AETF: Autoencoding Topographic Factors

This code provides a reference implementation of the AETF algorithm described in the following publications:

• Autoencoding Topographic Factors.
  Moretti, A.*, Atkinson-Stirn, A.*, Marks, G.*, Pe'er, I.
  Journal of Computational Biology, 2019 26(6):546–560. PMID: 30526005

• Auto-Encoding Topographic Factors.
  Moretti, A.*, Atkinson-Stirn, A.*, Pe'er, I.
  Joint IJCAI-ICML Workshop on Computational Biology, 2018.

AETF is an extension of the TFA algorithm from the following publication. As a reference, TFA is also supported in the repo.

• Topographic Factor Analysis.
  Manning, J., Raganath, R., Norman, K., Blei, D.
  Plos One, 2014

Installation

The code is written in Python 3.6. It should also run in Python 2.7 with the following dependencies:

• Tensorflow
• numpy
• scipy
• matplotlib

To checkout, run git@github.com:amoretti86/AETF.git

Demo

Original	Inferred