[Feature Request] Molecule Feature Extraction by RDKit

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#71 opened on Dec 29, 2021 0 comments 0 reactions 0 assignees View on GitHub

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enhancement

Dominant language: Python
Stars: 2.5k
Forks: 374
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Description

Summary

This techical report describes the features used in Graphormer in KDD Cup 2021 quantum chemistry track. They are extracted by RDKit and could be found at here. We may consider to import it in v2.0 for molecule dataset.

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First steps

Read the whole issue, then the project's contributing guide.
Comment on the issue to say you are picking it up — it saves two people doing the same work.
Fork the repository and make your change on a branch.
Open a pull request that references the issue number.

Research direction

Start with the linked Graphormer technical report and OGB-LSC/graphormer/src/pcq_wrapper.py to understand the RDKit-derived features. Then locate the molecule-dataset integration point in the v2.0 code and confirm the expected feature representation. Done means the extraction is integrated for the molecule dataset with coverage for the supported feature set.

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Assessment

Tech stack: python
Domain: machine-learning
Issue type: Feature
Difficulty: 4/5
Estimated time: 3-5 days
Activity status: Stale
Clarity: Needs clarification
Newbie friendliness: 35/100

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