This work proposes a new self-supervised pretraining task for 3D graph neural networks: pretrained on 542k SwissProt protein structures from the AlphaFold Database, the model predicts the Euclidean distance between the geometric centroid of each protein subgraph (2-hop ego networks centered on 10% of amino acids) and the global geometric centroid of the whole protein, discretized into 10 equal bins and trained with cross-entropy; across ProNet, SchNet, and GCN backbones and ca_base, ca_angles, and ca_bb featurizations, it improves Fold, Superfamily, Family, and React classification by up to about 6% over no-pretraining and edge-distance pretraining baselines, without multiple views, augmentations, or masking strategies.
This work proposes a new self-supervised pretraining task for 3D graph neural networks: pretrained on 542k SwissProt protein structures from the AlphaFold Database, the model predicts the Euclidean distance between the geometric centroid of each protein subgraph (2-hop ego networks centered on 10% of amino acids) and the global geometric centroid of the whole protein, discretized into 10 equal bins and trained with cross-entropy; across ProNet, SchNet, and GCN backbones and ca_base, ca_angles, and ca_bb featurizations, it improves Fold, Superfamily, Family, and React classification by up to about 6% over no-pretraining and edge-distance pretraining baselines, without multiple views, augmentations, or masking strategies.