bayesian_bootstrap
bayesian_bootstrap
is a package for Bayesian bootstrapping in Python. For an overview of the Bayesian bootstrap, I highly recommend reading Rasmus Bååth's writeup. This Python package is similar to his R package.
This README contains some examples, below. For the documentation of the package's API, see the docs.
This package is on pypi  you can install it with pip install bayesian_bootstrap
.
bootstrap
module
Overview of the The main module in the bayesian_bootstrap
package is the bootstrap
module. The bootstrap
module contains tools
for doing approximate bayesian inference using the Bayesian Bootstrap introduced in Rubin's The Bayesian Bootstrap.
It contains the following:

The
mean
andvar
functions, which simulate the posterior distributions of the mean and variance 
The
bayesian_bootstrap
function, which simulates the posterior distribution of an arbitrary statistic 
The
BayesianBootstrapBagging
class, a wrapper allowing users to generate ensembles of regressors/classifiers using Bayesian Bootstrap resampling. A base class with a scikitlearn like estimator needs to be provided. See also thebayesian_bootstrap_regression
function. 
The
central_credible_interval
andhighest_density_interval
functions, which compute credible intervals from posterior samples.
For more information about the function signatures above, see the examples below or the docstrings of each function/class.
One thing that's worth making clear is the interpretation of the parameters of the bayesian_bootstrap
, BayesianBootstrapBagging
, and bayesian_bootstrap_regression
functions, which all do sampling within each bootstrap replication:

The number of replications is the number of times the statistic of interested will be replicated. If we think about the classical bootstrap, this is the number of times your dataset is resampled. If we think about it from a bayesian point of view, this is the number of draws from the posterior distribution.

The resample size is the size of the dataset used to calculate the statistic of interest in each replication. More is better  you'll probably want this to be at least as large as your original dataset.
Example: Estimating the mean
Let's say that we observe some data points, and we wish to simulate the posterior distribution of their mean.
The following code draws four data points from an exponential distribution:
X = np.random.exponential(7, 4)
Now, we are going to simulate draws from the posterior of the mean. bayesian_bootstrap
includes a mean
function in
the bootstrap
module that will do this for you.
The code below performs the simulation and calculates the 95% highest density interval using 10,000 bootstrap replications. It also uses the wonderful
seaborn
library to visualize the histogram with a Kernel density estimate.
Included for reference in the image is the same dataset used in a classical bootstrap, to illustrate the comparative smoothness of the bayesian version.
from bayesian_bootstrap.bootstrap import mean, highest_density_interval
posterior_samples = mean(X, 10000)
l, r = highest_density_interval(posterior_samples)
plt.title('Bayesian Bootstrap of mean')
sns.distplot(posterior_samples, label='Bayesian Bootstrap Samples')
plt.plot([l, r], [0, 0], linewidth=5.0, marker='o', label='95% HDI')
The above code uses the mean
method to simulate the posterior distribution of the mean. However, it is a special
(if very common) case, along with var
 all other statistics should use the bayesian_bootstrap
method. The
following code demonstrates doing this for the posterior of the mean:
from bayesian_bootstrap.bootstrap import bayesian_bootstrap
posterior_samples = bayesian_bootstrap(X, np.mean, 10000, 100)
Example: Regression modelling
Let's take another example  fitting a linear regression model. The following code samples a few points in the plane. The mean is y = x, and normally distributed noise is added.
X = np.random.normal(0, 1, 5).reshape(1, 1)
y = X.reshape(1, 1).reshape(5) + np.random.normal(0, 1, 5)
We build models via bootstrap resampling, creating an ensemble of models via bootstrap aggregating. A
BayesianBootstrapBagging
wrapper class is available in the library, which is a bayesian analogue to scikitlearn's
BaggingRegressor
and BaggingClassifer
classes.
m = BayesianBootstrapBagging(LinearRegression(), 10000, 1000)
m.fit(X, y)
Once we've got our ensemble trained, we can make interval predictions for new inputs by calculating their HDIs under the ensemble:
X_plot = np.linspace(min(X), max(X))
y_predicted = m.predict(X_plot.reshape(1, 1))
y_predicted_interval = m.predict_highest_density_interval(X_plot.reshape(1, 1), 0.05)
plt.scatter(X.reshape(1, 1), y)
plt.plot(X_plot, y_predicted, label='Mean')
plt.plot(X_plot, y_predicted_interval[:,0], label='95% HDI Lower bound')
plt.plot(X_plot, y_predicted_interval[:,1], label='95% HDI Upper bound')
plt.legend()
plt.savefig('readme_regression.png', bbox_inches='tight')
Users interested in accessing the base models can do so via the base_models_
attribute of the object.
Contributions
Interested in contributing? We'd love to have your help! Please keep the following in mind:

Bug fixes are welcome! Make sure you reference the issue number that is being resolved, and that all test cases in
tests
pass on both Python 2.7 and 3.4/3.5. 
New features are welcome as well! Any new features should include docstrings and unit tests in the
tests
directory. 
If you want to contribute a case study or other documentation, feel free to write up a githubflavored markdown document or ipython notebook and put it in the
examples
folder before issuing a pull request.
Credit for past contributions:
 roya0045 implemented the original version of the lowmemory optimizations.