# fbgan

**Repository Path**: jarckry/fbgan

## Basic Information

- **Project Name**: fbgan
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: AGPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2019-11-27
- **Last Updated**: 2021-07-09

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Feedback GAN for DNA

## System Requirements and Installation
```pip install -r requirements.txt```
- Python 3.6.3
- PSIPRED libraries should be installed by downloading from [here](http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/) and following [this installation guide](http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README)

## Demo Instructions
All default arguments for demo are provided.

1) Run `python wgan_gp_gene` to pretrain WGAN with Gradient Penalty to produce valid gene sequences.
  - **Expected Output**
    - `sample/$RUN_NAME` will contain sample gene sequences from every 100 iterations, as well as loss and distance curves.
    - `checkpoint/$RUN_NAME` will contain checkpoints for both generator and discriminator

2) Pretrain Analyzer:
  - AMP Analyzer: run `python amp_predictor_pytorch`
    - **Expected Output**
      - `checkpoint/$RUN_NAME` will contain analyzer checkpoints
      - At end of training, model will print training accuracy, test accuracy, etc.
  - Psipred Secondary Structure Analyzer: No pretraining necessary. `psipred_wrapper.py` provides a wrapper around the PSIPRED libraries.

3) Train FBGAN:
  - With AMP analyzer: run `python wgan_gp_lang_gene_analyzer`. Default arguments for demo are provided.
  - With Psipred analyzer: run `python wgan_psipred`. Default arguments for demo are provided.
  - **Expected Output**
    - `checkpoint/$RUN_NAME` will contain FBGAN checkpoints
    - `samples/$RUN_NAME/sampled_*_preds.txt` will contain sampled outputs from generator and their scores from analyzer from every epoch.
    - $RUN_NAME for AMP demo is default "fbgan_amp_demo"
    - $RUN_NAME for Psipred demo is default "fbgan_psipred_demo"
  -**Expected Runtime**
    - With a Nvidia GEFORCE GTX GPU, it takes roughly 2 minutes per epoch for FBGAN. Expect this to take at least 10 minutes per epoch on a desktop.

## LICENSE
  Source files are made available under the terms of the GNU Affero General Public License (GNU AGPLv3). See GNU-AGPL-3.0.txt for details.