Kernel regression with Numpy only

The kernel method is a powerful weapon for nonlinear data analysis. It frequently appears as a basic element of algorithms such as soft margin SVM, Gaussian process, and clustering. In this post, I tried to reproduce the procedure for solving a regression problem using the kernel method in Python.

TL;DR Please check this repository and see codes.

For knowledge about the kernel method, refer to the following books.

What is kernel regression?

Kernel functions and gram matrix

$ n $ data sample $ \ mathcal {D} = \ left \ {x ^ {(i)}, y ^ {(i)} \ right \} , (i = 1, \ dots n) Approximate the function $ y = f (x) $ from $. The regression model is expressed by the following equation using the kernel function $ k (\ cdot, \ cdot) $ and the parameter $ {\ alpha} _i , (i = 1 \ dots n) $.

\hat{y}^{(i)} = \sum\_{j=1}^{n} \alpha_j k(x^{(i)}, x^{(j)}) ~~~~ (i=1 \dots n)

The distance between the estimated value $ \ hat {y} ^ {(i)} $ and the true value $ y ^ {(i)} $ is calculated as the residual. Fit the model to the data sample, derive the sum (or average) of the residuals as the loss function of the model, and find the optimal parameters $ {\ alpha} _i , (i = 1 \ dots n) $.

\begin{align} residual(y^{(i)}, \hat{y}^{(i)}) &= y^{(i)} - \hat{y}^{(i)} \\\ &= y^{(i)} - \sum\_{j=1}^{n} \alpha\_j k(x^{(i)}, x^{(j)}) \end{align}

\begin{align} L(\alpha) &= \frac{1}{n} \sum\_{i=1}^{n} {residual(y^{(i)}, \hat{y}^{(i)}) }^{2} \\\ &= \frac{1}{n} \sum\_{i=1}^{n} { \left( y^{(i)} - \sum\_{j=1}^{n} \alpha\_j k(x^{(i)}, x^{(j)}) \right) }^{2} \\\ &= {({\bf y} - {\bf K} {\bf \alpha})}^{\mathrm{T}} ({\bf y} - {\bf K} {\bf \alpha}) \end{align}

where, \,\,\, {\bf K} = \begin{pmatrix} k(x^{(1)}, x^{(1)}) & \cdots & k(x^{(1)}, x^{(n)}) \\\ \vdots & \ddots & \vdots \\\ k(x^{(n)}, x^{(1)}) & \cdots & k(x^{(n)}, x^{(n)}) \end{pmatrix}

$ {\ bf K} $ is a matrix that is calculated from a data sample given a kernel function, and is called a Gram Matrix.

Parameter search by gradient descent

The naive gradient descent method is used to search for the parameter $ {\ alpha} \ _ i , (i = 1 \ dots n) $. The coefficient $ \ gamma $ is the learning rate.

\frac{\partial L(\alpha)}{\partial {\bf \alpha}} = -2 \cdot {\bf K}^{\mathrm{T}} ({\bf y} - {\bf K} {\bf \alpha}) \\\ {\alpha}\_{new} = {\alpha}\_{old} + \gamma \cdot \frac{\partial L(\alpha)}{\partial {\bf \alpha}} \mid\_{ \alpha = {\alpha}\_{old} }

RBF kernel (Gaussian kernel) is adopted as the kernel function.

k(x, x') := \exp \left( {\large - \frac{{|| x - x' ||}^2}{2 {\sigma}^{2}} } \right)

Implement kernel regression in Python (numpy only)

All the code can be found in the repository below. https://github.com/yumaloop/KernelRegression

import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline

# Kernel Function
class RBFkernel():
    def __init__(self, sigma=0.5):
        self.sigma = sigma
        
    def __call__(self, x, y):
        numerator = -1 * np.sum((x - y)**2)
        denominator = 2 * (self.sigma**2)
        return np.exp(numerator / denominator)
    
    def get_params(self):
        return self.sigma
    
    def set_params(self, sigma):
        self.sigma = sigma

# Regression Model
class KernelRegression():
    def __init__(self, kernel):
        self.kernel = kernel
        
    def fit_kernel(self, X, y, lr=0.01, nb_epoch=1000, log_freq=50):
        self.X = X
        self.y = y
        self.n = X.shape[0] # sample size
        self.alpha = np.full(self.n, 1) # param alpha: initialize
        self.gram_matrix = np.zeros((self.n, self.n))
        
        # Gradient Descent Algorithm to optimize alpha
        for epoch in range(nb_epoch):
            
            # Gram Matrix
            for i in range(self.n):
                for j in range(self.n):
                    self.gram_matrix[i][j] = self.kernel(self.X[i], self.X[j])
                    self.loss, self.loss_grad = self.mse(self.X, self.y, self.alpha, self.gram_matrix)
                    self.alpha = self.alpha - lr * self.loss_grad
                    
            if epoch % log_freq == 0:
                print("epoch: {} \t MSE of sample data: {:.4f}".format(epoch, self.loss))
                        
                        
    def mse(self, X, y, alpha, gram_matrix):
        loss = np.dot((y - np.dot(gram_matrix, alpha)), (y - np.dot(gram_matrix, alpha)))
        loss_grad = -2 * np.dot(gram_matrix.T, (y - np.dot(gram_matrix, alpha)))
        return loss, loss_grad
    
    def predict(self, X_new):
        n_new = X_new.shape[0]
        y_new = np.zeros(n_new)
        for i in range(n_new):
            for j in range(self.n):
                y_new[i] += self.alpha[j] * self.kernel(X_new[i], self.X[j])
        return y_new

# Experiment

def actual_function(x):
    return 1.7 * np.sin(2 * x) + np.cos(1.5 * x) + 0.5 * np.cos(0.5 * x) + 0.5 * x  + 0.1

sample_size = 100 # the number of data sample
var_noise = 0.7 # variance of the gaussian noise for samples

# make data sample
x_sample = np.random.rand(sample_size) * 10 - 5
y_sample = actual_function(x_sample) + np.random.normal(0, var_noise, sample_size)

# variables for plot (actual function)
x_plot = np.linspace(-5, 5, 100)
y_plot = actual_function(x_plot)

# plot figure
plt.plot(x_plot, y_plot, color="blue", linestyle="dotted", label="actual function")
plt.scatter(x_sample, y_sample, alpha=0.4, color="blue", label="data sample")
plt.title("Actual function & Data sample (N={})".format(sample_size))
plt.legend(loc="upper left")
plt.xlabel("x")
plt.ylabel("y")
plt.show()

# set kernel
sigma=0.2
kernel = RBFkernel(sigma=sigma)

# generate model
model = KernelRegression(kernel)

# fit data sample for the model
model.fit_kernel(x_sample, y_sample, lr=0.01, nb_epoch=1000, log_freq=100)
  epoch: 0      MSE of sample data: 35.2988
  epoch: 100 	 MSE of sample data: 30.3570
  epoch: 200 	 MSE of sample data: 29.4241
  epoch: 300 	 MSE of sample data: 28.8972
  epoch: 400 	 MSE of sample data: 28.5597
  epoch: 500 	 MSE of sample data: 28.3322
  epoch: 600 	 MSE of sample data: 28.1736
  epoch: 700 	 MSE of sample data: 28.0598
  epoch: 800 	 MSE of sample data: 27.9759
  epoch: 900 	 MSE of sample data: 27.9122

# check Gram Matrix of the model
print(model.gram_matrix)
  array([[1.00000000e+000, 3.24082380e-012, 1.86291046e-092, ...,
        3.45570112e-030, 7.50777061e-016, 6.18611768e-129],
       [3.24082380e-012, 1.00000000e+000, 5.11649994e-039, ...,
        1.78993799e-078, 1.05138357e-053, 1.15421467e-063],
       [1.86291046e-092, 5.11649994e-039, 1.00000000e+000, ...,
        6.88153992e-226, 4.47677881e-182, 8.98951607e-004],
       ...,
       [3.45570112e-030, 1.78993799e-078, 6.88153992e-226, ...,
        1.00000000e+000, 4.28581263e-003, 2.58161981e-281],
       [7.50777061e-016, 1.05138357e-053, 4.47677881e-182, ...,
        4.28581263e-003, 1.00000000e+000, 3.95135557e-232],
       [6.18611768e-129, 1.15421467e-063, 8.98951607e-004, ...,
        2.58161981e-281, 3.95135557e-232, 1.00000000e+000]])

# check loss
print(model.loss)
  12.333081499130776

# array for plot (predicted function)
x_new = np.linspace(-5, 5, 100)
y_new = model.predict(x_new)

 plot result
plt.plot(x_plot, y_plot, color="blue", linestyle="dotted", label="actual function")
plt.scatter(x_sample, y_sample, alpha=0.3, color="blue", label="data sample")
plt.plot(x_new, y_new, color="red", label="predicted function")
plt.title("Kernel Regression \n RBF kernel (sigma={}), sample size ={}".format(sigma, sample_size))
plt.legend(loc="upper left")
plt.xlabel("x")
plt.ylabel("y")
plt.show()

that's all. Thank you for reading to the end!