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.