lda-cython

This repo contains Cython implementations of Gibbs sampling for latent Dirichlet allocation and its supervised variants.

Installation

Dependencies

GNU Scientific Library

This module depends on GSL, please install it. For macosx users using homebrew, this is as simple as

$ brew install gsl

pypolyagamma

This package depends on pypolyagamma, which is a bit of a pain for two reasons:

1. The pypolyagamma module that is installed using pip does not have Python 3 support. However, there is a fork that does. So if you want Python 3 support, you are going to have to clone this fork and pip install it from the repo's main directory like this:

   $ pip install /path/to/pypolyagamma/

2. pypolyagamma requies a C/C++ compiler with OpenMP support. Unfortunately for macosx users, Apple's native compiler, clang, does not ship with that support, so you need to install and use one that does. For macosx users using homebrew, this is as simple as

   $ brew install gcc --without-multilib

   This will install a version of gcc with OpenMP support. However, Apple makes things worse by aliasing gcc to point to clang! So you need to explicitly tell pip which gcc compiler to use. As of the writing of this README, brew installs major version 5 of gcc, and as a result will create a binary called gcc-5 in your path. So pip install pypolyagamma as follows:

   $ CC=gcc-5 CXX=gcc-5 pip install pypolyagamma

   or if you are installing directly from code for Python 3 support:

   $ CC=gcc-5 CXX=gcc-5 pip install /path/to/pypolyagamma/

Instructions

We first need to compile the C code in this repository. To do this, clone this repository to your local machine, change into the main directory, start up a virtualenv, make sure that Cython, CythonGSL and Numpy are installed (all listed in requirements.txt), and run

$ python setup.py build_ext --inplace

Now you can pip install lda-cython:

$ CC=gcc-5 CXX=gcc-5 pip install /path/to/lda-cython

Again, the C flags are required for pypolyagamma, as I've explained above. If you want Python 3 support, you need to install pypolyagamma, as described above, before pip installing lda-cython.