https://github.com/GPflow/GPflow
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README.md
# GPflow

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[Website](https://gpflow.org) |
[Documentation](https://gpflow.readthedocs.io/en/master/) |
[Tips & Tricks](https://github.com/GPflow/GPflow/blob/develop/doc/source/notebooks/tips_and_tricks.ipynb)

GPflow is a package for building Gaussian process models in python, using [TensorFlow](http://www.tensorflow.org). It was originally created and is now managed by [James Hensman](http://jameshensman.github.io/) and [Alexander G. de G. Matthews](http://mlg.eng.cam.ac.uk/?portfolio=alex-matthews).
The full list of [contributors](http://github.com/GPflow/GPflow/graphs/contributors) (in alphabetical order) is Alexander G. de G. Matthews, Alexis Boukouvalas, Artem Artemev, Daniel Marthaler, David J. Harris, Hugh Salimbeni, Ivo Couckuyt, James Hensman, Keisuke Fujii, Mark van der Wilk, Mikhail Beck, Pablo Leon-Villagra, Rasmus Bonnevie, ST John, Tom Nickson, Valentine Svensson, Vincent Dutordoir, Zoubin Ghahramani. GPflow is an open source project so if you feel you have some relevant skills and are interested in contributing then please do contact us.

## What does GPflow do?

GPflow implements modern Gaussian process inference for composable kernels and likelihoods. The [online user manual (develop)](http://gpflow.readthedocs.io/en/develop/)/[(master)](http://gpflow.readthedocs.io/en/master/) contains more details. The interface follows on from [GPy](http://github.com/sheffieldml/gpy), and the docs have further [discussion of the comparison](http://gpflow.readthedocs.io/en/develop/intro.html#what-s-the-difference-between-gpy-and-gpflow).

GPflow uses [TensorFlow](http://www.tensorflow.org) for running computations, which allows fast execution on GPUs, and uses Python 3.5 or above.

## Install

### 1) Quick install
GPflow latest release can be installed using `pip`:

```
pip install gpflow
```

### 2) Alternative method
A different option to install GPflow requires installation of TensorFlow first. Please see [instructions on the main TensorFlow webpage](https://www.tensorflow.org/install/). You will need at least version 1.10 (we aim to support the latest version). We find that for most users pip installation is the fastest way to get going. Then, for those interested in modifying the source of GPflow, we recommend

```
python setup.py develop
```

but installation should work well too:

```
python setup.py install
```

You can run the tests with `python setup.py test`.

## Getting Started

Get started with our [examples and tutorials](https://nbviewer.jupyter.org/github/GPflow/GPflow/blob/nbviewer/doc/source/notebooks/manual/intro.ipynb),
and for more information check out the [online user manual (develop)](http://gpflow.readthedocs.io/en/develop/)/[(master)](http://gpflow.readthedocs.io/en/master/). TODO: change path to develop once this branch is merged!


## Compiling documentation

Online documentation of the latest GPflow release can be found at https://gpflow.readthedocs.io/en/master/
(If you are using the "develop" branch off github, you can find corresponding documentation at https://gpflow.readthedocs.io/en/develop/)

To compile the GPflow documentation locally:

1. Install doc dependencies
```
pip install sphinx sphinx_rtd_theme numpydoc nbsphinx
```
2. Install pandoc 
```
pip install pandoc
```
If pandoc does not install via pip, or step 4 does not work, go to pandoc.org/installing.html

3. Change directory to `doc`
```
cd doc
```

4. Compile the documentation as html
```
make html
```

5. Check documentation locally by opening (in a browser) doc/build/html/index.html

### Docker image

We also provide a [Docker image](https://hub.docker.com/r/gpflow/gpflow/) which can be run using

```
docker run -it -p 8888:8888 gpflow/gpflow
```

The image can be generated using our [Dockerfile](Dockerfile).

## Getting help
Please use GitHub issues to start discussion on the use of GPflow. Tagging enquiries `discussion` helps us distinguish them from bugs.

## Contributing
All constructive input is gratefully received. For more information, see the [notes for contributors](contributing.md).

## Compatibility

GPflow heavily depends on TensorFlow and as far as TensorFlow supports forward compatibility, GPflow should as well. The version of GPflow can give you a hint about backward compatibility. If the major version has changed then you need to check the release notes to find out how the API has been changed.

Unfortunately, there is no such thing as backward compatibility for GPflow _models_, which means that a model implementation can change without changing interfaces. In other words, the TensorFlow graph can be different for the same models from different versions of GPflow.

## Projects using GPflow

A few projects building on GPflow and demonstrating its usage are listed below.

| Project | Description |
| --- | --- |
| [GPflowOpt](https://github.com/GPflow/GPflowOpt)       | Bayesian Optimization using GPflow. |
| [VFF](https://github.com/jameshensman/VFF)       | Variational Fourier Features for Gaussian Processes. |
| [Doubly-Stochastic-DGP](https://github.com/ICL-SML/Doubly-Stochastic-DGP)| Deep Gaussian Processes with Doubly Stochastic Variational Inference.|
| [BranchedGP](https://github.com/ManchesterBioinference/BranchedGP) | Gaussian processes with branching kernels.|
| [heterogp](https://github.com/Joshuaalbert/heterogp) | Heteroscedastic noise for sparse variational GP. |
| [widedeepnetworks](https://github.com/widedeepnetworks/widedeepnetworks) | Measuring the relationship between random wide deep neural networks and GPs.| 
| [orth_decoupled_var_gps](https://github.com/hughsalimbeni/orth_decoupled_var_gps) | Variationally sparse GPs with orthogonally decoupled bases| 


Let us know if you would like your project listed here.

## Citing GPflow

To cite GPflow, please reference the [JMLR paper](http://www.jmlr.org/papers/volume18/16-537/16-537.pdf). Sample Bibtex is given below:

```
@ARTICLE{GPflow2017,
   author = {Matthews, Alexander G. de G. and {van der Wilk}, Mark and Nickson, Tom and
	Fujii, Keisuke. and {Boukouvalas}, Alexis and {Le{\'o}n-Villagr{\'a}}, Pablo and
	Ghahramani, Zoubin and Hensman, James},
    title = "{{GP}flow: A {G}aussian process library using {T}ensor{F}low}",
  journal = {Journal of Machine Learning Research},
  year    = {2017},
  month = {apr},
  volume  = {18},
  number  = {40},
  pages   = {1-6},
  url     = {http://jmlr.org/papers/v18/16-537.html}
}
```
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