Kernel Density Estimation from Scratch

Implementing KDE with Julia

J. Duncan


Why am I writing about KDE’s? At the recommendation of Will Kurt’s probability blog I’ve been reading a great book on data analysis by Philipp K. Janert:

This book has a great intro to KDEs that explain the motivation. My own abbreviated version are that KDEs provide a useful technique to visualize a variables distribution. Visualizing your data is an important step to take early in the data analysis stage. In fact, there are many metrics that we commonly use to understand a variable that have an implicit assumption that your data are unimodal (having a single peak). If your data doesn’t have this structure then you may be mislead by measures of central tendency (mean/median/mode), outliers, or other statistical methods (linear regression, t-tests, etc.).

This post’s structure follows closely with how I commonly learn topics. I start at a high level, using a pre-canned solution for the algorithm, and then work backward to find out what’s going on underneath.

I use a small example I discovered on the Wikipedia page for KDEs. It uses a handful of data points for a single variable:

Sample Value
1 -2.1
2 -1.3
3 -0.4
4 1.9
5 5.1
6 6.2

Let’s start with a basic dot plot of these points. I’ll be using the Julia Programming Language for these examples.

using StatsPlots

# initialize an array of the samples
x = [-2.1; -1.3; -0.4; 1.9; 5.1; 6.2];
# plot it out
scatter(x, zeros(length(x)), legend = false)

KDE with KernelDensity.jl

Now applying the quick and easy solution: a package. This package has a function named kde that takes a one dimensional array (or vector), a bandwidth argument, and a chosen kernel (we’ll use the default). So let’s see it:

import KernelDensity

KernelDensity.kde(x, bandwidth = sqrt(2.25)) |>
  x -> plot!(x, legend = false)

There we go, we’ve applied KDE to these data points and we can now see the bimodal nature of this data. If all we wanted to do was visualize the distribution then we’re done. I’d like to dig a bit deeper though.

KDE with Distributions.jl

What is the kernel part of this about? What was the default kernel we used in the previous section? The kde function from the package used a default kernel associated with the Normal distribution. But to understand what this all means we need to take a look at the definition of Kernel Density Estimation:

\[ D_h(x; {x_i}) = \sum_{i=1}^n \frac{1}{nh} K\left(\frac{x - x_i}{h}\right) \]

Breaking down this formula a bit: The kernel is the function shown above as $K$ and Janert describes it like so:

To form a KDE, we place a kernel —that is, a smooth, strongly peaked function—at the position of each data point. We then add up the contributions from all kernels to obtain a smooth curve, which we can evaluate at any point along the x axis

We are effectively calculating weighted distances from our data points to points along the x axis. There is a great interactive introduction to kernel density estimation here. I highly recommend it because you can play with bandwidth, select different kernel methods, and check out the resulting effects.

As I mentioned before, the default kernel for this package is the Normal (or Gaussian) probability density function (pdf):

\[ K(x) = \frac{1}{\sqrt{2\pi}}\text{exp}\left(-\frac{1}{2}x^2\right) \]

Since we are calculating pdfs I’ll use the Distributions.jl package to create each distribution, calculate the densities, and sum the results.

using Distributions

dists = Normal.(x, sqrt(2.25))
6-element Array{Distributions.Normal{Float64},1}:
 Distributions.Normal{Float64}(μ=-2.1, σ=1.5)
 Distributions.Normal{Float64}(μ=-1.3, σ=1.5)
 Distributions.Normal{Float64}(μ=-0.4, σ=1.5)
 Distributions.Normal{Float64}(μ=1.9, σ=1.5)
 Distributions.Normal{Float64}(μ=5.1, σ=1.5)
 Distributions.Normal{Float64}(μ=6.2, σ=1.5)

Here we see a neat feature of the Julia language. Any Julia function can be vectorized (or broadcasted) by the application of the . (or “dot”) operator. See this blog post if you want to learn more about it. Above we applied the Normal method element-wise creating an array of Normal distributions. The mean of our individual distributions being our data points and a variance of 2.25 (aka our chosen bandwidth). Let’s plot each of these distributions:

plot(dists, legend = false)

Summing up their probability densities across all of x.

# create an iterator
x_d = range(-7, 11, length = 100)
# find the kde with a gaussian kernel
dens = sum(pdf.(eachdist, x_d) for eachdist in dists)

plot!(x_d, dens)

The resulting shape of the KDE is identical to the one we first calculated. We could stop here except this is really just a special case where we are using the gaussian kernel. Let’s extrapolate a bit so we could use different kernels.

Kernel Density from Scratch

To apply a new kernel method we can just write the KDE code from scratch. Below I’ve defined the KDE function as D and the kernel argument as K to mimic the math above.

# define some kernels:
# gaussian kernel
kgauss(x) = 1/sqrt(2π) * exp(-1/2 * x^2)
# boxcar
kbox(x) = abs(x) <= 1 ? 1/2 : 0
# triangular
ktri(x) = abs(x) <= 1 ? 1 - abs(x) : 0

# define the KDE function
D(x, h, xi, K) =
  1/(length(xi) * h) * sum(K.((x .- xi) / h))

# evaluate KDE along the x-axis using comprehensions
dens = [D(xstep, sqrt(2.25), x, K) for xstep in x_d, K in (kgauss, kbox, ktri)]

# visualize the kernels
plot(x_d, dens, label = ["Gaussian", "Box", "Triangular"])

In my example above I used some shorthand Julia syntax. The ?: syntax is called a ternary operator and makes a conditional if-else statement more compact. I also used Julia’s Assignment form for my function definitions above because it looks a lot more like the math involved. You could have easily defined each of these functions to look more like so:

function foo(x)
  if ...
  return ...

What’s next?

A short post on cumulative distribution functions (cdf) using Julia will likely follow this one. Janert introduces both kdes and cdfs in his chapter A Single Variable: Shape and Distribution and they complement each other really well. Thanks for reading!