Fixed the problem with the evaluation quality metric

facebookresearch / PoincareMaps

The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

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Fixed the problem with the evaluation quality metric #6

Closed klanita closed 3 years ago

klanita commented 3 years ago

Updated the code to be compatible with pytorch 1.7.1.
Updated the code to be compatible with the latest version of scanpy.
Fixed the issue in the quality score: use geodesic distances instead of euclidean distances in high dimensional space
Added example notebook on how to run the quality metric.
Added docstrings to the quality metrics functions. Cleaned the code file with quality metrics removing unused functions.
Changed default plots format from pdf to png.