There is a mountain of publicly available resources teaching deep learning. While they are helpful for learning specific topics, tutorials on how to implement a type of neural network are only useful if you know which model is the right one for your problem.

To fill the gap my labmate Alex Lee and I are giving a workshop to explain the connections between biological problems and deep learning solutions. Our goal is to give high level overviews of various ideas in deep learning and their practical applications to empower you to learn the details of applicable models on your own.

Our workshop will contain lectures on concepts in deep learning and demonstrations of their application in biology. If you’re interested, you can sign up here to receive a link to the workshop. After the workshop is done you will receive links to the lecture slides and demo materials. If you want more information, descriptions of the workshop sessions are below.


The workshop will take place on October 29 from 11 am to 2pm EDT.


What is Deep Learning
A brief introduction to the overarching ideas in deep learning, the basic parts of a deep learning system, and rules of thumb for when to use deep learning methods.

Basic Neural Network Demo
A demonstration of how to implement and train a basic deep learning model in PyTorch.

Convolutional Neural Networks
A presentation of the potential applications of convolutional neural networks, the assumptions they make about the input data, and problems in biology where they can be useful.

DeepSEA Demo
A demonstration of convolutional neural networks outside of image data. This demo shows that CNNs can be used to predict noncoding variants’ effects and how to use preexisting models from Kipoi.

Dimensionality Reduction Methods
An introduction on what dimensionality reduction methods are and why they are useful, a walk through the conceptual idea behind some well known compression methods including PCA and VAEs, and examples of how people have used these methods in biology.

Recurrent Neural Networks
A presentation about the motivation for using recurrent neural networks and related models, the ideas behind how these methods work, and some examples of their use in biology.


If you would like to receive a link to the workshop and the lecture materials, sign up here! If you’re reading this post after October 29, there will be links below.

The workshop is complete! You can find a recording of the workshop here.

The workshop materials, including the presentation slides and demo notebooks can be found here.