Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pytorch. Idea proposed and accepted at ICLR 2021

Related tags

Deep Learningdeep-learningprotein-structureartficial-intelligencebiomoleculeequivariance
Overview

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-perceptron

Functionality

  • 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 from torch-geometric package. Still not tested.

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
)

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
)

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},
    note={under review}
}
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Comments
  • Adds MPNN wrapper

    Adds MPNN wrapper

    Could you double check it?

    I've tried to follow the original implementation ( https://github.com/drorlab/gvp/ see src/models.py ) but it's weird since they seem to mix the edge_attrs and the node features and return a mix of them, but later they seem to discard them so :man_shrugging: (whereas i only return node features - bc idk how to modify edge_attrs in an easy way -> the aggregation is always node-based)

    opened by hypnopump 3
  • Fixes edge issues and distinguishes between covalent and proximity bonds

    Fixes edge issues and distinguishes between covalent and proximity bonds

    • Gets all covalent bonds for a protein conformation (different than proximity)
    • Reduces unused computations
    • Fixes edges (now undirected graph)
    • Adapts denoising example accordingly (not in reconstruction example yet)
    opened by hypnopump 0
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Phil Wang
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