Torch-TDA
A package used to do automatic differentiation in Pytorch for topological data analysis.
This package provides utilities for using constructions in topological data analysis with automatic differentiation. It wraps functionality from
- BATS for Basic Applied Topology computation.
- persim for computations comparing persistence diagrams.
- hera a library for fast calculation of bottleneck distance and Wasserstein distance on persistence diagrams.
- topologylayer for polynomial features of barcodes.
The design is heavily inspired by topologylayer. Key differences are that we uses bats
for faster topological computations.
Here is the documentation and examples.
Use
Package installation provides a package under the torch_tda
namespace. Functionality is primarily under torch_tda.nn
, which provides several PyTorch layers.
import torch_tda
Installation
Attension: please use Linux OS to install for now and the support for Mac OS will come soon.
First, it is recommended to set up a conda environment
conda create -n bats
conda activate bats
If you are installing torch_tda
from the development version, please install the development version of BATS.py, install it from source.
Otherwise, you can use the latest release of BATS.py
pip install bats-tda
Now, to use torch_tda
, you will need Pytorch pre-installed and then
pip install torch-tda
Hera
If you want to compute bottleneck distance, you will need to install hera by 1. following their installation description to build from source and install the Python binding 2. (Optional if you can put the Python package in the correct position) write a simple setup.py
file to install the package into environment path.
Build from source
If you want to install from source, after cloning the repository, you can setup with setup.py
python setup.py install
Attention:
-
Note that installing by
pip install torch-tda
in the cloned repository will probably install the older version from remote, see the explanation. So, DO NOT usepip
if you want to build from the latest source. -
If you have installed an older version of
torch-tda
and want to update to the newest version, please uninstall it first bypip uninstall torch-tda
.
Documentation
If you want to contribute to the documenation, you can add some jupyter notebooks to the docs/examples
folder and then generate documentation using Sphinx
cd docs
pip install -r requirements.txt
make html
xdg-open _build/html/index.html # or just open this file