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PHATE 2.0 (Fast scalable PHATE)
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@scottgigante scottgigante released this 31 May 23:59
· 525 commits to main since this release
v0.2.0
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Version 2.0 implements fast scalable PHATE in Python (2.7, >=3.5), MATLAB and R.

PHATE now runs in seconds to minutes on tens of thousands of cells. Benchmarking shows runtime of ~3 hours on >1,000,000 cells.

Key changes:

  • t is automatically chosen using Von Neumann Entropy using t='auto' by default.
  • n_landmark determines the number of landmarks to use for scalable PHATE. n_landmark=None ([] on MATLAB, NA in R) specifies exact PHATE.
  • default parameters have changed: k=15, a=10 but is ignored if n_cells>=n_landmark.
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