Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training

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Deep Learning LPIGAC
Overview

Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training

Code for our paper "Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training" (IEEE BIBM 2021)

Requirements

The code has been tested running under Python 3.7.4, with the following packages and their dependencies installed:

numpy==1.16.5
pytorch==1.3.1
sklearn==0.21.3

Usage

git clone https://github.com/zhanglabNKU/LPIGAC.git
cd LPIGAC
python fivefoldcv.py

Options

We adopt an argument parser by package argparse in Python, and the options for running code are defined as follow:

parser = argparse.ArgumentParser()
parser.add_argument('--no-cuda', action='store_true', default=False,
                    help='Disables CUDA training.')
parser.add_argument('--seed', type=int, default=1, help='Random seed.')
parser.add_argument('--epochs', type=int, default=300,
                    help='Number of epochs to train.')
parser.add_argument('--lr', type=float, default=0.01,
                    help='Learning rate.')
parser.add_argument('--weight_decay', type=float, default=1e-7,
                    help='Weight decay (L2 loss on parameters).')
parser.add_argument('--hidden', type=int, default=144,                    help='Dimension of representations')
parser.add_argument('--alpha', type=float, default=0.5,
                    help='Weight between lncRNA space and protein space')
parser.add_argument('--beta', type=float, default=1.0,
                    help='Hyperparameter beta')

args = parser.parse_args()
args.cuda = not args.no_cuda and torch.cuda.is_available()

Data

Files of data are listed as follow:

  • LncRNAName.txt includes the names of all lncRNAs.
  • ProteinName.txt includes the names of all proteins.
  • interaction.txt is a matrix Y that shows lncRNA-protein associations. Y[i,j]=1 if lncRNA i and protein j are known to be associated, otherwise 0.
  • protfeat.txt is the feature matrix of proteins.
  • rnafeat.txt is the feature matrix of lncRNAs.

Citation

@inproceedings{jin2021lpigac,
    author = {Jin, Chen and Shi, Zhuangwei and Zhang, Han and Yin, Yanbin},
    title = {Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training},
    year = {2021},
    booktitle = {IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
}
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