Ryan-Rhys Griffiths comments

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                                            Ryan-Rhys Griffiths

String kernels can exploit biases in SMILES string format, skewing performance metrics

Thanks for raising this! I made a change to the photoswitch dataset to canonicalise all SMILES as a preprocessing step a couple of weeks ago, will make sure this is...

String kernels can exploit biases in SMILES string format, skewing performance metrics

Interesting! @henrymoss and I will keep track of this conversation you guys are having in DeepChem!

Support for random walk kernel

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

Question about Tanimoto kernel, ARD

Hi Mohammad, Thanks for your comment! The FlowMO library: https://github.com/Ryan-Rhys/FlowMO/blob/master/GP/kernels.py is probably a better example for the Tanimoto kernel. `sigma_f` in this instance is the output scale for the kernel...

Question about Tanimoto kernel, ARD

Hi Mohammad, Are you referring to the numpy implementation here or to the Tanimoto kernel in FlowMO? Best, Ryan

Question about Tanimoto kernel, ARD

Hi Mohammad, Judging from the test for the Tanimoto kernel in `test_mlhgp.py` module it seems that the input is assumed to be `[No. of Observations, 1]`. If you would prefer...

Where to look for composition-based optimization and how to implement with custom dataset

Hi Sterling, Our physics lab experiments fell through on the experimental side unfortunately and so we didn't end up running the heteroscedastic BO algorithm over material composition space! I'm currently...

Where to look for composition-based optimization and how to implement with custom dataset

@sgbaird I guess the key for the composition-based problem is setting the bounds to be a simplex i.e. modifying the following line: `bounds = np.array([0, 10]).reshape(-1, 1) # bounds of...