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STAT718/BIO703

Spring 2026

Genomic Data Science: AI & Bioinformatics

Instructor: Yen-Yi Ho

Office: LeConte 216A

Class Meetings:

Monday/Wednesday 14:20-15:35PM

Classroom: LeConte 206

Dr. Ho's office Hours: Thursday afternoon 16:00-17:00PM, Friday 10-11:30AM or by appointment (LeConte 216A)

Email: hoyen@stat.sc.edu

Course Website: https://people.stat.sc.edu/hoyen/STAT718/STAT718.html

Textbook:

1. Introduction to Data Science: Data Wrangling and Visualization with R by Rafael A. Irizarry (Required)

2. Python Data Science Handbook by Jake VanderPlas

available at https://jakevdp.github.io/PythonDataScienceHandbook/

3. Python for Biologists Tutorial. Available at https://www.pythonforbiologists.org/

4. Machine Learning for Biology Tutorial. Available at https://pythonforbiologists.com/

5. Deep Learning by Ian Goodfellow, Yoshua Bengio and Aaron Courville. Available at https://github.com/janishar/mit-deep-learning-book-pdf or https://www.deeplearningbook.org

6. Understanding deep learning by Simon J.D. Prince 2023, the MIT press. Available at https://udlbook.github.io/udlbook/

Recommended

1. Python Crash Course, 3rd Edition: A Hands-On, Project-Based Introduction to Programming by Eric Mattens.

2. Deep Learning by PyTorch: Build, Train, and Tune Neural Networks Using Python Tools by Eli Stevens, Luca Antiga and Thomas Viehmann

Announcements:

Approximate course outline: (Lecture notes will be updated often)

Date	Weekly topic	Homework	Code	Reading
Week 1 Jan 12	Syllabus Lecture 1: Introduction to Genomic Data Getting Started with Jupyter Notebook and JupyterLab R Markdown (Chapter 20.2 in Rafa)	Homework Submission Instruction Homework1 Homework 1 Notebook Homework 1 Solution	Google Colab Coupon Link for Requesting HPC account (Choose Research Computing Account creation)
Week 2 Jan 19	Jan 19: No Class Python Basic 1 Data Types NumPy	Presentation Schedule Paper presented by Macro Paper presented by John Darden Paper presented by Kasra Paper presented by Jianyu Paper1 presented by Grant Paper2 presented by Grant Cellpose paper presented by Xiuchuan CGMega paper presented by Meysam Cox-PASNet paper presented by Elaina Nucleotide Transformer paper presented by Anderson	Python Basic 1 Notebook1 Python Basic 2 Notebook2	Python Data Science Handbook Chap 2 &3
Week 3 Jan 26	Plots in Python Python Functions If and Loops Modules and Packages		Python Basic 3 Notebook3 Python Basic 4 Notebook4	Python Data Science Handbook Chap 4
Week 4 Feb 2	Data Manipulation with Pandas Biopython Tutorial	Homework1Due (Monday Feb 02) Homework2 Homework 2 Notebook Homework 2 Solution Paper about Chopsticks Gene	df3.csv adata1_counts.csv.gz adata2_counts.csv.gz adata1_cell_metadata.csv adata2_cell_metadata.csv gene_metadata.csv Python Basic 5 Notebook5 myseq.fa Biopython Case Studies Biopython Case Studies Notebook	Deep Learning by Prince Chap 1, 2, 3
Week 5 Feb 9	Lecture 7: Machine Learning Part I (KNN) Lecture 8: Machine Learning Part II (Linear Classifier) Lecture 9: Regularization, Optimization and Performance Metric The Good, the Bad and the Ugly	Homework 3 Homework 3 Notebook TCGA Pancancer Expression Data TCGA Pancancer Meta Data	KNN Classifier Notebook Linear Classifier Linear Notebook	Deep Learning by Goodfellow et al. Chap 5 Deep Learning by Prince Chap 4, 5, 6
Week 6 Feb 16	Lecture 10: Neural Networks & Backpropagation Lecture 11: Convolutional Neuron Networks	Homework2Due (Monday Feb 16)	Identifying hand-written digits using PyTorch Notebook	Deep Learning by Goodfellow et al. Chap 6 & 7 Deep Learning by Prince Chap 7, 8, 9
Week 7 Feb 23	Lecture 11: DNA Convolutional Neuron Networks and Applications in Regulatory Genomics: DeepBind DNA methylation: DeepCpG		Genomics_CNN Genomics_CNN.ipynb	Deep Learning by Goodfellow et al. Chap 8 & 9 Deep Learning by Prince Chap 10
Week 8 March 2		Homework3 Due (Monday March 02) Homework 3 solution Notebook		Deep Learning by Goodfellow et al. Chap 10 & 11 Deep Learning by Prince Chap 11
Week 9 March 9	Spring Break: No Classes
Week 10 March 16	Lecture 12: CNN for Gene Coexpression (CNNC) in Single-Cell Data	Homework 4 Homework 4 Notebook Final Project Proposal template		Deep Learning by Goodfellow et al. Chap 14 Deep Learning by Prince Chap 12 & 13
Week 11 March 23	From Language Models to Cell Types: Transformers in Genomic Data Science Lecture 13: Transformer and Attention	Final Project Instruction	HPC tutorial Linux Commands Linux File Transfer	Deep Learning by Prince Chap 14 & 15
Week 12 March 30	Single-Cell Best Practice Book	Homework 4 Due (Monday March 30) Final Project Proposal Due (Monday March 30)	scBERT Slides Transformer Encoder Example Transformer Encoder Notebook	Deep Learning by Prince Chap 16 & 17
Week 13 April 6	Graphical Neural Networks	Final Project Template Final Project Template Notebook	Karate Club Example Karate Club Example Notebook Alphafold simplified example Alphafold simplified example notebook	Deep Learning by Prince Chap 18 & 19
Week 14 April 13	Graphical Neural Networks	Homework 4 Solution Homework 4 Solution Notebook	Convolutional Layer Convolutional Layer Notebook	Deep Learning by Prince Chap 20 & 21
Week 15 April 20	Student Presentation	Final Project Presentation Presentation Rubric
Week 16 April 27	Student Presentation	Final Project Due Monday May 4 before 5PM