Geometric Vector Perceptron
Implementation of Geometric Vector Perceptron, a simple circuit with 3d rotation equivariance for learning over large biomolecules, in Pytorch. The repository may also contain experimentation to see if this could be easily extended to self-attention.
Install
$ pip install geometric-vector-perceptronFunctionality
-
GVP: Implementing the basic geometric vector perceptron. -
GVPDropout: Adapted dropout for GVP in MPNN context -
GVPLayerNorm: Adapted LayerNorm for GVP in MPNN context -
GVP_MPNN: Adapted instance of Message Passing class fromtorch-geometricpackage. Still not tested. -
GVP_Network: Functional model architecture ready for working with arbitary point clouds.
Usage
import torch
from geometric_vector_perceptron import GVP
model = GVP(
dim_vectors_in = 1024,
dim_feats_in = 512,
dim_vectors_out = 256,
dim_feats_out = 512,
vector_gating = True # use the vector gating as proposed in https://arxiv.org/abs/2106.03843
)
feats, vectors = (torch.randn(1, 512), torch.randn(1, 1024, 3))
feats_out, vectors_out = model( (feats, vectors) ) # (1, 256), (1, 512, 3)With the specialized dropout and layernorm as described in the paper
import torch
from torch import nn
from geometric_vector_perceptron import GVP, GVPDropout, GVPLayerNorm
model = GVP(
dim_vectors_in = 1024,
dim_feats_in = 512,
dim_vectors_out = 256,
dim_feats_out = 512,
vector_gating = True
)
dropout = GVPDropout(0.2)
norm = GVPLayerNorm(512)
feats, vectors = (torch.randn(1, 512), torch.randn(1, 1024, 3))
feats, vectors = model( (feats, vectors) )
feats, vectors = dropout(feats, vectors)
feats, vectors = norm(feats, vectors) # (1, 256), (1, 512, 3)TF implementation:
The original implementation in TF by the paper authors can be found here: https://github.com/drorlab/gvp/
Citations
@inproceedings{anonymous2021learning,
title = {Learning from Protein Structure with Geometric Vector Perceptrons},
author = {Anonymous},
booktitle = {Submitted to International Conference on Learning Representations},
year = {2021},
url = {https://openreview.net/forum?id=1YLJDvSx6J4}
}@misc{jing2021equivariant,
title = {Equivariant Graph Neural Networks for 3D Macromolecular Structure},
author = {Bowen Jing and Stephan Eismann and Pratham N. Soni and Ron O. Dror},
year = {2021},
eprint = {2106.03843},
archivePrefix = {arXiv},
primaryClass = {cs.LG}
}
