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Sparse fast alpha and gamma informational distances
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@scottgigante scottgigante released this 08 Jun 02:04
v0.2.7
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PHATE now implements a sparse, fast alpha decay kernel which has minimal memory requirements, compared to the old alpha decay which required a parwise distance matrix. Alpha decay now runs by default. In order to use the k nearest neighbors kernel, run with a=None.

Other notable changes:

  • graphtools implementation of kernel matrices
  • gamma replaces potential_method for the selection of informational distances. gamma=1 is equivalent to a log potential (default) and gamma=0 is equivalent to a square root potential
  • arguments alpha_decay and potential_method are deprecated.
  • PHATE is now implemented as a visualization method in Scanpy: https://scanpy.readthedocs.io/
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