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cran2367 / sgt

Sequence Graph Transform
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Creating network graph from SGT Embedding #13

Open sdattaIDBS opened 11 months ago

sdattaIDBS commented 11 months ago

Hello,

Thank you for developing and sharing a unique algorithm for sequence embedding. I am currently implementing your SGT algorithm for protein embedding. While reading your paper, I could see in fig 2(a) that SGT embedding could be transformed to network graph. I intend to create graph and feed to Vanilla Graph Neural Network (am new to GNN). I am facing issue in creating graph out of the SGT embedding. I was thinking to unwrap the tuple columns to be as source and destination nodes and the decimal values to be as weight values. However. I was struggling with the graph.x (torch geometric) dimension.

I was wondering if you could help me on how to create create network graph from SGT embedding.

Thanks in advance.

cran2367 commented 11 months ago

Hi, SGT provides the adjacency matrix. I believe you are already using the adjacency matrix to create the (source, destination, weight) tuples. I am now sure of how to work with graph.x. If there is anything specific you are looking in SGT, please let me know.