Non-negative matrix factorization - Githubissues

cellarium-ai / cellarium-ml

Distributed single-cell data analysis.

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Non-negative matrix factorization #196

Open sjfleming opened 3 months ago

sjfleming commented 3 months ago

Implement NMF.

Uses the algorithm of Mairal et al. from their online learning paper.

Current issues:

[ ] Find a good solver for non-negative least squares regression
- Mairal et al. recommend LARS (least angle)
- Gao et al. (Welch group) recommend ANLS (but their implementation is in R)
- Others use HALS and BPP (including nmf-torch package)
[ ] Benchmark against existing algorithms (https://pypi.org/project/nmf-torch/)
- Complicated by the fact that NMF is non-convex
[ ] Implement cNMF

Looking forward

Think about implementing different kinds of losses (other than L2 Frobenius norm), especially beta divergences, because the beta=1 beta divergence loss turns NMF into Poisson NMF (this is mentioned in the original Lee and Seung paper I think)