https://github.com/divya031090/phyLoSTM

https://github.com/divya031090/phyLoSTM

Last synced: about 2 months ago
JSON representation

• Host: GitHub
• URL: https://github.com/divya031090/phyLoSTM
• Owner: divya031090
• Created: 2021-01-08T18:12:18.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2021-08-12T19:13:52.000Z (over 3 years ago)
• Last Synced: 2024-08-01T16:18:40.978Z (5 months ago)
• Language: Python
• Size: 13.8 MB
• Stars: 3
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-rm-omics - **phyLoSTM** - Sharma - combined modeling using CNN for feature extraction and LSTM for temporal dependency analysis - [phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data](https://doi.org/10.1093/bioinformatics/btab482) (Software packages and methods / Machine Learning/Artificial Neural Networks (Deep Learning) Methods)

README

        
# phyLoSTM

A combined modeling using CNN for feature extraction and LSTM for temporal dependency analysis in microbiome data.

DIABIMMUNE three country cohort and DiGuilio study have been used as the data for implementation of the method.

temporal.py is the file for longitudinal analysis and CNN.py is the file for CNN based feature extraction 

The datafiles are OTU_data_revised.csv and Diguilio.xlsx

Prerequisites:

Python 2.7

CUDA

cuDNN

Conda

TensorFlow

NumPy pandas

Keras