Foundations of Data Analysis
Instructor : Jeff Phillips (email) | Office hours: Thursdays 9-10am (MEB 3404, Zoom) and directly after each class
TAs: Meysam Alishahi (meysam.alishahi@gmail.com) | Office hours: Fridays 10am-noon (WEB 2426)
         Anna Bell (abell.datascience@gmail.com) | Office hours: Tuesdays 12:30pm-2:30pm (WEB 2426)
         Peter Jacobs (u1266560@utah.edu) | Office hours: Mondays 8:30am - 10:30am (WEB 2426)
         Xinyuan Yan (u1320974@utah.edu) | Office hours: Mondays 11am-1pm (WEB 2426)
         Ananya Smirti (u1419404@umail.utah.edu) | Office hours: Wednesdays 4-6pm (WEB 2426)

Fall 2022 | Tuesday, Thursday 10:45 am - 12:05 pm
WEB L104 ( Zoom / YouTube )
Catalog number: CS/DS 3190 01
and meets with COMP 5960 01 (meant for non-SoC graduate and non-matriculated students)
Google Calendar of all lectures & office hours


Syllabus
Description:
This class will be an introduction to computational data analysis, focusing on the mathematical foundations, but providing some basic experience in analysis techniques. The goal will be to carefully develop and explore several core topics that form the backbone of modern data analysis topics, including Machine Learning, Data Mining, Artificial Intelligence, and Visualization. This will include some background in probability and linear algebra, and then various topics including Bayes Rule and its connection to inference, linear regression and its polynomial and high dimensional extensions, principal component analysis and dimensionality reduction, as well as classification and clustering. We will also focus on modern PAC (probably approximately correct) and cross-validation models for algorithm evaluation.
Some of these topics are often very breifly covered at the end of a probability or linear algebra class, and then are often assumed knowledge in advanced data mining or machine learning classes. This class fills that gap. The planned pace will be closer to CS3130 or Math2270 than the 5000-level advanced data analysis courses.

We will use Python in the class to demonstrate and explore basic concepts. But programming will not be the main focus.
Former TA Hasan Poormahmood created a short python tutorial on loading, manipulating, processing, and plotting data in python in colab. Here is the python notebook so you can follow along.

Book: Mathematical Foundations of Data Analysis (v1.0)
A free version (v0.6) is free and available online as pdf. The formatting and page numbering is updated, and the writing is improved in spots in the v1.0. Some content is also added in v1.0, but it does not affect the part covered in this course.
More outside online resources are listed below.

Videos: Lecture will be given in person, and live streamed on Zoom/ YouTube. Soonafter videos will automatically appear on the YouTube playlist

Prerequisits:
The official pre-requisites are CS 2100, CS 2420, and Math 2270. These are to ensure a certain very basic mathematical maturity (CS 2100) a basic understanding of how to store and manipulate data with some efficiency (CS2420), and basics of linear algebra and high dimensions (MATH 2270).
We have as a co-requisite CS 3130 (or Math 3070) to ensure some familiarity with probability.
A few lectures will be devoted to review linear algebra and probability, but at a fast pace and a focus on the data interpretation of these domains. I understand students now obtain background in data analysis in a variety of different ways, contact instructor if you think you may manage without these pre-requisites.
This course is a pre-requisite for CS 5350 (Machine Learning) and CS 5140 (Data Mining), and is required course for the BS in Data Science.
The COMP 5960 course meant for non-SoC graduate students, and non-matriculated students, does not have pre-requisites.

Schedule:
Date Chapter Video Topic Assignment
Tue 8.23 YT Class Overview
Thu 8.25 Ch 1 - 1.2 YT Probability Review : Sample Space, Random Variables, Independence
Quiz 0
Tue 8.30 Ch 1.3 - 1.6 YT Probability Review : PDFs, CDFs, Expectation, Variance, Joint and Marginal Distributions(colab) HW1 out
Thu 9.01 Ch 1.7 YT Bayes' Rule: MLEs and Log-likelihoods
Tue 9.06 Ch 1.8 YT Bayes Rule : Bayesian Reasoning
Thu 9.08 Ch 2.1 - 2.2 YT Convergence : Central Limit Theorem and Estimation (colab)
Quiz 1
Tue 9.13 Ch 2.3 YT Convergence : PAC Algorithms and Concentration of Measure HW 1 due
Thu 9.15 Ch 3.1 - 3.2 YT Linear Algebra Review : Vectors, Matrices, Multiplication and Scaling HW 2 out
Tue 9.20 Ch 3.3 - 3.5 YT Linear Algebra Review : Norms, Linear Independence, Rank and numpy (colab)
Thu 9.22 Ch 3.6 - 3.8 YT Linear Algebra Review : Inverse, Orthogonality
Quiz 2
Tue 9.27 Ch 5.1 YT Linear Regression : explanatory & dependent variables (colab) HW 2 due
Thu 9.29 Ch 5.2-5.3 YT Linear Regression : multiple regression (colab), polynomial regression (colab)
Tue 10.04 Ch 5.4 YT Linear Regression : overfitting and cross-validation (colab) HW 3 out
Thu 10.06 Ch 5 YT Linear Regression : mini review + slack (colab)
Quiz 3
Tue 10.11
FALL BREAK
Thu 10.13
FALL BREAK
Tue 10.18 Ch 6.1 - 6.2 YT Gradient Descent : functions, minimum, maximum, convexity & gradients
Thu 10.20 Ch 6.3 YT Gradient Descent : algorithmic & convergence (colab)
Tue 10.25 Ch 6.4 YT Gradient Descent : fitting models to data and stochastic gradient descent HW 3 due
Thu 10.27 Ch 7.1 - 7.2 YT Dimensionality Reduction : project onto a basis
Quiz 4
Tue 11.01 Ch 7.2 - 7.3 YT Dimensionality Reduction : SVD and rank-k approximation (colab) HW 4 out
Thu 11.03 Ch 7.4 YT Dimensionality Reduction : eigndecomposition and power method (colab)
Tue 11.08 Ch 7.5 - 7.6 YT Dimensionality Reduction : PCA, centering (colab), and MDS (colab)
Thu 11.10 Ch 8.1 YT Clustering : Voronoi Diagrams + Assignment-based Clustering
Quiz 5
Tue 11.15 Ch 8.3 YT Clustering : k-means (colab) HW 4 due
Thu 11.17 Ch 8.4, 8.7 YT Clustering : EM, Mixture of Gaussians, Mean-Shift
Tue 11.22 Ch 9.1 YT Classification : Linear prediction HW 5 out
Thu 11.24
THANKSGIVING
Tue 11.29 Ch 9.2 YT Classification : Perceptron Algorithm
Thu 12.01 Ch 9.3 YT Classification : Kernels and SVMs
Quiz 6
Tue 12.06 Ch 9.4 - 9.5 YT Classification : Neural Nets, Decision Trees, etc
Thu 12.08 YT Semester Review
Fri 12.09 HW 5 due
Mon 12.12
FINAL EXAM overlaps with (10:30am - 12:30pm)
 (practice)


Class Organization: The class will be run through this webpage and Canvas. The schedule, notes, and links will be maintained here. All homeworks will be turned in through Canvas.


Grading: There will be one final exam with 20% of the grade. Homeworks will be worth 60% of the grade. There will be 5 homeworks and the lowest one can be dropped. Quizzes will be worth 20% of the grade. There will be 6 or 7 (the first, Quiz 0, is worth fewer points).

The homeworks will usually consist of an analytical problems set, and sometimes light programming exercizes in python. When python will be used, we typically will work through examples in class first.


Late Policy: To get full credit for an assignment, it must be turned in through Canvas by the end of the day it is due, specifically 11:50 pm. Once the 11:50pm deadline is missed, those turned in late will lose 10%. Every subsequent 24 hours until it is turned another 10% is deducted. That is, a homework 30 hours late worth 10 points will have lost 2 points. Once the graded assignment is returned, or 48 hours has passed, any assignment not yet turned in will be given a 0.


Academic Conduct Policy: The Utah School of Computing has an academic misconduct policy, which requires all registered students to sign an Acknowledgement Form. This form must be signed and turned into the department office before any homeworks are graded.

This class has the following collaboration policy:
For assignments, students may discuss answers with anyone, including problem approach, proofs, and code. But all students must write their own code, proofs, and write-ups. If you collaborated with another student on homeworks to the extent that you expect your answers may start to look similar, you must explain the extent to which you collaborated explicitly on the homework. Students whose homeworks appear too similar, and did not explain the collaboration will get a 0 on that assignment.

More Resources:
I hope the book provide all information required to understand the material for the class .. and for a solid footing beyond. However, it is sometimes useful to also explore other sources. Wikipedia is often a good source on many of these topics. In the past students have also enjoyed 3 Blue 1 Brown.

Here are a few other books that cover some of the material, but at a more advanced level:
Understanding ML | Foundations of Data Science | Introduction to Statistical Learning

Here is a list nice resources I believe may be useful with relevant parts at roughly the right level for this course, but often with disparate notation:
  • Probability: ProbStat course | P1 | P2
  • Bayes Rule/Reasoning: B1 | B2 | B3 | B4
  • Linear Algebra: No-BS Book | LA1 | LA2 | LA3
  • Linear Regression: LR1 | LR2
  • Gradient Descent: GD1 | GD2
  • PCA: PCA1 | PCA2 | PCA3 | PCA4
  • Clustering: C1 | C2 | C3 | C4
  • Classification: L1 | L2 | L3