MATH:5760:0AAA Mathematical Biology II
Spring 2026
Time: 12:30P - 1:45P TTh    Location: S118 LC

Instructor:  Dr. Isabel K. Darcy
Department of Mathematics and AMCS
University of Iowa
Office: MLH 25J
Phone: 319-335- 0770
Email: isabel-darcy AT uiowa.edu

Ways to get help:

Your grade will be based on

Grading will be based on a point system, so if you have earned enough points for your desired grade, you do not need to take the final exam. Your main focus in this class is to create a project/portfolio so that it is an excellent resource for you to review techniques in future years.

TENTATIVE CLASS SCHEDULE-ALL DATES SUBJECT TO CHANGE (click on date/section for file of corresponding class material):

Tentative ScheduleHW/Announcements -- replace with references
Week 1
1/20 Introduction to data analysis HW: Create github account
1/22 LAB 1: Introduction to Github 1,
Introduction to Python,
Week 2
1/27 Intro to ML ,     Linear Regression HW:
1/29 LAB 2: Introduction to Github 2;
Python: creating artificial data OR downloading real data, linear regression on unclean data
Week 3
2/3 Data cleaning,    
Linear Regression, p-values
HW: due Friday 2/6
Lab 1
2/5 LAB 3: Introduction to Github 3, intro to cleaning data, linear regression on partially cleaned data
Week 4
2/10 Noise Data cleaning, PCA,   
p-values, data cleaning Linear Regression, Variance
HW: due Friday 2/13
Lab 2,   Create personal webpage on Github
2/12 Lab 4: Introduction to Git, Intro to PCA, Linear regression
Week 5
2/17 Logistic Regression HW: due Friday 2/20
Lab 3,    Project draft 1,    poster idea
2/19 Lab 5:
Week 6
2/24 Logistic Regression part 2 HW: due Friday 2/27
Lab 4,    poster draft
2/26 Lab 6:
Week 7
3/3 Presentations: Illustrate something you have learned.
Variance, PCA
HW: due Friday 3/6
Lab 5,    Project draft 2   
3/5 Review,    Lab 7:
Week 8
3/10 Midterm Exam HW: due Friday 3/13
Lab 6
3/12 Lab 8:
***** Spring Break March 15 - 22 ****
Week 9
3/23 Test/Train, Data Leakage, Bias/Variance, Shrinkage HW: due Friday 3/26
Lab 7,    Idea for poster,    python script
3/25 Shrinkage Lab 9:
Week 10
3/31 k-nearest neighbors, HW: due Friday 4/3
Lab 8,    Poster draft,    Project draft 3   
Voronoi (6:06 min) and k-means (9:10 min)
4/2 Lab 10:
Week 11
4/7 k-means clustering,    Hierarchical Clustering,    HW: due Friday 4/10
Lab 9,   
4/9 Clustering
Lab 11:
Week 12
4/14 Presentations: Use artificial or real data to illustrate something.
neural networks and deep learning
HW: due Friday 4/17
Lab 10,    Project draft 4   
4/16 neural networks and deep learning
Lab 12:
Week 13
4/21 neural networks and deep learning HW: due Friday 4/24
Lab 11,    Poster draft 1 due Friday 4/19
4/23 neural networks and deep learning
Lab 13
Week 14
4/28 Ethics, reproducible research, publication bias, data privacy HW: due Friday 5/1
Lab 12,    Project draft 5,    Poster draft 2 due Friday 4/26
4/30 Lab wrap-up
Week 15
5/5 Presentations HW: due Friday 5/8
Lab 13,    Poster draft 3 and written project
5/7 Presentations, Review
Final's week
TBA Final exam: TBA

References:

An Introduction to Statistical Learning with applications in Python, http://www.statlearning.com
Scikit-learn Machine Learning in Python, available at https://scikit-learn.org
StatQuest: eg: https://statquest.org/video-index/, https://statquest.org/neural-networks-part-1-inside-the-black-box/