] for i in target],
alpha=0.5)
plt.title('Origin Data')
except:
pass
figure2 = plt.figure(2)
k = 1
for kernel in ['linear', 'rbf', 'poly', 'sigmoid']: # 线性核即是原始的pca
plt.subplot(1, 4, k)
k += 1
kpca = decomposition.KernelPCA(n_components=2, kernel=kernel)
data_reduced = kpca.fit_transform(data)
plt.scatter(data_reduced[:, 0],
data_reduced[:, 1],
c=[color[i] for i in target])
plt.title(kernel)
plt.suptitle('The Comparasion Between KPCA')
plt.show()
def plot_KPCA_sigmoid(*data):
"""
绘制经过使用sigmoid核的KernelPCA降维到二维之后的样本点
"""
x,y = data
fig = plt.figure()
colors = ((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0.5,0,0.5),\
(0,0.5,0.5),(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),\
(0.5,0.3,0.2),)
"""
下面的Params列表中的每一个元素是sigmoid核参数的排列组合
gamma的取值为:0.01,0.1,0.2
coef0的取值为:0.1,0.2
因此，排列组合数为6
"""
Params=[(0.01,0.1),(0.01,0.2),(0.1,0.1),(0.1,0.2),(0.2,0.1),\
(0.2,0.2)]
for i,(gamma,r) in enumerate(Params):
kpca = decomposition.KernelPCA(n_components=2,kernel="sigmoid",\
gamma=gamma,coef0=r)
kpca.fit(x)
x_r = kpca.transform(x)
ax = fig.add_subplot(3,2,i+1)
for label,color in zip(np.unique(y),colors):
position=y==label
ax.scatter(x_r[position,0],x_r[position,1],\
label="target=%d" % label,color=color)
ax.set_xlabel("x[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("x[1]")
ax.legend(loc="best")
ax.set_title(r"$\tanh(%s(x\cdot z)+%s)$"%(gamma,r))
plt.suptitle("KPCA-sigmoid")
plt.show()
def plot_KPCA_sigmoid(*data):
x, y = data
fig = plt.figure()
colors = ((1, 0, 0), (0, 1, 0), (0, 0, 1), (0.5, 0.5, 0), (0, 0.5, 0.5), (0.5, 0, 0.5), (0.4, 0.6, 0), (0.6, 0.4, 0) \
, (0, 0.6, 0.4), (0.5, 0.3, 0.2))
Params = [(0.01, 0.1), (0.01, 0.2), (0.1, 0.1), (0.1, 0.2), (0.2, 0.1),
(0.2, 0.2)]
for i, (gamma, r) in enumerate(Params):
kpca = decomposition.KernelPCA(n_components=2,
kernel='sigmoid',
gamma=gamma,
coef0=r)
kpca.fit(x)
x_r = kpca.transform(x)
ax = fig.add_subplot(3, 2, i + 1)
for label, color in zip(np.unique(y), colors):
position = y == label # 这里的position类型为bool类型
ax.scatter(x_r[position, 0],
x_r[position, 1],
label="target=%d" % label,
color=color)
ax.set_xlabel("x[0]")
ax.set_xticks([]) # 修改轴的刻度
ax.set_yticks([])
ax.set_ylabel("x[1]")
ax.legend(loc="best")
ax.set_title(r"$\tanh(%s(x\cdot z)+%s)$" % (gamma, r))
plt.suptitle("KPCA-sigmoid")
plt.show()
def plot_KPCA_rbf(*data):
"""
绘制经过使用rbf核的kernelPCA降维到二维之后的样本点
"""
x,y = data
fig = plt.figure()
colors = ((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0.5,0,0.5),\
(0,0.5,0.5),(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),\
(0.5,0.3,0.2),)
Gammas=[0.5,1,4,10] #rbf核的参数组成的列表，每个参数就是gamma值
for i,gamma in enumerate(Gammas):
kpca = decomposition.KernelPCA(n_components=2,kernel="rbf",\
gamma=gamma)
kpca.fit(x)
x_r = kpca.transform(x) #将原始数据降到二维
ax = fig.add_subplot(2,2,i+1)
for label,color in zip(np.unique(y),colors):
position=y==label
ax.scatter(x_r[position,0],x_r[position,1],\
label="target=%d" % label,color=color)
ax.set_xlabel("x[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("x[1]")
ax.legend(loc="best")
ax.set_title(r"$\exp(-%s||x-z||^2)$"%gamma)
plt.suptitle("KPCA-rbf")
plt.show()
def feature_analysis(data=None,
feature=None,
pca_components=None,
graph=False,
start=None,
end=None):
X = data[feature].values.reshape(-1, len(feature))
X_train = data[feature].ix[start:end].values.reshape(-1, len(feature))
pca = decomposition.KernelPCA(n_components=pca_components)
pca.fit(X_train)
pcaresult = pca.transform(X)
# print(pca.components_)
ica = decomposition.FastICA(n_components=pca_components)
ica.fit(X_train)
icaresult = ica.transform(X)
pcaresult = (pcaresult.T.reshape(pca_components, -1))
icaresult = (icaresult.T.reshape(pca_components, -1))
for n in range(pca_components):
data['%s-pcomponent' % str(n + 1)] = pcaresult[n]
data['%s-icomponent' % str(n + 1)] = icaresult[n]
# print(pca.explained_variance_ratio_.cumsum())
if graph is True:
for j in range(1, pca_components + 1):
plt.clf()
data['%i-pcomponent' % j].plot()
plt.legend()
plt.plot()
plt.show()
return data
def dimension_redu(_data, _method):
'''
A subfunction to transform a multi-dimensional dataset from the high-diemsnional space to a one-dimensional space
:param _data: a multi-dimensional dataset
:param _method: one or multiple dimensionality-reduction techniques
:return: a one-dimensional vector
'''
min_max_scaler = preprocessing.MinMaxScaler()
# print(_data[:, :-2])
z_data = min_max_scaler.fit_transform(_data)
# print(z_data)
from sklearn import decomposition
# Choose one method
if _method == 'PCA':
dim_redu_method = decomposition.PCA(n_components=1)
elif _method == 'FA':
dim_redu_method = decomposition.FactorAnalysis(n_components=1, max_iter=5000)
elif _method == 'KernelPCA':
dim_redu_method = decomposition.KernelPCA(kernel='cosine', n_components=1)
elif _method == 'TruncatedSVD':
dim_redu_method = decomposition.TruncatedSVD(1)
dimension_redu_vector = dim_redu_method.fit_transform(z_data)
z_dimension_redu_vector = np.ndarray.tolist(min_max_scaler.fit_transform(dimension_redu_vector))
return z_dimension_redu_vector
def preprocess(normalization=False, standarization=False, pca=False, whitening=False, kpca=False):
global train_inputs, test_inputs, input_size
if normalization:
train_inputs = preprocessing.normalize(train_inputs)
test_inputs = preprocessing.normalize(test_inputs)
if standarization:
train_inputs = preprocessing.StandardScaler().fit_transform(train_inputs)
test_inputs = preprocessing.StandardScaler().fit_transform(test_inputs)
if pca:
train_inputs = decomposition.PCA(n_components='mle', whiten=whitening, svd_solver='full').fit_transform(train_inputs)
test_inputs = decomposition.PCA(n_components='mle', whiten=whitening, svd_solver='full').fit_transform(test_inputs)
if kpca:
train_inputs = decomposition.KernelPCA(kernel='rbf', remove_zero_eig=True).fit_transform(train_inputs)
test_inputs = decomposition.KernelPCA(kernel='rbf', remove_zero_eig=True).fit_transform(test_inputs)
input_size = len( train_inputs[0] )
def plot_KPCA_sigmoid(*data):
'''
graph with sigmoid kernel
:param data: train_data, train_value
:return: None
'''
X,y=data
fig=plt.figure()
colors=((1,0,0),(0,1,0),(0,0,1),(0.5,0.5,0),(0,0.5,0.5),(0.5,0,0.5),
(0.4,0.6,0),(0.6,0.4,0),(0,0.6,0.4),(0.5,0.3,0.2),)
Params=[(0.01,0.1),(0.01,0.2),(0.1,0.1),(0.1,0.2),(0.2,0.1),(0.2,0.2)]# parameter of sigmoid kernel
# gamma,coef0
# gamma ： 0.01，0.1，0.2
# coef0 ： 0.1,0.2
# 6 combination
for i,(gamma,r) in enumerate(Params):
kpca=decomposition.KernelPCA(n_components=2,kernel='sigmoid',gamma=gamma,coef0=r)
kpca.fit(X)
X_r=kpca.transform(X)
ax=fig.add_subplot(3,2,i+1)
for label ,color in zip( np.unique(y),colors):
position=y==label
ax.scatter(X_r[position,0],X_r[position,1],label="target= {0}".format(label),
color=color)
ax.set_xlabel("X[0]")
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title(r"$\tanh({0}(x\cdot z)+{1})$".format(gamma,r))
plt.suptitle("KPCA-sigmoid")
plt.show()
def pca(self, X):
pca = decomposition.KernelPCA(n_components=None, kernel='linear', gamma=None, degree=3, coef0=1, kernel_params=None, alpha=1.0,
fit_inverse_transform=False, eigen_solver='auto', tol=0, max_iter=None, remove_zero_eig=False,
random_state=None, copy_X=True, n_jobs=1)
pca.fit(X)
X = pca.transform(X)
return X
def plot_kpca(*data):
x, y = data
fig = plt.figure()
colors = ((1, 0, 0), (0, 1, 0), (0, 0, 1))
gammas = [0.5, 1, 4, 10]
for i, gamma in enumerate(gammas):
print("-" * 50)
print(gamma)
kpca = decomposition.KernelPCA(n_components=2,
kernel="rbf",
gamma=gamma)
kpca.fit(x)
x_r = kpca.transform(x)
# 展示
ax = fig.add_subplot(2, 2, i + 1)
for label, color in zip(np.unique(y), colors):
print(label, " ", color)
position = y == label
ax.scatter(x_r[position, 0],
x_r[position, 1],
label="target=%d" % label,
color=color)
ax.set_xlabel("x[0]")
ax.set_ylabel("x[1]")
ax.set_xticks([])
ax.set_yticks([])
ax.legend(loc="best")
ax.set_title(r"$\exp(-%s||x-z||^2)$" % gamma)
plt.suptitle("KPCA-rbf")
plt.show()
def plot_KPCA(*data):
X, Y = data
kernels = ['linear', 'poly', 'rbf', 'sigmoid']
fig = plt.figure()
colors = (
(1, 0, 0),
(0, 1, 0),
(0, 0, 1),
(0.5, 0.5, 0),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
(0.4, 0.6, 0),
(0.6, 0.4, 0),
(0, 0.6, 0.4),
(0.5, 0.3, 0.2),
)
for i, kernel in enumerate(kernels):
kpca = decomposition.KernelPCA(n_components=2, kernel=kernel)
kpca.fit(X)
X_r = kpca.transform(X)
ax = fig.add_subplot(2, 2, i + 1)
for label, color in zip(np.unique(Y), colors):
position = Y == label
ax.scatter(X_r[position, 0],
X_r[position, 1],
label="target=%d" % label,
color=color)
ax.set_xlabel("X[0]")
ax.set_ylabel("X[1]")
ax.legend(loc="best")
ax.set_title("kernel=%s" % kernel)
plt.suptitle("KPCA")
plt.show()
def test_KPCA(*data):
X, Y = data
kernels = ['linear', 'poly', 'rbf', 'sigmoid']
for kernel in kernels:
kpca = decomposition.KernelPCA(n_components=None, kernel=kernel)
kpca.fit(X)
print("kernel=%s-->lambdas:%s" % (kernel, kpca.lambdas_))
def plot_kpca(*data):
x, y = data
fig = plt.figure()
colors = ((1, 0, 0), (0, 1, 0), (0, 0, 1))
kernels = ["linear", "poly", "rbf", "sigmoid"]
for i, kernel in enumerate(kernels):
print("-" * 50)
kpca = decomposition.KernelPCA(n_components=None, kernel=kernel)
kpca.fit(x)
x_r = kpca.transform(x)
ax = fig.add_subplot(2, 2, i + 1)
for label, color in zip(np.unique(y), colors):
print(label, " ", color)
position = y == label
ax.scatter(x_r[position, 0],
x_r[position, 1],
label="target=%d" % label,
color=color)
ax.set_xlabel("x[0]")
ax.set_ylabel("y[0]")
ax.legend(loc="best")
ax.set_title("kernel=%s" % kernel)
plt.suptitle("KPCA")
plt.show()
def _gen_gbdt_features(self, pool):
final = []
col_gbdts = ['gbdt_' + str(i) for i in range(self.n_tree)]
for g in pool.groupby(self.kcols):
(keys, df) = g
train = df[df.time_window_start < pd.datetime(2016, 10, 18)]
train_x = train.drop([*self.timecols, *self.kcols, self.vcol], axis=1)
train_y = train[self.vcol]
regor = GradientBoostingRegressor(
loss='huber',
n_estimators=self.n_tree, max_leaf_nodes=10)
model = regor.fit(train_x, train_y)
gbdt_features = []
df_x = df.drop([*self.timecols, *self.kcols, self.vcol], axis=1)
assert len(model.estimators_) == self.n_tree, 'n_tree is not match!'
for tree in model.estimators_:
gbdt_features.append(tree[0].apply(df_x))
gbdt_features = np.array(gbdt_features).T
df_gbdts = pd.DataFrame(gbdt_features, columns=col_gbdts)
# ignore_index will drop column names, so we do not use it here
df.reset_index(drop=True, inplace=True)
df_gbdts.reset_index(drop=True, inplace=True)
final.append(pd.concat([df, df_gbdts], axis=1))
final = pd.concat(final)
# one-hot code
origs = final[list(set(final.columns) - set(col_gbdts))]
gbdts = final[col_gbdts]
for gbdtcol in col_gbdts:
gbdts[gbdtcol] = gbdts[gbdtcol].astype('category')
gbdts_dummies = pd.get_dummies(gbdts).reset_index(drop=True)
n_feature = int(origs.shape[1] / 4)
# remove duplicated gdbt features
gbdts = gbdts_dummies.T.drop_duplicates().T
#gbdts = preprocessing.RobustScaler().fit_transform(gbdts)
#gbdts = decomposition.TruncatedSVD(
# n_components=int(origs.shape[1] / 4), n_iter=20
gbdts = decomposition.KernelPCA(
n_components=n_feature
).fit_transform(gbdts)
gbdts = pd.DataFrame(
gbdts, columns=['gbdt_{0}'.format(i) for i in range(n_feature)])
print('GDBT Feature Shape:', gbdts.shape, origs.shape)
origs.reset_index(drop=True, inplace=True)
gbdts.reset_index(drop=True, inplace=True)
return pd.concat([origs, gbdts], axis=1)
def add_kernel_pca_reduction(self, n_components: int = None,
kernel: str = Union['linear', 'poly', 'rbf', 'sigmoid', 'cosine', 'precomputed'],
gamma: float = None, degree: int = 3, coef0: float = 1, n_jobs: int = -1,
remove_zero_eig: bool = False, fit_inverse_transform: bool = False, **kwargs):
# n_components can also be 'mle' or a number in [0,1]
self._pca.append(decomposition.KernelPCA(n_components=n_components, kernel=kernel, gamma=gamma, degree=degree,
coef0=coef0, fit_inverse_transform=fit_inverse_transform, n_jobs=-1,
remove_zero_eig=remove_zero_eig, **kwargs))