Winter 2025
MATH - BIOINF- STAT 547: Mathematics of Data
Instructor: Prof. INDIKA Rajapakse (indikar@umich.edu)
Graduate Student Instructor (GSI): MARC Andrew Choi (machoi@umich.edu)
Location: 2140 SKB (School of Kinesiology Building)
Class Time: Tuesday and Thursday, 2:30 PM - 4:00 PM
Office Hours:
INDIKA Rajapakse - Wednesday and Friday, 3:00 PM - 5:00 PM: https://meet.google.com/dnm-zipr-tsb or in person after class
MARC Choi - Wednesday 2:00-3:00 PM (Zoom) and Thursday 12:00-1:00 PM (East Hall Lower Atrium)
Links
Topics and Timeline (Topics and Timeline subject to change without notice. Please check regularly)
Piazza (Please sign in and add yourself to the course if you have not already)
References of Interest
MATLAB: 1) MATLAB Tutorial 2) Basic Functions Reference
Digital Library: An unofficial digital library I maintain that contains books and papers on topics related to my research and teaching
Great book with codes: Cleve Moler . Numerical computing with MATLAB. Society for Industrial and Applied Mathematics, (2004)
Gilbert Strang's Book
Lars Eldén's Book
Stephen Boyd's book: Introduction to applied linear algebra: vectors, matrices, and least squares
Cover TM. Elements of information theory. John Wiley & Sons; 1999.
Great Blogs! I visit these from time to time, and they have many great articles
Amazing TED Talk: The mathematician who cracked Wall Street | Jim Simons
PROBLEM OF THE DAY (POD)
PROBLEM SETS
This section includes assignments, solutions, and helpful resources.
Problem Set 1: Due Thursday, January 30
Problem Set 2: Due Monday, February 17
Problem Set 3: Due Tuesday, March 11
Problem Set 4: Due Tuesday, April 1
Problem Set 5: Due Tuesday, April 22
FINAL Project: Due April 26 (no extensions!)
Project Proposal Slide: Due Tuesday, March 25
NOTES, SLIDES, AND PAPERS
Date: 01-09-2025
Introduction: Slides
Date: 01-14-2025
"You can always recognize truth by its beauty and simplicity"―Richard P. Feynman
Papers
Lieberman-Aiden, Erez, ..., Groudine Mark, ..., Lander Eric. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293.
Turk, Matthew, and Alex Pentland. "Eigenfaces for recognition." Journal of cognitive neuroscience 3.1 (1991): 71-86. (Classic! just browse)
Martin CD, Porter MA. The extraordinary SVD. The American Mathematical Monthly. 2012 Dec 1;119(10):838-51. (Excellent Review!)
Date: 01-16-2025
"If you don’t believe in yourself why is anyone else going to believe in you?" ― Tom Brady
Eckhart-Young Theorem and Low Rank Approximations
Poincare Diagram: Stability diagram classifying Poincaré maps as stable or unstable according to their features
Image Compression with Low-Rank SVD: Example
My talk yesterday (1/15/2025)
Date: 01-21-2025
Quote of the Day
"Young man, in mathematics you don't understand things. You just get used to them" ― John von Neumann
Guest Lecture: Dr. Cleve Moler
MathWorks Co-Founder and Chief Mathematician Cleve B. Moler
Direct link to YouTube: https://www.youtube.com/watch?v=R9UoFyqJca8
Date: 1-23-2025
Quote of the Day
"Everything is practice" ― Pele
Scree Plots and Optimal Hard Threshold (OHT)
Low Rank Approximations
Additional Reading
Gavish, Matan, and David L. Donoho. "The optimal hard threshold for singular values is 4/sqrt(3)." IEEE Transactions on Information Theory 60.8 (2014): 5040-5053. (Amazing Paper!)
Excellent book chapter (Please read pages 31 - 32)
Donoho, David, Matan Gavish, and Elad Romanov. "ScreeNOT: Exact MSE-optimal singular value thresholding in correlated noise." The Annals of Statistics 51, no. 1 (2023): 122-148.
Udell, Madeleine, and Alex Townsend. "Why are big data matrices approximately low rank?." SIAM Journal on Mathematics of Data Science 1.1 (2019): 144-160.
Thibeault, Vincent, Antoine Allard, and Patrick Desrosiers. "The low-rank hypothesis of complex systems." Nature Physics 20, no. 2 (2024): 294-302.
Date: 1-28-2025
Quote of the Day
"Nature has a great simplicity and therefore a great beauty" ― Richard Feynman
Poincare Diagram: Stability diagram classifying Poincaré maps as stable or unstable according to their features
Dynamic Mode Decomposition (DMD)
Book
Kutz, J. Nathan, et al. Dynamic mode decomposition: data-driven modeling of complex systems. Society for Industrial and Applied Mathematics, 2016.
Chapter 1: Dynamic Mode Decomposition: An Introduction
Additional Reading
Schmid, Peter J. "Dynamic mode decomposition of numerical and experimental data." Journal of fluid mechanics 656 (2010): 5-28.
Schmid, Peter J. "Dynamic mode decomposition and its variants." Annual Review of Fluid Mechanics 54 (2022): 225-254.
Tu, Jonathan H. "Dynamic mode decomposition: Theory and applications." PhD diss., Princeton University, 2013.
Date: 1-30-2025
Quote of the Day
"Be constantly on the lookout for hype"―David Heckerman
Guest Lecture: Causal discovery from data (Dr. David Heckerman from Amazon)
Please visit and like these GitHub:
Date: 2-04-2025
Quote of the Day
"I think one of the things about creativity is not to be afraid of saying the wrong thing " ― Sydney Brenner
Papers
Von Luxburg, Ulrike. "A tutorial on spectral clustering." Statistics and computing 17.4 (2007): 395-416. (Excellent Review!)
Belkin, Mikhail, and Partha Niyogi. "Laplacian eigenmaps and spectral techniques for embedding and clustering." Advances in neural information processing systems. 2002.
Ng, Andrew Y., Michael I. Jordan, and Yair Weiss. "On spectral clustering: Analysis and an algorithm." Advances in neural information processing systems 2 (2002): 849-856.
Eliasof, Moshe, Eldad Haber, and Eran Treister. "Graph neural reaction diffusion models." SIAM Journal on Scientific Computing 46, no. 4 (2024): C399-C420.
Date: 2-06-2025
Quote of the Day
"You have to spend some energy and effort to see the beauty of mathematics" ― Maryam Mirzakhani
Working with Data (PS2: 5 and 6)
Joshua Pickard, Cooper Stansbury, Amit Surana, Anthony Bloch, and Indika Rajapakse. "Biomarker Selection for Adaptive Systems." arXiv preprint arXiv:2405.09809 (2024).
Cooper Stansbury will present a Bioinformatics PhD Defense
Date: 2-11-2025
Quote of the Day
"Imagination will often carry us to worlds that never were. But without it we go nowhere" ― Carl Sagan
Joshua L. Proctor, Philip A. Eckhoff. "Discovering dynamic patterns from infectious disease data using dynamic mode decomposition." International Health, Volume 7, Issue 2, March 2015
OHT revisited: Slides from Matan Gavish
K-Means Clustering
Date: 2-13-2025
Quote of the Day
"I believe in my game, and I believe in me. At the end of the day, I'm my biggest fan" ― Serena Williams
Low rank matrices (Let's do it one more time!)
Papers
Udell, Madeleine, and Alex Townsend. "Why are big data matrices approximately low rank?." SIAM Journal on Mathematics of Data Science 1.1 (2019): 144-160.
Date: 02- 18-2025
"Stay hungry, stay foolish" ― Steve Jobs
Papers
Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha MS, Bloch A, Brockett R, Rajapakse I. "Algorithm for cellular reprogramming." Proceedings of the National Academy of Sciences. 2017 Nov 7;114(45):11832-7. Data-guided Control (DGC) Supporting Information and Slides from Scott Ronquist
Proctor, Joshua L., Steven L. Brunton, and J. Nathan Kutz. "Dynamic mode decomposition with control." SIAM Journal on Applied Dynamical Systems 15, no. 1 (2016): 142-161.
Date: 02- 20-2025
"I don’t think limits” ― Usain Bolt
Date: 02- 25-2025
"The only way to learn mathematics is to do mathematics ” ― Paul Halmos
Linear Dimension Reduction
Date: 02- 27-2025
"Simplicity makes me happy ” ― Alicia Keys
Nonlinear Dimension Reduction
Other Loss functions
Good post that explains some common ones: https://www.geeksforgeeks.org/ml-common-loss-functions/
Papers
UMPAP: McInnes, Leland, John Healy, and James Melville. "Umap: Uniform manifold approximation and projection for dimension reduction." arXiv preprint arXiv:1802.03426 (2018).
t-SNE: Van der Maaten, Laurens, and Geoffrey Hinton. "Visualizing data using t-SNE." Journal of machine learning research 9.11 (2008).
Wang, Y., Huang, H., Rudin, C. and Shaposhnik, Y., 2021. Understanding how dimension reduction tools work: an empirical approach to deciphering t-SNE, UMAP, TriMAP, and PaCMAP for data visualization. The Journal of Machine Learning Research, 22(1), pp.9129-9201.
Remark: This is a really nice review in general, but the most relevant parts are pages 8, 9, and 10
Winter Vacation (March 1 - March 10, 2025): Suggested Reading!
Strogatz S. Sync: The emerging science of spontaneous order.
uring, Alan Mathison. "The chemical basis of morphogenesis." Bulletin of mathematical biology 52.1-2 (1990): 153-197.
Date: 03- 12-2025
"Study hard what interests you the most in the most undisciplined, irreverent and original manner possible ” ― Richard P. Feynman
The Pleasure of Finding Things Out
Nonlinear Dimension Reduction
Papers
Wang, Y., Huang, H., Rudin, C. and Shaposhnik, Y., 2021. Understanding how dimension reduction tools work: an empirical approach to deciphering t-SNE, UMAP, TriMAP, and PaCMAP for data visualization. The Journal of Machine Learning Research, 22(1), pp.9129-9201.
Remark: This is a really nice review in general, but the most relevant parts are pages 8, 9, and 10
Date: 3-13-2025
Quote of the Day
"The true delight is in the finding out rather than in the knowing"―Isaac Asimov
Tensors = Multi-Dimensional Arrays, Graphs represented with adjacency matrix and Hypergraphs represented with adjacency tensor
Tensors and Hypergraphs (Notes)
Tensors (Slides) and Hypergraphs (Slides)
Hypergraphs: STEPHEN WOLFRAM and Wolfram Physics Project Launch
Other Resources: Dr. Charles Van Loan
Papers
Kolda, Tamara G., and Brett W. Bader. "Tensor decompositions and applications." SIAM review 51.3 (2009): 455-500. (Excellent Review!)
Williams, Alex H., et al. "Unsupervised discovery of demixed, low-dimensional neural dynamics across multiple timescales through tensor component analysis." Neuron 98.6 (2018): 1099-1115.
Wolf, Michael M., Alicia M. Klinvex, and Daniel M. Dunlavy. "Advantages to modeling relational data using hypergraphs versus graphs." 2016 IEEE High Performance Extreme Computing Conference (HPEC). IEEE, 2016.
Date: 3-18-2025
Quote of the Day
"The best way to have a good idea is to have a lot of ideas"― Linus Pauling
Links for Programming Demo:
Papers
Pickard J, Can C, Salman R, Stansbury C, Kim S, Surana A, Rajapakse I. “HAT: Hypergraph Analysis Toolbox,” PLOS Computational Biology, 2023
Date: 3-27-2025
"No great discovery was ever made without a bold guess" ― Isaac Newton
Tensors and Hypergraphs (Notes)
Slides: Hypergraph Similarity
Papers
Donnat, Claire, and Susan Holmes. "Tracking network dynamics: A survey using graph distances." The Annals of Applied Statistics 12.2 (2018): 971-1012.
Surana A, Chen C, Rajapakse I. "Hypergraph Similarity Measures." IEEE Transactions on Network Science and Engineering, 2022
Date: 4-01-2025
Quote of the Day
"The only way to do great work is to love what you do" ― Steve Jobs
1. Topological Data Analysis 2. The Shape of Data:Nice introduction by Gunnar Carlsson
Chapter 2: Charles Pugh. Real mathematical analysis. (Excellent Exposition!)
Introduction: These slides deck includes slides from my good friend Yuan Yao
Papers
Carlsson G. Topological methods for data modelling. Nature Reviews Physics 2, no. 12 (2020): 697-708.
Wasserman L. Topological data analysis. Annual Review of Statistics and Its Application. 2018 Mar 7;5:501-32.
Lum PY, Singh G, Lehman A, Ishkanov T, Vejdemo-Johansson M, Alagappan M, Carlsson J, Carlsson G. Extracting insights from the shape of complex data using topology. Scientific reports. 2013 Feb 7;3(1):1-8.
Date: 4-03-2025
Quote of the Day
"The more we know, the more we realize there is to know" ― Jennifer Doudna
Introduction: These slides deck includes slides from my good friend Yuan Yao
Convex Optimization Tools: CVX
Remark: Condition Number and Hierarchical Clustering
Papers
Koren Y, Bell R, Volinsky C. Matrix factorization techniques for recommender systems. Computer. 2009 Aug 7;42(8):30-7.
Van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ, Burdziak C, Moon KR, Chaffer CL, Pattabiraman D, Bierie B. Recovering gene interactions from single-cell data using data diffusion. Cell. 2018 Jul 26;174(3):716-29. MAGIC
Davis, George J., and Cleve B. Moler. Sensitivity of matrix eigenvalues. International Journal for Numerical Methods in Engineering 12, no. 9 (1978): 1367-1373. Blog post
GENERAL READING
I will add to this list throughout the semester
Rajapakse, Indika. "Conversation with Dr. Steve Smale and Dr. Lee Hartwell." NOTICES OF THE AMERICAN MATHEMATICAL SOCIETY 68, no. 9.
Aksoy SG, Hagberg A, Joslyn CA, Kay B, Purvine E, Young SJ. Models and Methods for Sparse (Hyper) Network Science in Business, Industry, and Government. NOTICES OF THE AMERICAN MATHEMATICAL SOCIETY.;69(2).
Vaswani, Ashish, et al. "Attention is all you need." Advances in neural information processing systems 30 (2017).
Kolda T. Mathematics: The Tao of Data Science. (2020).
Turing, Alan Mathison. "The chemical basis of morphogenesis." Bulletin of mathematical biology 52.1-2 (1990): 153-197.