Exploring PyTorch and Transformers for Genomic Sequence Classification

Location: Wellcome Genome Campus, UK Date: Wednesday, October 16, 2024

Overview

This repository contains all the materials for the workshop conducted at the Explainable AI in Biology Conference, 2024. The session will focus on applying deep learning techniques, using oublicly available HuggingFace models and a simple Convolutional Neural Network, to classify genomic sequences. The tutorial is designed for participants with a basic understanding of biology and programming, and it covers both theoretical and practical aspects.

Contents

• Jupyter Notebook: The notebook for the workshop can be found in the main folder. It contains:
• An introduction to Deep Learning theory.
• Cases of deep learning applications in genomics.
• A step-by-step guide for implementing publicly available HuggingFace models
• A second implementation for manually-developed models
• Images: The images folder contains diagrams and figures used in the notebook.

Execution

The Jupyter Notebook is adapted to be executed in Google Colab, it can be accessed in this link: https://colab.research.google.com/github/judz03/Pytorch-and-HF-for-genomic-sequence-classification/blob/main/sequence_classification_with_deep_learning.ipynb Remeber to configure the runtime type to a T4 GPU instance for accelerated training.