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microsoft / Graphormer

Graphormer is a general-purpose deep learning backbone for molecular modeling.
MIT License
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Node classification #12

Closed steelman97 closed 3 years ago

steelman97 commented 3 years ago

What do I have to modify the code in order to try the model on ogbn-proteins? (Wrapper, collator..)

chengxuanying commented 3 years ago

Hi @steelman97 , I think writing a new dataset for node tasks is better. Please refer to the class MyGraphPropPredDataset if you want to do so.

There are some tips for trying the model on ogbn-proteins:

  1. Implement a proper graph sampling strategy as mentioned in our paper.
  2. Some parts of the code need to rewrite to fit for larger graph. (E.g., the floyd-warshall algorithm is n^3 regarding the number of nodes, you may need to choose an alternative metric for efficient spatial encoding.)