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
Codes accompanying the paper "Believe What You See: Implicit Constraint Approach for Offline Multi-Agent Reinforcement Learning" (NeurIPS 2021 Spotlight

Implicit Constraint Q-Learning This is a pytorch implementation of ICQ on Datasets for Deep Data-Driven Reinforcement Learning (D4RL) and ICQ-MA on SM

42 Dec 23, 2022
This repo holds codes of the ICCV21 paper: Visual Alignment Constraint for Continuous Sign Language Recognition.

VAC_CSLR This repo holds codes of the paper: Visual Alignment Constraint for Continuous Sign Language Recognition.(ICCV 2021) [paper] Prerequisites Th

Yuecong Min 64 Dec 19, 2022
[Official] Exploring Temporal Coherence for More General Video Face Forgery Detection(ICCV 2021)

Exploring Temporal Coherence for More General Video Face Forgery Detection(FTCN) Yinglin Zheng, Jianmin Bao, Dong Chen, Ming Zeng, Fang Wen Accepted b

57 Dec 28, 2022
Vision Transformer for 3D medical image registration (Pytorch).

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio

Junyu Chen 192 Dec 20, 2022
Boosted neural network for tabular data

XBNet - Xtremely Boosted Network Boosted neural network for tabular data XBNet is an open source project which is built with PyTorch which tries to co

Tushar Sarkar 175 Jan 04, 2023
Neural style in TensorFlow! 🎨

neural-style An implementation of neural style in TensorFlow. This implementation is a lot simpler than a lot of the other ones out there, thanks to T

Anish Athalye 5.5k Dec 29, 2022
Implementation of "Learning to Match Features with Seeded Graph Matching Network" ICCV2021

SGMNet Implementation PyTorch implementation of SGMNet for ICCV'21 paper "Learning to Match Features with Seeded Graph Matching Network", by Hongkai C

87 Dec 11, 2022
CLIP + VQGAN / PixelDraw

clipit Yet Another VQGAN-CLIP Codebase This started as a fork of @nerdyrodent's VQGAN-CLIP code which was based on the notebooks of @RiversWithWings a

dribnet 276 Dec 12, 2022
Transport Mode detection - can detect the mode of transport with the help of features such as acceeration,jerk etc

title emoji colorFrom colorTo sdk app_file pinned Transport_Mode_Detector 🚀 purple yellow gradio app.py false Configuration title: string Display tit

Nishant Rajadhyaksha 3 Jan 16, 2022
ICSS - Interactive Continual Semantic Segmentation

Presentation This repository contains the code of our paper: Weakly-supervised c

Alteia 9 Jul 23, 2022
Research on Tabular Deep Learning (Python package & papers)

Research on Tabular Deep Learning For paper implementations, see the section "Papers and projects". rtdl is a PyTorch-based package providing a user-f

Yura Gorishniy 510 Dec 30, 2022
Fast and robust certifiable relative pose estimation

Fast and Robust Relative Pose Estimation for Calibrated Cameras This repository contains the code for the relative pose estimation between two central

42 Dec 06, 2022
Bravia core script for python

Bravia-Core-Script You need to have a mandatory account If this L3 does not work, try another L3. enjoy

5 Dec 26, 2021
This repository provides an unified frameworks to train and test the state-of-the-art few-shot font generation (FFG) models.

FFG-benchmarks This repository provides an unified frameworks to train and test the state-of-the-art few-shot font generation (FFG) models. What is Fe

Clova AI Research 101 Dec 27, 2022
High level network definitions with pre-trained weights in TensorFlow

TensorNets High level network definitions with pre-trained weights in TensorFlow (tested with 2.1.0 = TF = 1.4.0). Guiding principles Applicability.

Taehoon Lee 1k Dec 13, 2022
Product-based-recommendation-system - A product based recommendation system which uses Machine learning algorithm such as KNN and cosine similarity

Product-based-recommendation-system A product based recommendation system which

Prem Jha 2 Feb 15, 2022
Jax/Flax implementation of Variational-DiffWave.

jax-variational-diffwave Jax/Flax implementation of Variational-DiffWave. (Zhifeng Kong et al., 2020, Diederik P. Kingma et al., 2021.) DiffWave with

YoungJoong Kim 37 Dec 16, 2022
A Lightweight Face Recognition and Facial Attribute Analysis (Age, Gender, Emotion and Race) Library for Python

deepface Deepface is a lightweight face recognition and facial attribute analysis (age, gender, emotion and race) framework for python. It is a hybrid

Sefik Ilkin Serengil 5.2k Jan 02, 2023
A data-driven approach to quantify the value of classifiers in a machine learning ensemble.

Documentation | External Resources | Research Paper Shapley is a Python library for evaluating binary classifiers in a machine learning ensemble. The

Benedek Rozemberczki 188 Dec 29, 2022
HiFi-GAN: High Fidelity Denoising and Dereverberation Based on Speech Deep Features in Adversarial Networks

HiFiGAN Denoiser This is a Unofficial Pytorch implementation of the paper HiFi-GAN: High Fidelity Denoising and Dereverberation Based on Speech Deep F

Rishikesh (ऋषिकेश) 134 Dec 27, 2022