Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Adding more grover layers #3277

Merged
merged 5 commits into from
Mar 17, 2023
Merged

Adding more grover layers #3277

merged 5 commits into from
Mar 17, 2023

Conversation

arunppsg
Copy link
Contributor

Pull Request Template

Description

I am breaking down #3272 into two pull requests. Here is the part one, containing some layers in the grover pretrain model.

Type of change

Please check the option that is related to your PR.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
    • In this case, we recommend to discuss your modification on GitHub issues before creating the PR
  • Documentations (modification for documents)

Checklist

  • My code follows the style guidelines of this project
    • Run yapf -i <modified file> and check no errors (yapf version must be 0.32.0)
    • Run mypy -p deepchem and check no errors
    • Run flake8 <modified file> --count and check no errors
    • Run python -m doctest <modified file> and check no errors
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • I have added tests that prove my fix is effective or that my feature works
  • New unit tests pass locally with my changes
  • I have checked my code and corrected any misspellings

@arunppsg arunppsg mentioned this pull request Mar 14, 2023
Merged
15 tasks
rbharath
rbharath reviewed Mar 15, 2023
View reviewed changes
Copy link
Member

@rbharath rbharath left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Mostly minor comments here requesting improvements to the docs

deepchem/models/torch_models/grover_layers.py Outdated
the number of attention heads.
atom_embedding_output_type: str
the type of output aggregation after message passing.
atom_messages: True False
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is the formatting here messed up? It looks strange

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Fixed it

deepchem/models/torch_models/grover_layers.py Show resolved Hide resolved
deepchem/models/torch_models/grover_layers.py Outdated
class GroverBondVocabPredictor(nn.Module):
"""Layer for learning contextual information for bonds.

The layer is used in `Grover <https://drug.ai.tencent.com/publications/GROVER.pdf>`_
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Can you add a References section and move the link there?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

added reference section

deepchem/models/torch_models/grover_layers.py Show resolved Hide resolved
deepchem/models/torch_models/grover_layers.py Outdated
"""Grover Atom Vocabulary Prediction Module.

The GroverAtomVocabPredictor module is used for predicting atom-vocabulary
for the self-supervision task in `Grover. <https://drug.ai.tencent.com/publications/GROVER.pdf>`_
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Same comments as before. Can you add References and can you add a usage example?

deepchem/models/torch_models/grover_layers.py Show resolved Hide resolved
rbharath
rbharath reviewed Mar 15, 2023
View reviewed changes
Copy link
Member

@rbharath rbharath left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

One minor fix needed on the docstring and we should be good to go

deepchem/models/torch_models/grover_layers.py Outdated
in_features: int, default: 128
Input feature size of bond embeddings.

Example
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This should be in the main docstring above and not in the init docstring

rbharath
rbharath approved these changes Mar 17, 2023
View reviewed changes
Copy link
Member

@rbharath rbharath left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM. Feel free to merge in once CI looks good

@arunppsg arunppsg merged commit 7011045 into deepchem:master Mar 17, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@rbharath rbharath rbharath approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@arunppsg @rbharath