This is a Python 3 implementation of ARD-NMF from Tan & Févotte (IEEE Transactions on Pattern Analysis and Machine Intelligence, 2013). The code here is based on Févotte's MATLAB implementation, in some cases copying code and comments verbatim.
The only required software is Python 3.
We include a list of required packages in requirements.txt. We recommend using Conda to install Python 3, and then install the required packages.
Beyond installing the dependencies above, no compilation of is required.
The implementation of ARD-NMF was written to match the coding guidelines of scikit-learn, and is provided as a Python module. In that way, the main usage is to import the module (e.g. by running the Python shell in this directory):
from ardnmf import ARDNMF
model = ARDNMF(a=10)
H = model.fit_transform(X)
W = model.components_
The value for beta determines the cost function and controls the assumed statistics of the observation noise. It can be learned from training data by cross-training but this package expects beta to be a fixed value (default value for beta is 1). beta = 0 implies multiplicative Gamma observation noise, beta = 1 implies Poisson noise and beta = 2 implies Gaussian additive noise. For mutation signature extraction, the assumption of Poisson noise is reasonable.
They impose inverse-Gamma priors on each relevance weight where a is the (non-negative) shape hyperparameter and b is the scale hyperparameter. The value for b is computed using the algorithm originally described by Fevotte et al. Estimating the value for a is more difficult so it is required as an input. Fevotte et al. recommend a small value for a.
The PCAWG version of SignatureAnalyzer uses a=10, b=5 and phi=1 as the default parameters. They use an exponential prior for W (the signatures) and a half normal prior for H (the exposures). The algorithm for computing b assumes that the same prior is used for both W and H.
We include an example application of ARDNMF to the "swimmer" dataset described in Tan & Févotte in examples/swimmer.