Error in plotting the decision boundary for SVC Laplace kernel

Question

I'm trying to plot the decision boundary of the SVM classifier using a precomputed Laplace kernel (code below) on the similar lines of this scikit-learn post. I'm taking test points as mesh grid values (xx, yy) just like as mentioned in the post and train points as X and y. I'm able to fit the pre-computed kernel using train points.

import numpy as np
#from sklearn.model_selection import train_test_split
import matplotlib.pyplot as plt
from sklearn.datasets import load_iris
from sklearn.svm import SVC
from sklearn.metrics.pairwise import laplacian_kernel

#Load the iris data
iris_data = load_iris()

#Split the data and target
X = iris_data.data[:, :2]
y = iris_data.target

#Step size in mesh plot
h = 0.02

#Convert X and y to a numpy array
X = np.array(X)
y = np.array(y)

#Using Laplacian kernel - https://scikit-learn.org/stable/modules/metrics.html#laplacian-kernel
K = np.array(laplacian_kernel(X, gamma=.5))
svm = SVC(kernel='precomputed').fit(K, np.ravel(y))

# create a mesh to plot in
x_min, x_max = X[:, 0].min() - 1, X[:, 0].max() + 1
y_min, y_max = X[:, 1].min() - 1, X[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, h),
                     np.arange(y_min, y_max, h))

# Plot the decision boundary. For that, we will assign a color to each
# point in the mesh [x_min, x_max]x[y_min, y_max].
#plt.subplot(2, 2, i + 1)
#plt.subplots_adjust(wspace=0.4, hspace=0.4)

# Calculate the gram matrix for test points. Here is where the error is coming. xx- test, X-train.
K_test = np.array(laplacian_kernel(xx, X,  gamma=.5)) 

#Predict using the gram matrix for test
Z = svm.predict(np.c_[K_test])

# Put the result into a color plot
Z = Z.reshape(xx.shape)
plt.contourf(xx, yy, Z, cmap=plt.cm.coolwarm, alpha=0.8)

# Plot also the training points
plt.scatter(X[:, 0], X[:, 1], c=y, cmap=plt.cm.coolwarm)
plt.xlabel('Sepal length')
plt.ylabel('Sepal width')
plt.xlim(xx.min(), xx.max())
plt.ylim(yy.min(), yy.max())
plt.xticks(())
plt.yticks(())
plt.title('SVC with Laplace kernel')

plt.show()

However, when I try to plot the decision boundary on graph for grid points, I get the below error.

Traceback (most recent call last):
  File "/home/user/Src/laplce.py", line 37, in 
    K_test = np.array(laplacian_kernel(xx, X,  gamma=.5)) 
  File "/home/user/.local/lib/python3.9/site-packages/sklearn/metrics/pairwise.py", line 1136, in laplacian_kernel
    X, Y = check_pairwise_arrays(X, Y)
  File "/home/user/.local/lib/python3.9/site-packages/sklearn/utils/validation.py", line 63, in inner_f
    return f(*args, **kwargs)
  File "/home/user/.local/lib/python3.9/site-packages/sklearn/metrics/pairwise.py", line 160, in check_pairwise_arrays
    raise ValueError("Incompatible dimension for X and Y matrices: "
ValueError: Incompatible dimension for X and Y matrices: X.shape[1] == 280 while Y.shape[1] == 2

So, how do I resolve the error and plot the decision boundary for iris data ? Thanks in advance

user_12258459 · Answer

The issue is getting your meshgrid into the same dimensions as the training matrix, before applying the laplacian. So if we run the code below to fit the svm :

import numpy as np
import matplotlib.pyplot as plt
from sklearn.datasets import load_iris
from sklearn.svm import SVC
from sklearn.metrics.pairwise import laplacian_kernel

iris_data = load_iris()

X = iris_data.data[:, :2]
y = iris_data.target
h = 0.02

K = laplacian_kernel(X,gamma=.5)
svm = SVC(kernel='precomputed').fit(K, y)

Create the grid like you did:

x_min, x_max = X[:, 0].min() - 1, X[:, 0].max() + 1
y_min, y_max = X[:, 1].min() - 1, X[:, 1].max() + 1
x_test = np.meshgrid(np.arange(x_min, x_max, h),
                     np.arange(y_min, y_max, h))

xx,yy = np.meshgrid(np.arange(x_min, x_max, h),np.arange(y_min, y_max, h))

Your original input into the laplacian was (150,2) so you need to basically put your xx,yy into 2 columns:

x_test = np.vstack([xx.ravel(),yy.ravel()]).T

K_test = laplacian_kernel(x_test, X,  gamma=.5)
Z = svm.predict(K_test)
Z = Z.reshape(xx.shape)

Then plot:

plt.contourf(xx, yy, Z, cmap=plt.cm.coolwarm, alpha=0.8)
plt.scatter(X[:, 0], X[:, 1], c=y, cmap=plt.cm.coolwarm)
plt.xlabel('Sepal length')
plt.ylabel('Sepal width')
plt.xlim(xx.min(), xx.max())
plt.ylim(yy.min(), yy.max())

The points are more or less correct, you can see it does not resolve 1,2 very well:

pd.crosstab(y,svm.predict(K))

col_0   0   1   2
row_0           
0   49  1   0
1   0   35  15
2   0   11  39

Error in plotting the decision boundary for SVC Laplace kernel

1 Answers