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SALMON 🐟

SALMON: Survival Analysis Learning with Multi-Omics Neural Networks

SALMON architecture with the implementation of Cox proportional hazards regression networks:

SALMON Architecture

Publication:

Huang, Zhi, et al. "SALMON: Survival Analysis Learning with Multi-Omics Neural Networks on Breast Cancer." Frontiers in Genetics 10 (2019): 166. [Link]

1. Installation

Download Anaconda from https://www.anaconda.com/download/#linux/ with python 3 version.
Install Pytorch, tqdm, imblearn, and lifelines.

conda install pytorch torchvision -c pytorch
conda install -c conda-forge tqdm
conda install -c conda-forge imbalanced-learn
conda install -c conda-forge lifelines

Alternative installation

To install the libraries with the specified version, requirements.txt can be used as a configuration file with the following command:

pip install -r requirements.txt

2. Run the main routine

cd experiments
python main.py