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genome-minimizer: Generative Models for Genomic Sequence Generation

Code developed by Stacy Shcherbakova and Chris P Barnes

Requirements

Libraries: PyTorch, numpy, pandas, seaborne, matplotlib, sklearn, biopython

Create a venv enviroment using the following commands inside the repository:

python -m venv GM_env source GM_env/bin/activate pip install -r requiremnet.txt

Data

The data folders: data These can be obtained from the Zenodo repository and should be placed in the top level directory of the package.

Some Acronyms/File names:

  • Extras: Extra functions
  • Training: Files which include training loops
  • Directories: Directories paths
  • BD: Horesh et. al. dataset (±7.5k samples)
  • Final: Cut down Horesh et. al. dataset (±5k samples)
  • GS: Gradient Clipping and Scheduling
  • AHPT: After Hyperparameter Tuning

Usage