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Ryan-Rhys / FlowMO

Library for training Gaussian Processes on Molecules
MIT License
36 stars 15 forks source link

Support for random walk kernel #29

Open JuliusSchwartz opened 3 years ago

JuliusSchwartz commented 3 years ago

Converting the work done in https://github.com/leojklarner/GProTorch/blob/kernels/gprotorch/kernels/graph_kernels/random_walk.py from pytorch to tensorflow and using https://www.jmlr.org/papers/volume11/vishwanathan10a/vishwanathan10a.pdf as a reference.

Have only implented eigendecomposition approach so far (meaning that one test for which GraKel uses Conjugate Gradient Descent only passes if method_type="baseline" is specified as an argument to the constructor of GraKel's random walk kernel)

Tests with non-null values of p don't pass although I suspect this might be due to a bug in GraKel (see https://github.com/ysig/GraKeL/issues/71)

Ryan-Rhys commented 3 years ago

I'll just add Leo to the review since he coded up the random walk kernel in GProTorch.

JuliusSchwartz commented 3 years ago

I'll just add Leo to the review since he coded up the random walk kernel in GProTorch.

Good idea (I don't seem to be able to add people myself)