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

Last update: Nov 24, 2022

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}
}

Comments

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
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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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

Overview

Geometric Vector Perceptron

Install

Functionality

Usage

TF implementation:

Citations

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Comments

Adds MPNN wrapper

Fixes edge issues and distinguishes between covalent and proximity bonds

Releases(0.0.14)

0.0.14(Jun 8, 2021)

0.0.12(Mar 7, 2021)

0.0.11(Mar 5, 2021)

0.0.10(Mar 3, 2021)

0.0.9(Mar 1, 2021)

0.0.8(Feb 24, 2021)

0.0.7(Feb 21, 2021)

0.0.6(Jan 27, 2021)

0.0.5(Jan 24, 2021)

0.0.3(Jan 24, 2021)

0.0.2(Jan 14, 2021)

0.0.1(Jan 13, 2021)

Owner

Phil Wang

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