@KevinKaichuang I enjoyed your talk! Have you considered using some of the more recently developed equivariant architectures to incorporate more refined geometric information for the structural component of your architecture? 🙂
That's interesting, thanks! I would have thought that being able to incorporate structural info about neighbors that are nearby in space but not necessarily in sequence order could be useful, but maybe it depends on how much training data are available or something like that.
@mspells That's what the MIF and MIF-ST papers do right? I just didn't think the architectures were that recent.
Maybe I'm misunderstanding, but I thought that the MIF work just used the backbone torsion angles of neighbors in sequence order; I was thinking that structural info derived from Cartesian coordinates of some number of nearest neighbors (in 3D space for the folded structure, not in sequence order space, I mean) might also be informative.
@KevinKaichuang Sorry for being unclear; I'm suggesting that, rather than using the rotation-invariant attributes of torsion angles for neighbors along the sequence, you could use a set of learned, rotation invariant attributes that represent the geometry of the nearby point cloud (i.e. not restricted to neighbors as you travel along the sequence, but rather k-nearest neighbors in 3D) for each amino acid. Sorry again if my point is still unclear; happy to clarify further if it would help!
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