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Add Gaussian Process Model #18

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muammar opened this issue Aug 1, 2019 · 1 comment
Open

Add Gaussian Process Model #18

muammar opened this issue Aug 1, 2019 · 1 comment
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@muammar
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enhancement New feature or request

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@muammar
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muammar commented Aug 1, 2019 •
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Another one to the zoo.
@muammar muammar self-assigned this Aug 3, 2019
@muammar muammar added the enhancement New feature or request label Aug 3, 2019
muammar added a commit that referenced this issue Aug 3, 2019
@muammar
General improvements and addition of Gaussian process regression
2c8e259 
- ml4chem/data/parser.py: improved FakeCalculator class and its
  docstrings.
- ml4chem/models/kernelridge.py:
    * New `class_name` parameter is saved to operate with universal
      loading of models.
    * get_kernel_matrix() function can handle more input cases.
    * Improvement in docstrings.
- ml4chem/potentials.py: universal loading of models.
- setup.py: now the `ml4chem` command line tool is installed with pip.
- ml4chem/models/gaussian_process.py: the new gaussian process
  regression model for ml4chem. It uses the KernelRidge class in the
  kernelridge module as a base class to then compute the extra step
  referring to the inference variance. This is related to #18.
- Updated examples/.
@muammar
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muammar commented Aug 3, 2019

I think this is implemented now but the following aspects have to be improved:

  1. Compute training data K just once at inference time. See https://github.com/muammar/ml4chem/blob/master/ml4chem/models/gaussian_process.py#L171 and https://github.com/muammar/ml4chem/blob/master/ml4chem/potentials.py#L331.
  2. Add some tools to plot the kernels.

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