# SALMON 🐟

SALMON: Survival Analysis Learning with Multi-Omics Neural Networks

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

![SALMON Architecture](figures/Figure1.png)

### Publication:

Huang, Zhi, et al. "SALMON: Survival Analysis Learning with Multi-Omics Neural Networks on Breast Cancer." Frontiers in Genetics 10 (2019): 166. [[Link]](https://www.frontiersin.org/articles/10.3389/fgene.2019.00166/abstract)

## 1. Installation

* Download Anaconda from https://www.anaconda.com/download/#linux/ with python 3 version.

* Install Pytorch, tqdm, imblearn, and lifelines.

```bash

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:

```bash

pip install -r requirements.txt

```

## 2. Run the main routine

```bash

cd experiments

python main.py

```