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SALMON

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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](https://github.com/huangzhii/SALMON/blob/master/figures/Figure1.png?raw=true)

### 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
```

	a/README.md		b/README.md
1	# SALMON 🐟	1	# SALMON 🐟
2	SALMON: Survival Analysis Learning with Multi-Omics Neural Networks	2	SALMON: Survival Analysis Learning with Multi-Omics Neural Networks
3		3
4	### SALMON architecture with the implementation of Cox proportional hazards regression networks:	4	### SALMON architecture with the implementation of Cox proportional hazards regression networks:
5	![SALMON Architecture](figures/Figure1.png)	5	![SALMON Architecture](https://github.com/huangzhii/SALMON/blob/master/figures/Figure1.png?raw=true)
6		6
7	### Publication:	7	### Publication:
8	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)	8	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)
9		9
10		10
11	## 1. Installation	11	## 1. Installation
12	* Download Anaconda from https://www.anaconda.com/download/#linux/ with python 3 version.	12	* Download Anaconda from https://www.anaconda.com/download/#linux/ with python 3 version.
13	* Install Pytorch, tqdm, imblearn, and lifelines.	13	* Install Pytorch, tqdm, imblearn, and lifelines.
14		14
15	```bash	15	```bash
16	conda install pytorch torchvision -c pytorch	16	conda install pytorch torchvision -c pytorch
17	conda install -c conda-forge tqdm	17	conda install -c conda-forge tqdm
18	conda install -c conda-forge imbalanced-learn	18	conda install -c conda-forge imbalanced-learn
19	conda install -c conda-forge lifelines	19	conda install -c conda-forge lifelines
20	```	20	```
21		21
22	### Alternative installation	22	### Alternative installation
23	To install the libraries with the specified version, `requirements.txt` can be used as a configuration file with the following command:	23	To install the libraries with the specified version, `requirements.txt` can be used as a configuration file with the following command:
24		24
25	```bash	25	```bash
26	pip install -r requirements.txt	26	pip install -r requirements.txt
27	```	27	```
28		28
29	## 2. Run the main routine	29	## 2. Run the main routine
30		30
31		31
32	```bash	32	```bash
33	cd experiments	33	cd experiments
34	python main.py	34	python main.py
35	```	35	```