Deep Learning in Genomics Course Material

This page contains material for the GENE46100 Deep learning in genomics course.
Find the 2025 syllabus here.
Edit github source here

See all notes here

Preprocessing and clustering

The data used in this basic preprocessing and clustering tutorial was collected from bone marrow mononuclear cells of healthy human donors and was part of openproblem’s…

Unit 04 Single Cell Genomics

© HakyImLab and Listed Authors - CC BY 4.0 License

Seurat - Guided Clustering Tutorial

gene46100

tutorial

For this tutorial, we will be analyzing the a dataset of Peripheral Blood Mononuclear Cells (PBMC) freely available from 10X Genomics. There are 2,700 single cells that were…

Borzoi prediction from personal genome - qmd version

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notebook

Using Borzoi for predicting on a personal genome, derived from VCF

Predicting alternative polyadenylation with Borzoi

notebook

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Borzoi is a deep learning model that, similarily to Enformer:

homework 6

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homework

If you run the analysis locally, make sure you clone the gene46100 conda environment and install the python packages as needed. See this jupyter notebook for an example.…

Enformer Architecture

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Enformer is a deep learning model designed for predicting gene expression and other functional genomics signals directly from DNA sequence. It was introduced by DeepMind and…

unit 03

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Slides for Unit 3 - Enformer, Borzoi, and PrediXcan link

Enformer usage neanderthal - qmd version

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notebook

predict neanderthal epigenome with enformer

Enformer training

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notebook

train enformer on human and mouse

Enformer usage neanderthal - jupyter notebook version

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notebook

predict neanderthal epigenome with enformer

homework 5

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homework

© HakyImLab and Listed Authors - CC BY 4.0 License

Genomic language model training with nanoGPT - qmd version

notebook

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Henry’s genomic language model trained on human reference genome with nanogpt

homework 4

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homework

Watch Karpathy’s nanoGPT tutorial on youtube link and answer the questions in the form

Building a GPT - companion notebook annotated

Companion notebook from Karpathys video on building a minimal GPT, annotated by cursors LLM with summary from gemini.

Andrey Karpathy

Building a GPT - companion notebook backup

Andrey Karpathy

homework 3

gene46100

homework

© HakyImLab and Listed Authors - CC BY 4.0 License

Calibrating hyperparameters with weights and biases

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project

notebook

Weights and biases is a platform used for AI developers to track, visualize and manage their ML models and experiments. The coolest part is that W&B allows you to log…

TF binding prediction challenge

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project

Competition details for TF binding prediction challenge

homework 2

gene46100

homework

© HakyImLab and Listed Authors - CC BY 4.0 License

Updated - DNA score prediction with Pytorch

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notebook

created by Erin Wilson. Downloaded from here.

TF Binding prediction project

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project

notebook

The goal of this project is to create a neural network model that predicts TF binding strength in a DNA sequence.

homework 1

gene46100

homework

© HakyImLab and Listed Authors - CC BY 4.0 License

DO NOT USE FOR REPURPOSING - DNA score prediction with Pytorch

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notebook

Quick introduction to deep learning

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notebook

Understand and implement gradient descent to fit a linear model

Boxiang Liu, modified by Haky Im

preparing environment for unit 00

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how-to

setting up conda environement and installing packages

Building a GPT From Scratch summary

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slides

gpt

Karpathy’s gpt_dev.ipynb summarized by gemini, reviewed by me.

Borzoi prediction from personal genome - jupyter notebook

gene46100

notebook

Using Borzoi for predicting on a personal genome, derived from VCF

© HakyImLab and Listed Authors - CC BY 4.0 License