Gaussian Process Regression With Varying Noise


David Tolpin
5 min read

In Gaussian process regression for time series forecasting, all observations are assumed to have the same noise. When this assumption does not hold, the forecasting accuracy degrades. Student’s t-processes handle time series with varying noise better than Gaussian processes, but may be less convenient in applications. In this article, we introduce a weighted noise kernel for Gaussian processes allowing to account for varying noise when the ratio between noise variances for different points is known, such as in the case when an observation is the sample mean of multiple samples, and the number of samples varies between observations. A practical example of this setting is forecasting of mean visitor value based on revenues and numbers of visitors over fixed time intervals.


Gaussian process regression

Gaussian process is a non-parameteric regression model in which the vector of values of the target variable in any finite combination of points follows the normal (Gaussian) distribution. A Gaussian process defines a distribution over functions:

$$f \sim \mathcal{GP}(m(\cdot), k(\cdot, \cdot))$$

Here, $m(\cdot)$ is called the mean function, and $k(\cdot, \cdot)$ the kernel. Given any vector of points $\pmb{x}$, the distribution of the function values at these points follows multivariate normal distribution:

$$f(\pmb{x}) \sim \mathcal{N}(m(\pmb{x}), k(\pmb{x}, \pmb{x}))$$

Posterior inference is performed by computing the mean and standard deviation at each point of interest based on values of the target variable at the observed points.

Inference depends on the process kernel. Kernels can be combined by addition and multiplication, and most kernels are parameterized by a small number of hyperparameters. The hyperparameters are inferred (‘tuned’), e.g. by maximizing the likelihood on the training set.

White noise kernel

To deal with noisy observations, a small constant $\sigma_n^2$ is customarily added to the diagonal of the covariance matrix $\Sigma$:

$$\Sigma \gets \Sigma + \sigma_n^2I$$

The constant $\sigma_n^2$ is interpreted as the variance of observation noise, normally distributed with zero mean. Instead of adding the noise to the covariance matrix, a white noise kernel term can be added to the process kernel. The white noise kernel $k_n(\cdot, \cdot)$ is specified as:

$$k_n(x, x’) = \sigma_n^2 \text{ if } x \equiv x’, 0 \mbox{ otherwise.}$$

Here, $\equiv$ means that $x$ and $x’$ refer to the same point, rather than just to a pair of possibly different points with the same coordinates.

Weighted white noise kernel

White noise kernel allows to learn the observation noise from data, but does that under the assumption that all observations have the same Gaussian noise. Approximating symmetric non-Gaussian noise with Gaussian noise will work sufficiently well in most cases (see the Central limit theorem), however observations with strongly varying noise will result in either overestimating the noise variance or overfitting the data.

In certain important cases, such as the mentioned cases of forecasting the mean from observations of the empirical mean over varying sample sizes, the relative variance in each point can be accurately approximated, and only a single parameter, the variance factor, must be learned. This leads to the weighted white noise kernel:

$$k_{wn}(x, x’) = w(x) \sigma_n^2 \text{ if } x \equiv x’, 0 \mbox{ otherwise.}$$

Here $w(x)$ is the noise weight of observation $x$, which in the case of empirical mean forecasting is the reciprocal of the number of samples.

Learning the noise

The weighted white noise kernel $k_{wn}(\cdot, \cdot)$, just like $k_n(\cdot, \cdot)$, has a single hyperparameter $\sigma_n^2$.

In addition to the kernel itself, the derivative $k’_{wn}(\cdot, \cdot)$ of the kernel by $\log \sigma_n^2$ is required for learning the hyperparameter:

$$k’_{wn}(x, x’) = w(x)\sigma_n^2 \text{ if } x \equiv x’, 0 \mbox{ otherwise.}$$


There are two options for forecasting:

  1. The white noise is just ignored in forecasting (the true mean is forecast).
  2. The white noise is included (the empirical mean is forecast), but cannot be known in advance unless the noise weights of future observations are known (and in general the weights are unknown).

It is tempting to adopt the first approach, however this breaks consistency with the unweighted kernel. A simple assumption in the second case is that the average precision of observations in future data is the same as in the training data. This is tantamount to setting the noise weight of all future points to the harmonic mean of noise weights of the observed points $x_1, x_2, \dots, x_N$:

$$w^+(\cdot) = \left( \frac 1 N {\sum\limits_{i=1}^N \frac 1 {w(x_i)}} \right)^{-1}$$

The implementation in the case study uses the latter noise estimate.

Case study

For the case study, we obtained a time series where the empirical mean is computed at each point, and the number of samples varies in broad bound between points. Figure 1 shows the empirical means and the numbers of samples. Obviously, the empirical mean has higher variance at points with lower numbers of samples.

Empirical mean and numbers of samples
Figure 1. Empirical means and numbers of samples.

We implemented a weighted white noise kernel for the scikit-learn version of Gaussian processes, using the WhiteKernel as the starting point and modifying the code to accept observation weights. Figure 2 compares forecasting with uniform (orange) and weighted (green) noise. The weighted noise kernel gives much tighter confidence bounds, while still closely following the dynamics of the average visit value.

Visit value forecasting with weighted noise
Figure 2. Forecasting with uniform and weighted noise.

Two examples where weighted noise kernel noticeably improves forecasting are hours $23$ and $44$, marked in red on the plot. In both cases, weighted forecast (green) is closer to the empirical mean (and to the apparent true mean). Unweighted noise forecast is disturbed by noisy observations during hours $20–22$, either immediately preceding the forecast ($23$), or influencing the forecast through the daily seasonal component of the kernel ($44$).

The implementation of the weighted white kernel for scikit-learn used in the study is available at

David Tolpin
As the Head of our Data Science department, David likes to say he does two things well - write cool programs that work, from design to support, and conduct cutting-edge AI research, from idea to publication.