Since this shows up in homomeric proteins, maybe the issue is because symmetry breaking in quartinary structure happens late in training. This is just a guess tho... but aligns with my intuitions on training dynamics. I would also guess that this would get ironed out in the tails of the loss curve, if we push out further in training. I think the PLDDT loss would first learn to stack homomers on top of one another and then spread them out. I haven't used alphafold too much but the smoking gun plot id be interested in is clashes in heteromers vs clashes in homomers. It's a curious little detail, thanks for sharing this finding!
Since this shows up in homomeric proteins, maybe the issue is because symmetry breaking in quartinary structure happens late in training. This is just a guess tho... but aligns with my intuitions on training dynamics. I would also guess that this would get ironed out in the tails of the loss curve, if we push out further in training. I think the PLDDT loss would first learn to stack homomers on top of one another and then spread them out. I haven't used alphafold too much but the smoking gun plot id be interested in is clashes in heteromers vs clashes in homomers. It's a curious little detail, thanks for sharing this finding!