marcoplacenti/protein_generation

This repo contains code and resources used for the project "Proteins Generation using Language Model" for the course 02456 Deep Learning at DTU - Fall 2020.

Mini-ProGen: Learning the Amino Acid Language of Protein Families

This repo contains code and resources used in "Mini-ProGen: Learning the Amino Acid Language of Protein Families" developed as part of the course 02456 Deep Learning at DTU - Fall 2020.

To train the model

python mini-progen.py

To run in Jupyter Notebook/Colab use mini-progen.ipynb

protein_generation's Issues

Create script that can download data from the UniProt SPARQL API

Implement downloading GO-terms via the UniProt SPARQL API

Implement cleaning of data using PySpark

Reason: PySpark is great for managing huge data sets

Create virtual Python environment

Create virtual Python environment to ensure that we all have the needed Python packages for the different scripts.
See here and here.

Further process data from SPARQL API such that we have one row per sequence

Implement sinusoidal positional encoder in "gpt2_from_scratch.py"