This is a major version update of MELD, and it will break backwards compatibility with previous workflows due to a significant change in nomenclature accompanying our revised manuscript forthcoming in Nature Biotechnology.
You can find an up-to-date version of our article on BioRxiv with the revised language. The main difference is that we have dropped the "RES" and "EES" language for a more rigorous probabilistic interpretation inspired by an update to the algorithm made during the review process.
The output of `meld.MELD().fit_transform` is now referred to as the `sample_densities` and is the output of a kernel density estimation of each sample over that cell similarity graph. We then calculate the ratio of these densities using `meld.utils.normalize_densities` to calculate `sample_likelihoods`.
This framework reflects the interpretation of the MELD algorithm as a kernel density estimation over a graph. The tutorial and documentation have also been updated.