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

Related tags

Deep LearningLPIGAC
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)},
}
Owner
zhanglabNKU
Data Mining Lab. Prof. Han Zhang
zhanglabNKU
GitHub Repository
Implementation of Deep Deterministic Policy Gradiet Algorithm in Tensorflow

ddpg-aigym Deep Deterministic Policy Gradient Implementation of Deep Deterministic Policy Gradiet Algorithm (Lillicrap et al.arXiv:1509.02971.) in Ten

Steven Spielberg P 247 Dec 07, 2022
PyTorch implementation of DeepUME: Learning the Universal Manifold Embedding for Robust Point Cloud Registration (BMVC 2021)

DeepUME: Learning the Universal Manifold Embedding for Robust Point Cloud Registration [video] [paper] [supplementary] [data] [thesis] Introduction De

Natalie Lang 10 Dec 14, 2022
Exemplo de implementação do padrão circuit breaker em python

fast-circuit-breaker Circuit breakers existem para permitir que uma parte do seu sistema falhe sem destruir todo seu ecossistema de serviços. Michael

James G Silva 17 Nov 10, 2022
Code for the paper titled "Prabhupadavani: A Code-mixed Speech Translation Data for 25 languages"

Prabhupadavani: A Code-mixed Speech Translation Data for 25 languages Code for the paper titled "Prabhupadavani: A Code-mixed Speech Translation Data

Ayush Daksh 12 Dec 01, 2022
Nonnegative spatial factorization for multivariate count data

Nonnegative spatial factorization for multivariate count data This repository contains supporting code to facilitate reproducible analysis. For detail

Will Townes 24 Dec 19, 2022
An example to implement a new backbone with OpenMMLab framework.

Backbone example on OpenMMLab framework English | 简体中文 Introduction This is an template repo about how to use OpenMMLab framework to develop a new bac

Ma Zerun 22 Dec 29, 2022
This project aims to segment 4 common retinal lesions from Fundus Images.

This project aims to segment 4 common retinal lesions from Fundus Images.

Husam Nujaim 1 Oct 10, 2021
Official Pytorch Implementation of: "ImageNet-21K Pretraining for the Masses"(2021) paper

ImageNet-21K Pretraining for the Masses Paper | Pretrained models Official PyTorch Implementation Tal Ridnik, Emanuel Ben-Baruch, Asaf Noy, Lihi Zelni

574 Jan 02, 2023
PyTorch implementation for NED. It can be used to manipulate the facial emotions of actors in videos based on emotion labels or reference styles.

Neural Emotion Director (NED) - Official Pytorch Implementation Example video of facial emotion manipulation while retaining the original mouth motion

Foivos Paraperas 89 Dec 23, 2022
Cross-Image Region Mining with Region Prototypical Network for Weakly Supervised Segmentation

Cross-Image Region Mining with Region Prototypical Network for Weakly Supervised Segmentation The code of: Cross-Image Region Mining with Region Proto

LiuWeide 16 Nov 26, 2022
Use .csv files to record, play and evaluate motion capture data.

Purpose These scripts allow you to record mocap data to, and play from .csv files. This approach facilitates parsing of body movement data in statisti

21 Dec 12, 2022
The official implementation of You Only Compress Once: Towards Effective and Elastic BERT Compression via Exploit-Explore Stochastic Nature Gradient.

You Only Compress Once: Towards Effective and Elastic BERT Compression via Exploit-Explore Stochastic Nature Gradient (paper) @misc{zhang2021compress,

46 Dec 07, 2022
Evaluating deep transfer learning for whole-brain cognitive decoding

Evaluating deep transfer learning for whole-brain cognitive decoding This README file contains the following sections: Project description Repository

Armin Thomas 5 Oct 31, 2022
Adversarial Robustness Toolbox (ART) - Python Library for Machine Learning Security - Evasion, Poisoning, Extraction, Inference - Red and Blue Teams

Adversarial Robustness Toolbox (ART) is a Python library for Machine Learning Security. ART provides tools that enable developers and researchers to defend and evaluate Machine Learning models and ap

3.4k Jan 04, 2023
A solution to ensure Crowd Management with Contactless and Safe systems.

CovidTrack A Solution to ensure Crowd Management with Contactless and Safe systems. ML Model Mask Detection Social Distancing Detection Analytics Page

Om Khare 1 Nov 10, 2021
FB-tCNN for SSVEP Recognition

FB-tCNN for SSVEP Recognition Here are the codes of the tCNN and FB-tCNN in the paper "Filter Bank Convolutional Neural Network for Short Time-Window

Wenlong Ding 12 Dec 14, 2022
SciKit-Learn Laboratory (SKLL) makes it easy to run machine learning experiments.

SciKit-Learn Laboratory This Python package provides command-line utilities to make it easier to run machine learning experiments with scikit-learn. O

ETS 528 Nov 25, 2022
This is the code for "HyperNeRF: A Higher-Dimensional Representation for Topologically Varying Neural Radiance Fields".

HyperNeRF: A Higher-Dimensional Representation for Topologically Varying Neural Radiance Fields This is the code for "HyperNeRF: A Higher-Dimensional

Google 702 Jan 02, 2023
A PyTorch Implementation of PGL-SUM from "Combining Global and Local Attention with Positional Encoding for Video Summarization", Proc. IEEE ISM 2021

PGL-SUM: Combining Global and Local Attention with Positional Encoding for Video Summarization PyTorch Implementation of PGL-SUM From "PGL-SUM: Combin

Evlampios Apostolidis 35 Dec 22, 2022
A python bot to move your mouse every few seconds to appear active on Skype, Teams or Zoom as you go AFK. 🐭 🤖

PyMouseBot If you're from GT and annoyed with SGVPN idle timeouts while working on development laptop, You might find this useful. A python cli bot to

Oaker Min 6 Oct 24, 2022