--- a/README.md +++ b/README.md @@ -1,35 +1,35 @@ -# SALMON 🐟 -SALMON: Survival Analysis Learning with Multi-Omics Neural Networks - -### SALMON architecture with the implementation of Cox proportional hazards regression networks: - - -### 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 -``` +# SALMON 🐟 +SALMON: Survival Analysis Learning with Multi-Omics Neural Networks + +### SALMON architecture with the implementation of Cox proportional hazards regression networks: + + +### 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 +```