Machine Learning Primer -- Basics
Claudius Gros, WS 2024/25
Institut für theoretische Physik
Goethe-University Frankfurt a.M.
Machine Learning - Linear Classifier
linear classifier
- A method using a linear combination of features
for the characterization or the separation of
two or more classes of objects or events.
- The resulting combination may be used as a linear
classifier, or, more commonly, for dimensionality
reduction before later classification.
$\qquad\quad
y= f(\mathbf{w}\cdot\mathbf{x}-b),
\qquad\quad
\mathbf{w}\cdot\mathbf{x}=\sum_{j=0}^{d-1} w_j x_j
$
- feature vector: $\ \ \mathbf{x}=(x_0,\,..,\,x_{d-1})$
weight vector: $\ \ \mathbf{w}=(w_0,\,..,\,w_{d-1})$
offset (threshold): $\ \ b$
- (non-linear) transfer function: $\ \ f(z)$
hyperplane
$$ \mathbf{x}\qquad \mathrm{such\ that}
\qquad
\fbox{$\phantom{\big|}\mathbf{w}\cdot\mathbf{x}=b\phantom{\big|}$}
$$
- a $(d-1)$ dimensional hyperplane divides a $d$ dimensional space into two halves
$$
\begin{array}{rcl}
\mathrm{right-side} &:& \mathbf{w}\cdot\mathbf{x}> b \\
\mathrm{left-side} &:& \mathbf{w}\cdot\mathbf{x}< b
\end{array}
$$
- use transfer function $\ \ f(z)=y(z) \ \ $ to map to feature class
$$
y(z<0)\ \to\ -1,\quad\qquad
y(z>0)\ \to\ 1,\quad\qquad
z=\mathbf{w}\cdot\mathbf{x}-b
$$
- also called 'perceptron' $\ \ \to \ \ $ neural networks
task
- determine "optimal"
weights $\ \ \mathbf{w}$
offset $\ \ b$
training / testing sets
supervised learning
- labeled data: $\ \ N=N_1+N_2$
$
\qquad
\begin{array}{rcl}
\mathrm{first\ feature} &:& \{\mathbf{x}_\alpha\}, \qquad \alpha\in[1,N_1] \\
\mathrm{second\ feature} &:& \{\mathbf{x}_\beta\}, \qquad \beta\in[N_1+1,N]
\end{array}
$
- divide randomly into training / test data
: typically 70/30, 80/20, ...
- non-optimized model parameters (hyper parameters)
may be fine tuned using a validation data set, if needed
center of mass of individual classes
$$
\mathbf{m}_1 = \frac{1}{N_1}\sum_\alpha \mathbf{x}_\alpha,
\quad\qquad
\mathbf{m}_2 = \frac{1}{N_2}\sum_\beta \mathbf{x}_\beta
$$
- implicit: sum is over training set
- intuition: $\ \ \mathbf{w}\ \propto \ \mathbf{m}_1-\mathbf{m}_2$
: only true for uniformly distributed data
covariance matrix
probability distribution
$\qquad\quad
p(\mathbf{x})\ge0,
\qquad\qquad
\int p(\mathbf{x})\,d\mathbf{x}=1
$
- generating the data
$
p(\mathbf{x}) \quad\longrightarrow
\quad \mathbf{x}_\alpha,
$
with mean (generic)
$
\mathbf{m} = \frac{1}{N}\sum_\alpha \mathbf{x}_\alpha
= \int \mathbf{x}\,p(\mathbf{x})\,d\mathbf{x}
= \langle \mathbf{x}\rangle
$
- Cartesian components
$$
\mathbf{x}=\left(\begin{array}{c}
x_0\\ \vdots \\ x_{d-1}\end{array}\right),\qquad\quad
\mathbf{m}=\left(\begin{array}{c}
m_0\\ \vdots \\ m_{d-1}\end{array}\right),\qquad\quad
\mathbf{x}^T=(x_0,\,\dots,x_{d-1})
$$
note: distinguish here between and vector $\ \ \mathbf{x}\ \ $ and
transposed vector $\ \ \mathbf{x}^T\ \ $
covariance matrix
$$
S_{ij} = \big\langle (x_i-m_i)(x_j-m_j)\big\rangle
$$
- symmetric
: eigenvalues are real
: they correspond to half-width of covariance ellipse
- matrix notation
$$
\hat S =
\big\langle (\mathbf{x}-\mathbf{m})\,(\mathbf{x}-\mathbf{m})^T\big\rangle,
\qquad\quad
S_{ij} = (\hat{S})_{ij},
\qquad\quad
\mathbf{x}=\left(\begin{array}{c}
x_0\\ \vdots \\ x_{d-1}
\end{array}\right)
$$
- outer product
$$ \mathbf{x}\,\mathbf{x}^T= \mathbf{x}\otimes\mathbf{x},
\qquad\quad \big(\mathbf{x}\,\mathbf{x}^T\big)_{ij}=x_ix_j
$$
note
$$ \mathbf{x}^T\mathbf{x} = \mathbf{x}\cdot\mathbf{x}
= \sum_i x_i x_i
$$
covariance ellipse
$$
\frac{x^2}{a^2}+\frac{y^2}{b^2} = 1,
\quad\qquad
\left\{\begin{array}{rcl}
x(t) &=& \sqrt{\lambda_1}\cos\Theta\cos t
-\sqrt{\lambda_2}\sin\Theta\sin t
\\[0.1ex]
y(t) &=& \sqrt{\lambda_1}\sin\Theta\cos t
+\sqrt{\lambda_2}\cos\Theta\sin t
\end{array}\right.
$$
- angle with x-axis: $\ \Theta$
- eigenvalues $\ \lambda_i$
$$
\mathbf{x} =
\hat{V} \cdot \hat{\Lambda} \cdot
\mathbf{T},
\quad\qquad
\mathbf{x} = {x\choose y},
\quad\qquad
\mathbf{T} = {\cos t\choose \sin t},
$$
- eigen-vector matrix $\ \hat{V}$
$$
\hat{V}=\left(\begin{array}{cc}
\cos\Theta & -\sin\Theta \\
\sin\Theta & \cos\Theta
\end{array}\right)
\quad\qquad
\hat{\Lambda}=\left(\begin{array}{cc}
\sqrt{\lambda_1} & 0 \\ 0 & \sqrt{\lambda_2},
\end{array}\right)
$$
plotting a covariance ellipse
-
if (__name__ == "__main__"):
not executed when imported as a module
allows to include testing
- $A=\sum_i\lambda_i |\lambda_i\rangle\langle\lambda_i|$
matrix decomposition in terms of eigensystem
projection operators $|\lambda\rangle\langle\lambda|$
are outer products
-
np.random.multivariate_normal(mean,
coVar, N)
draws N samples from a
multi-variate Gaussian with covariance matrix
coVar
- two covariance matrices:
for data generation and measured
#!/usr/bin/env python3
import math # math
import numpy as np # numerics
import matplotlib.pyplot as plt # plotting
from numpy import linalg as LA # linear algebra
# ***
# *** covariance matrix from data
# ***
def covarianceMatrix(data):
'''normalized covariance matrix of input data'''
nRow = len(data) # number of data points
nCol = len(data[0]) # dimension
mean = [0.0 for iCol in range(nCol)]
for thisRow in data: # loop over data points
mean += thisRow*1.0/nRow # vector-mean
#
coVar = np.zeros((nCol,nCol)) # empty matrix
for thisRow in data:
dataPoint = thisRow - mean # shifted data point
coVar += np.outer(dataPoint,dataPoint)/nRow # outer product
#
if (1==2):
print("\ninput data\n", data)
print("nRow, nCol\n", nRow, nCol)
print("mean\n", mean)
print("\n covariance matrix: measured \n",coVar)
#
return mean, coVar # returning both
# ***
# *** generate data for plotting an ellipse
# ***
def plotEllipseData(data):
"generates ellipse from symmetric 2x2 slice of the input matrix"
#
slice22 = [inner[:2] for inner in data[:2]] # slice
slice22[0][1] = slice22[1][0] # symmetrize
# ^ should not be necessary
eigenValues, eigenVectors = LA.eig(slice22) # eigensystem
#
if (eigenValues[0]<0.0) or (eigenValues[1]<0.0):
print("# plotEllipseData: only positive eigenvalues (variance)")
return
#
if (1==2):
print("\n# coVar \n", coVar )
print("\n# slice22 ", slice22)
print("\n# eigenValues ", eigenValues)
print("\n# eigenVectors\n",eigenVectors)
#
a = math.sqrt(eigenValues[0])
b = math.sqrt(eigenValues[1])
cTheta = eigenVectors[0][0]
sTheta = eigenVectors[1][0]
x = []
y = []
for i in range(nPoints:=101): # walrus assignment
tt = i*2.0*math.pi/(nPoints-1) # full loop
cc = math.cos(tt)
ss = math.sin(tt)
xx = a*cTheta*cc - b*sTheta*ss
yy = a*sTheta*cc + b*cTheta*ss
x.append(xx)
y.append(yy)
# print(xx,yy)
return x, y
# ***
# *** generate 2D test data
# ***
def testData(angle, var1, var2, nData, startMean=[0.0,0.0]):
"2D Gaussian for a given angle and main variances.\
A = \sum_i \lambda_i |lambda_i><lambda_i|"
#
eigen1 = [math.cos(angle),-math.sin(angle)]
eigen2 = [math.sin(angle), math.cos(angle)]
startCoVar = var1*np.outer(eigen1,eigen1)
startCoVar += var2*np.outer(eigen2,eigen2)
print("\n covariance matrix: data generation \n",startCoVar)
return np.random.multivariate_normal(startMean, startCoVar, nData)
# ***
# *** main (with a block)
# ***
if (__name__ == "__main__"): # blocking out-of-use access
#
dataMatrix = testData(0.3*math.pi, 1.0, 9.0, 100)
mean, coVar = covarianceMatrix(dataMatrix)
if (1==2):
print("\n#main: data\n", dataMatrix)
print("#main: mean\n", mean)
print("\n#main: coVar matrix \n",coVar)
xEllipse, yEllipse = plotEllipseData(coVar) # coVar-ellipse
xData = [thisRow[0] for thisRow in dataMatrix]
yData = [thisRow[1] for thisRow in dataMatrix]
Z_90 = math.sqrt(4.601) # 90% confidence
Z_95 = math.sqrt(5.991) # 95% confidence
Z_99 = math.sqrt(9.210) # 99% confidence
#
xE_90 = [Z_90*xx + mean[0] for xx in xEllipse]
yE_90 = [Z_90*yy + mean[1] for yy in yEllipse]
xE_99 = [Z_99*xx + mean[0] for xx in xEllipse]
yE_99 = [Z_99*yy + mean[1] for yy in yEllipse]
#
plt.plot(xE_90, yE_90, label="90%")
plt.plot(xE_99, yE_99, label="99%")
plt.plot(xData, yData, "ob", markersize=5)
#
plt.legend(loc="upper left")
plt.axis('square') # square plot
plt.savefig('foo.svg') # export figure
plt.show()
python intermezzo
- loading a privat module
:: plotting the covariance ellipse
-
__pycache__
:: directory created when importing private files
- imports are not transferred
#!/usr/bin/env python3
import math # math
import matplotlib.pyplot as plt # plotting
import ML_covarianceMatrix as CM # loading user-defined module
dataMatrix = CM.testData(0.3*math.pi, 1.0, 9.0, 100)
mean, coVar = CM.covarianceMatrix(dataMatrix)
xEllipse, yEllipse = CM.plotEllipseData(coVar) # coVar-ellipse
xData = [thisRow[0] for thisRow in dataMatrix]
yData = [thisRow[1] for thisRow in dataMatrix]
Z_90 = math.sqrt(4.601) # 90% confidence
Z_95 = math.sqrt(5.991) # 95% confidence
Z_99 = math.sqrt(9.210) # 99% confidence
xE_90 = [Z_90*xx + mean[0] for xx in xEllipse]
yE_90 = [Z_90*yy + mean[1] for yy in yEllipse]
xE_99 = [Z_99*xx + mean[0] for xx in xEllipse]
yE_99 = [Z_99*yy + mean[1] for yy in yEllipse]
plt.plot(xE_90, yE_90, label="90%")
plt.plot(xE_99, yE_99, label="99%")
plt.plot(xData, yData, "ob", markersize=5)
plt.legend(loc="upper left")
plt.axis('square') # square plot
plt.savefig('foo.svg') # export figure
plt.show()
multivariate Gaussians
- uni/multi-variate : one/multi-dimenional
- one-dimensional Gaussian
$$
N(x) = \frac{1}{\sqrt{2\pi\sigma^2}}e^{-(x-\mu)^2/(2\sigma^2)}
$$
- multivariate
$$
N(\mathbf{x}) = \frac{1}{\sqrt{(2\pi)^d|\hat{S}|}}
\exp\left(\frac{-1}{2}({\mathbf x}-{\mathbf m})^T{\hat{S}}^{-1}
({\mathbf x}-{\mathbf m})\right)
$$
diagonal case
$$
\hat{S}=\left(\begin{array}{ccc}
\sigma_0^2 & \dots & 0 \\
\vdots & \ddots & \vdots \\
0 & \dots & \sigma_{d-1}^2
\end{array}\right),
\qquad\quad
\sigma_k^2 = \big\langle (x_k-m_k)^2\big\rangle
$$
- if $\ \ \big\langle (x_i-m_i)(x_j-m_j)\big\rangle=0\quad \mbox{for}\quad i\ne j$
$i\ne j\ \ $ uncorrelated
$$
|\hat{S}| = \prod_k \sigma_k^2,
\qquad\quad
\hat{S}^{-1}=\left(\begin{array}{ccc}
1/\sigma_0^2 & \dots & 0 \\
\vdots & \ddots & \vdots \\
0 & \dots & 1/\sigma_{d-1}^2
\end{array}\right)
$$
- multivariate Gaussian factorizes
$$
N(\mathbf{x}) = \prod_k
\frac{\exp(-(x_k-m_k)^2/(2\sigma_k^2))}{\sqrt{2\pi\sigma_k^2}}
$$
statistics of features
- a linear classifiers combines data of features via
$\ \ \mathbf{w}\cdot\mathbf{x}_\alpha,\qquad \alpha=1,2$
- mean $\ \ \mu_\alpha=\mathbf{w}\cdot\mathbf{m}_\alpha$
- variance
$$
\sigma_\alpha^2=\left\langle
(\mathbf{w}\cdot\mathbf{x}_\alpha
-\mathbf{w}\cdot\mathbf{m}_\alpha)^2
\right\rangle = \left\langle
(\mathbf{w}\cdot(\mathbf{x}_\alpha -\mathbf{m}_\alpha))^2
\right\rangle = \left\langle
(\mathbf{w}^T(\mathbf{x}_\alpha -\mathbf{m}_\alpha))^2
\right\rangle
$$
or
$$
\sigma_\alpha^2=\left\langle
\mathbf{w}^T
(\mathbf{x}_\alpha -\mathbf{m}_\alpha)\,
(\mathbf{x}_\alpha -\mathbf{m}_\alpha)^T
\mathbf{w}
\right\rangle =
\mathbf{w}^T \left\langle
(\mathbf{x}_\alpha -\mathbf{m}_\alpha)\,
(\mathbf{x}_\alpha -\mathbf{m}_\alpha)^T
\right\rangle \mathbf{w}
$$
in terms of the covariance matrix
$$
\fbox{$\phantom{\big|}\sigma_\alpha^2=
\mathbf{w}^T \hat S_\alpha \mathbf{w}\phantom{\big|}$}
\qquad\quad
\hat S_\alpha =
\big\langle (\mathbf{x}_\alpha-\mathbf{m}_\alpha)\,
(\mathbf{x}_\alpha-\mathbf{m}_\alpha)^T\big\rangle
$$
linear discriminant analysis (LDA)
- linear discriminant, mean, variance
$$
\mathbf{w}\cdot\mathbf{x}_\alpha,\qquad\quad
\mu_\alpha=\mathbf{w}\cdot\mathbf{m}_\alpha,\qquad\quad
\sigma_\alpha^2=\mathbf{w}^T \hat S_\alpha \mathbf{w}
$$
- many linear classifier exist
Fisher objective function
- maximize $\ \ (\mu_1-\mu_2)^2\ \ $
keeping the combined variance $\ \ \sigma_1^2+\sigma_2^2\ \ $ constant
task
- find feature vector $\ \ \mathbf{w}\ \ $ maximizing
$$
S = \frac{(\mu_1-\mu_2)^2}{\sigma_1^2+\sigma_2^2}
= \frac{(\mathbf{w}\cdot(\mathbf{m}_1-\mathbf{m}_2))^2}
{\mathbf{w}^T (\hat{S}_1+\hat{S}_2) \mathbf{w}}
= \frac{\mathbf{w}^T(\mathbf{m}_1-\mathbf{m}_2)
(\mathbf{m}_1-\mathbf{m}_2)^T\mathbf{w}}
{\mathbf{w}^T (\hat{S}_1+\hat{S}_2) \mathbf{w}}
$$
$$
S = \frac{\mathbf{w}^T\hat{A}\mathbf{w}}
{\mathbf{w}^T \hat{B}\mathbf{w}}
\qquad\quad
\hat{A}=(\mathbf{m}_1-\mathbf{m}_2)(\mathbf{m}_1-\mathbf{m}_2)^T
\qquad\quad
\hat{B}=\hat{S}_1+\hat{S}_2
$$
- quantum mechanics:
$\mathbf{w}\ \ $ wavefunction
$\hat{A}\ \ $ Hamilton operator
$\hat{B}\ \ $ identiy matrix
$S\ \ $ expectation value of energy
LDA - maximization
$$
S = \frac{\mathbf{w}^T\hat{A}\mathbf{w}}
{\mathbf{w}^T \hat{B}\mathbf{w}}
\qquad\quad
\hat{A}=(\mathbf{m}_1-\mathbf{m}_2)(\mathbf{m}_1-\mathbf{m}_2)^T
\qquad\quad
\hat{B}=\hat{S}_1+\hat{S}_2
$$
- variation
$$
\delta S=
\frac{\mathbf{w}^T\hat{A}\,\delta\mathbf{w}}{\mathbf{w}^T \hat{B}\mathbf{w}}
-
\frac{\mathbf{w}^T\hat{A}\mathbf{w}}{(\mathbf{w}^T \hat{B}\mathbf{w})^2}
\mathbf{w}^T \hat{B}\,\delta\mathbf{w}
$$
plus terms in $\ \ (\delta\mathbf{w})^T$
- stationarity
$$
\delta S=0\qquad\quad
\big(\mathbf{w}^T \hat{B}\mathbf{w}\big)\big(\mathbf{w}^T\hat{A}\big)=
\big(\mathbf{w}^T \hat{A}\mathbf{w}\big)\big(\mathbf{w}^T\hat{B}\big)
$$
proportionality factors
$$
\mathbf{w}^T\hat{A}=\mathbf{w}^T
\big((\mathbf{m}_1-\mathbf{m}_2)(\mathbf{m}_1-\mathbf{m}_2)^T\big)
\propto
(\mathbf{m}_1-\mathbf{m}_2)^T
$$
- scalar quantities
$$
\mathbf{w}^T(\mathbf{m}_1-\mathbf{m}_2)\qquad\quad
\mathbf{w}^T \hat{A}\mathbf{w}\qquad\quad
\mathbf{w}^T \hat{B}\mathbf{w}
$$
- proportionality
$$
(\mathbf{m}_1-\mathbf{m}_2)^T\propto \mathbf{w}^T\hat{B}
\qquad\quad
\mathbf{m}_1-\mathbf{m}_2\propto
\hat{B}^T \mathbf{w}= \hat{B} \mathbf{w}
\qquad\quad
\hat{B}^T = \hat{B}
$$
- the solution for the feature vector
$$
\fbox{$\phantom{\big|}
\mathbf{w}\propto \big(\hat{S}_1+\hat{S}_2\big)^{-1}
\big(\mathbf{m}_1-\mathbf{m}_2\big)
\phantom{\big|}$}
\qquad
\hat{B}=\hat{S}_1+\hat{S}_2
$$
may be normalized to unity
regularization
- the system of linear equation
$$
\big(\hat{S}_1+\hat{S}_2\big)\mathbf{w}=
\mathbf{m}_1-\mathbf{m}_2
\qquad\quad
\hat{S}_1+\hat{S}_2\ \to\ (1-\lambda)\big(\hat{S}_1+\hat{S}_2\big)
+\lambda \hat{I}
$$
may be regularized for a singular combined covariance matrix
$\ \ \hat{S}_1+\hat{S}_2$
- shrinking intensity (regularization parameter): $\ \ \lambda$
- identity matrix: $\ \ \hat{I}$
LDA threshold
- already determined: $\ \ \mathbf{w}$
$$
z_\alpha=\mathbf{w}\cdot\mathbf{x}_\alpha\qquad\quad
\mu_\alpha=\mathbf{w}\cdot\mathbf{m}_\alpha\qquad\quad
\sigma_\alpha^2=\mathbf{w}^T \hat S_\alpha \mathbf{w}\qquad\quad
|\mathbf{w}|=1
$$
- determine now threshold $\ \ b:\quad\quad \mathbf{w}\cdot\mathbf{x}=b$
miss-classifications
$$
E= \int_{-\infty}^b p_2(z)\,dz + \int_b^{\infty} p_1(z)\,dz
$$
$$
\frac{\partial E}{\partial b} = 0
\qquad\quad
\fbox{$\phantom{\big|} p_1(b) = p_2(b)\phantom{\big|}$}
$$
- principle of equal probabilities
- threshold close to $\ \ (\mu_1+\mu_2)/2$
otherwise: Gaussian approximation
basic LDA code
- solving
$\displaystyle\qquad\qquad
\big(\hat{S}_1+\hat{S}_2\big)\mathbf{w}= \mathbf{m}_1-\mathbf{m}_2
$
-
numpy.linalg.inv
:: matrix inversion
-
numpy.matmul
:: matrix multiplication
-
np.sqrt(np.sum(vector**2))
:: vector norm
#!/usr/bin/env python3
import math # math
import matplotlib.pyplot as plt # plotting
import numpy as np
from numpy.linalg import inv # inverse matrix
import ML_covarianceMatrix as CM # loading user-defined module
#
# --- data generation
#
dataMatrix_A = CM.testData( 0.4*math.pi, 1.0, 9.0, 30, [ 6.0,0.0])
dataMatrix_B = CM.testData(-0.4*math.pi, 1.0, 9.0, 30, [-6.0,0.0])
mean_A, coVar_A = CM.covarianceMatrix(dataMatrix_A)
mean_B, coVar_B = CM.covarianceMatrix(dataMatrix_B)
#
# --- LDA
#
S_inverse = inv(coVar_A+coVar_B)
w_vector = np.matmul(S_inverse,mean_B-mean_A) # LDA
w_normalized = w_vector / np.sqrt(np.sum(w_vector**2)) # normalization
w_orthogonal = [w_normalized[1], -w_normalized[0]] # \perp vector
LL = 5.0
midPoint = 0.5*(mean_B+mean_A)
x_lower = midPoint[0] - LL*w_orthogonal[0]
y_lower = midPoint[1] - LL*w_orthogonal[1]
x_upper = midPoint[0] + LL*w_orthogonal[0]
y_upper = midPoint[1] + LL*w_orthogonal[1]
x_LDA_plane = [x_lower, x_upper]
y_LDA_plane = [y_lower, y_upper]
if (1==2):
print("\n#main w_orthogonal\n", w_orthogonal)
print("\n#main midPoint \n", midPoint )
#
# --- printing
#
xEllipse_A, yEllipse_A = CM.plotEllipseData(coVar_A) # coVar-ellipse
xEllipse_B, yEllipse_B = CM.plotEllipseData(coVar_B) # coVar-ellipse
xData_A = [thisRow[0] for thisRow in dataMatrix_A]
yData_A = [thisRow[1] for thisRow in dataMatrix_A]
xData_B = [thisRow[0] for thisRow in dataMatrix_B]
yData_B = [thisRow[1] for thisRow in dataMatrix_B]
Z_95 = math.sqrt(5.991) # 95% confidence
xE_95_A = [Z_95*xx + mean_A[0] for xx in xEllipse_A]
yE_95_A = [Z_95*yy + mean_A[1] for yy in yEllipse_A]
xE_95_B = [Z_95*xx + mean_B[0] for xx in xEllipse_B]
yE_95_B = [Z_95*yy + mean_B[1] for yy in yEllipse_B]
x_connectMean = [ mean_A[0], mean_B[0] ]
y_connectMean = [ mean_A[1], mean_B[1] ]
plt.plot(xE_95_A, yE_95_A, "k", linewidth=2.0, label="95%")
plt.plot(xE_95_B, yE_95_B, "b", linewidth=2.0, label="95%")
plt.plot(xData_A, yData_A, "ok", markersize=5)
plt.plot(xData_B, yData_B, "ob", markersize=5)
plt.plot(x_connectMean, y_connectMean, "r", linewidth=3.0)
plt.plot(x_connectMean, y_connectMean, "or", markersize=9.0)
plt.plot(x_LDA_plane, y_LDA_plane, "g", linewidth=4.0, label="LDA plane")
plt.legend(loc="upper left")
#plt.axis('square') # square plot
plt.savefig('foo.svg') # export figure
plt.show()
