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Node classification tasks #51
Description
Hi! First of all great job! I have been trying to do node classification in residue view, using my own node labels. However, I haven't been able to configure the NodePropertyPrediction task to use those labels instead of predicting the residue features. Do you have any guidance on how I can proceed to do this? Any help is appreciated
Activity
Oxer11 commentedon Oct 16, 2023
Hi! The
NodePropertyPredictiontask is orginally defined for sequence-based models. To adapt it to structure-based models, maybe you just need to add agraph_construction_modelpart following what we do intask.PropertyPrediction.mpedraza98 commentedon Oct 17, 2023
Thank you for your answer. I have a couple more questions, I have been trying to modify the AttributeMasking task for my node classification problem, however it is not clear to me how is the relation between the nodes id and the amino acids in the sequence. The only clue I've found so far is this note in the data/protein.py file "Nodes may have a different order with residues." Can you guide me on how to proceed?
Oxer11 commentedon Nov 27, 2023
Sorry for the late response. In
data.Protein, we usually usenodeandatominterchangably, whileresiduecorresponds to the real residue in proteins. You can usedata.Protein.atom2residueto learn which residue an atom belongs to.