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Kernel Density Estimation

Kernel density estimation is the process of estimating an unknown probability density function using a kernel function $K(u)$. While a histogram counts the number of data points in somewhat arbitrary regions, a kernel density estimate is a function defined as the sum of a kernel function on every data point. The kernel function typically exhibits the following properties:

Symmetry such that $K(u) = K(-u)$.
Normalization such that $\int_{-\infty}^{\infty} K(u) \ du = 1$ .
Monotonically decreasing such that $K'(u) < 0$ when $u > 0$.
Expected value equal to zero such that $\mathrm{E}[K] = 0$.

For more information about kernel density estimation, see for instance Wikipedia - Kernel density estimation.

A univariate kernel density estimator is implemented in sm.nonparametric.KDEUnivariate. In this example we will show the following:

Basic usage, how to fit the estimator.
The effect of varying the bandwidth of the kernel using the bw argument.
The various kernel functions available using the kernel argument.

In [1]:

%matplotlib inline
import numpy as np
from scipy import stats
import statsmodels.api as sm
import matplotlib.pyplot as plt
from statsmodels.distributions.mixture_rvs import mixture_rvs

A univariate example

In [2]:

np.random.seed(12345) # Seed the random number generator for reproducible results

We create a bimodal distribution: a mixture of two normal distributions with locations at -1 and 1.

In [3]:

# Location, scale and weight for the two distributions
dist1_loc, dist1_scale, weight1 = -1 , .5, .25
dist2_loc, dist2_scale, weight2 = 1 , .5, .75

# Sample from a mixture of distributions
obs_dist = mixture_rvs(prob=[weight1, weight2], size=250, 
                        dist=[stats.norm, stats.norm],
                        kwargs = (dict(loc=dist1_loc, scale=dist1_scale),
                                  dict(loc=dist2_loc, scale=dist2_scale)))

The simplest non-parametric technique for density estimation is the histogram.

In [4]:

fig = plt.figure(figsize=(12, 5))
ax = fig.add_subplot(111)

# Scatter plot of data samples and histogram
ax.scatter(obs_dist, np.abs(np.random.randn(obs_dist.size)), 
            zorder=15, color='red', marker='x', alpha=0.5, label='Samples')
lines = ax.hist(obs_dist, bins=20, edgecolor='k', label='Histogram')

ax.legend(loc='best')
ax.grid(True, zorder=-5)

Fitting with the default arguments

The histogram above is discontinuous. To compute a continuous probability density function, we can use kernel density estimation.

We initialize a univariate kernel density estimator using KDEUnivariate.

In [5]:

kde = sm.nonparametric.KDEUnivariate(obs_dist)
kde.fit() # Estimate the densities

We present a figure of the fit, as well as the true distribution.

In [6]:

fig = plt.figure(figsize=(12, 5))
ax = fig.add_subplot(111)

# Plot the histrogram
ax.hist(obs_dist, bins=20, normed=True, label='Histogram from samples', 
        zorder=5, edgecolor='k', alpha=0.5)

# Plot the KDE as fitted using the default arguments
ax.plot(kde.support, kde.density, lw=3, label='KDE from samples', zorder=10)

# Plot the true distribution
true_values = (stats.norm.pdf(loc=dist1_loc, scale=dist1_scale, x=kde.support)*weight1
              + stats.norm.pdf(loc=dist2_loc, scale=dist2_scale, x=kde.support)*weight2)
ax.plot(kde.support, true_values, lw=3, label='True distribution', zorder=15)

# Plot the samples
ax.scatter(obs_dist, np.abs(np.random.randn(obs_dist.size))/40, 
           marker='x', color='red', zorder=20, label='Samples', alpha=0.5)

ax.legend(loc='best')
ax.grid(True, zorder=-5)

/Users/taugspurger/Envs/statsmodels-dev/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "

In the code above, default arguments were used. We can also vary the bandwidth of the kernel, as we will now see.

Varying the bandwidth using the `bw` argument

The bandwidth of the kernel can be adjusted using the bw argument. In the following example, a bandwidth of bw=0.2 seems to fit the data well.

In [7]:

fig = plt.figure(figsize=(12, 5))
ax = fig.add_subplot(111)

# Plot the histrogram
ax.hist(obs_dist, bins=25, label='Histogram from samples', 
        zorder=5, edgecolor='k', normed=True, alpha=0.5)

# Plot the KDE for various bandwidths
for bandwidth in [0.1, 0.2, 0.4]:
    kde.fit(bw=bandwidth) # Estimate the densities
    ax.plot(kde.support, kde.density, '--', lw=2, color='k', zorder=10,
            label='KDE from samples, bw = {}'.format(round(bandwidth, 2)))

# Plot the true distribution
ax.plot(kde.support, true_values, lw=3, label='True distribution', zorder=15)

# Plot the samples
ax.scatter(obs_dist, np.abs(np.random.randn(obs_dist.size))/50, 
           marker='x', color='red', zorder=20, label='Data samples', alpha=0.5)

ax.legend(loc='best')
ax.set_xlim([-3, 3])
ax.grid(True, zorder=-5)

/Users/taugspurger/Envs/statsmodels-dev/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "

Comparing kernel functions

In the example above, a Gaussian kernel was used. Several other kernels are also available.

In [8]:

from statsmodels.nonparametric.kde import kernel_switch
list(kernel_switch.keys())

Out[8]:

['gau', 'epa', 'uni', 'tri', 'biw', 'triw', 'cos', 'cos2']

The available kernel functions

In [9]:

# Create a figure
fig = plt.figure(figsize=(12, 5))

# Enumerate every option for the kernel
for i, (ker_name, ker_class) in enumerate(kernel_switch.items()):
    
    # Initialize the kernel object
    kernel = ker_class()
    
    # Sample from the domain
    domain = kernel.domain or [-3, 3]
    x_vals = np.linspace(*domain, num=2**10)
    y_vals = kernel(x_vals)

    # Create a subplot, set the title
    ax = fig.add_subplot(2, 4, i + 1)
    ax.set_title('Kernel function "{}"'.format(ker_name))
    ax.plot(x_vals, y_vals, lw=3, label='{}'.format(ker_name))
    ax.scatter([0], [0], marker='x', color='red')
    plt.grid(True, zorder=-5)
    ax.set_xlim(domain)
    
plt.tight_layout()

The available kernel functions on three data points

We now examine how the kernel density estimate will fit to three equally spaced data points.

In [10]:

# Create three equidistant points
data = np.linspace(-1, 1, 3)
kde = sm.nonparametric.KDEUnivariate(data)

# Create a figure
fig = plt.figure(figsize=(12, 5))

# Enumerate every option for the kernel
for i, kernel in enumerate(kernel_switch.keys()):
    
    # Create a subplot, set the title
    ax = fig.add_subplot(2, 4, i + 1)
    ax.set_title('Kernel function "{}"'.format(kernel))
    
    # Fit the model (estimate densities)
    kde.fit(kernel=kernel, fft=False, gridsize=2**10)
    
    # Create the plot
    ax.plot(kde.support, kde.density, lw=3, label='KDE from samples', zorder=10)
    ax.scatter(data, np.zeros_like(data), marker='x', color='red')
    plt.grid(True, zorder=-5)
    ax.set_xlim([-3, 3])
    
plt.tight_layout()

A more difficult case

The fit is not always perfect. See the example below for a harder case.

In [11]:

obs_dist = mixture_rvs([.25, .75], size=250, dist=[stats.norm, stats.beta],
            kwargs = (dict(loc=-1, scale=.5), dict(loc=1, scale=1, args=(1, .5))))

In [12]:

kde = sm.nonparametric.KDEUnivariate(obs_dist)
kde.fit()

In [13]:

fig = plt.figure(figsize=(12, 5))
ax = fig.add_subplot(111)
ax.hist(obs_dist, bins=20, normed=True, edgecolor='k', zorder=4, alpha=0.5)
ax.plot(kde.support, kde.density, lw=3, zorder=7)
# Plot the samples
ax.scatter(obs_dist, np.abs(np.random.randn(obs_dist.size))/50, 
           marker='x', color='red', zorder=20, label='Data samples', alpha=0.5)
ax.grid(True, zorder=-5)

/Users/taugspurger/Envs/statsmodels-dev/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "

The KDE is a distribution

Since the KDE is a distribution, we can access attributes and methods such as:

entropy
evaluate
cdf
icdf
sf
cumhazard

In [14]:

obs_dist = mixture_rvs([.25, .75], size=1000, dist=[stats.norm, stats.norm],
                kwargs = (dict(loc=-1, scale=.5), dict(loc=1, scale=.5)))
kde = sm.nonparametric.KDEUnivariate(obs_dist)
kde.fit(gridsize=2**10)

In [15]:

kde.entropy

Out[15]:

1.314324140492138

In [16]:

kde.evaluate(-1)

Out[16]:

array([0.18085886])

Cumulative distribution, it's inverse, and the survival function

In [17]:

fig = plt.figure(figsize=(12, 5))
ax = fig.add_subplot(111)

ax.plot(kde.support, kde.cdf, lw=3, label='CDF')
ax.plot(np.linspace(0, 1, num = kde.icdf.size), kde.icdf, lw=3, label='Inverse CDF')
ax.plot(kde.support, kde.sf, lw=3, label='Survival function')
ax.legend(loc = 'best')
ax.grid(True, zorder=-5)

The Cumulative Hazard Function

In [18]:

fig = plt.figure(figsize=(12, 5))
ax = fig.add_subplot(111)
ax.plot(kde.support, kde.cumhazard, lw=3, label='Cumulative Hazard Function')
ax.legend(loc = 'best')
ax.grid(True, zorder=-5)

© 2009–2012 Statsmodels Developers
© 2006–2008 Scipy Developers
© 2006 Jonathan E. Taylor
Licensed under the 3-clause BSD License.
http://www.statsmodels.org/stable/examples/notebooks/generated/kernel_density.html