TDA Mapper

Data Visualization with TDA Mapper
Spring 2018

Instructor: Dr. Isabel K. Darcy, Department of Mathematics, AMCS, and Informatics, University of Iowa
Office: B1H MLH
Phone: 335-0778
Email: isabel-darcy AT uiowa.edu
Office hours: Tuesdays 8:50 - 9:15am and 12:30 - 2:00pm+, Thursday 8:50 - 9:15am, 12:30 - 12:40pm+and by appointment (Note + means I will normally be available for longer).

TA: Wako Bungula
Office: 325L MLH
Office hours: Tuesdays/Thursday 9:30 - 11:00am and by appointment.
Email: wako-bungula@uiowa.edu

Math 3900 syllabus including grading scheme

TDA Mapper was developed by Gurjeet Singh, Facundo Memoli and Gunnar Carlsson. The company Ayasdi is based on the Mapper algorithm. Both python versions and R versions are freely available. The algorithm is very simple (bin data into overlapping bins, cluster each bin, create a graph where vertices = clusters and two clusters are connected by an edge if they have points in common).

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

During the first 8 weeks we will introduce the TDA mapper algorithm including all needed background (e.g, clustering, PCA, some graph theory, etc.). On most Thursdays we will meet in the B5 MLH computer lab to run software related to the previous Tuesday's lecture. Explicit directions will be provided. The TA and I will be available to provide assistance. Labs can be incorporated into your project. In weeks 9 - 12, we will compare TDA mapper to other data analysis/visualization software. The remaining weeks will include lectures, mentoring talks and group presentations.

Click here for information regarding all assignments including ICON quizzes, HW, presentations, and project.

Week 1
Tentative Schedule		HW/Announcements
1/16	Professor Gunnar Carlsson Introduces Topological Data Analysis, Mapper slides	Icon Quiz 1 (Due 1/18 at 7am) over TDA Mapper videos: Intro, slides Examples, slides Summary, slides HW 1 (Due 1/18) --2 points Add your info (picture, name, interests) to our course wiki class list for Math 3900 or course wiki class list for Math 7450 HW 2 (Due 1/18) --5 points Complete worksheet
1/18	Meet in B5 MLH: Lab 1 files , Goals Start a draft of a poster introducing the TDA mapper algorithm.
Extracting insights from the shape of complex data using topology P. Y. Lum, G. Singh, A. Lehman, T. Ishkanov, M. Vejdemo-Johansson, M. Alagappan, J. Carlsson, G. Carlsson (2013) video, pptx, pdf Exploring data with topological tools, Marinka Zitnik, XRDS: Crossroads, The ACM Magazine for Students, 2014 FYI: Topological Methods for the Analysis of High Dimensional Data Sets and 3D Object Recognition G. Singh , F. Memoli, G. Carlsson (2007) http://yann.lecun.com/exdb/mnist/ Using the MNIST Dataset
Week 2
1/23	R/Rstudio, More TDA mapper: Filter functions I, Clustering I	HW 3 (Due 1/23) -- 5 points : Draft of a poster introducing the TDA mapper algorithm. (note poster can be printed on normal letter size paper -- make sure you use a readable font size) HW 4 (due Thursday 1/25, 10 points): Do a few Swirl submodules (1 point each for up to 10 submodules of any combination of Swirl courses).
1/25	Meet in B5 MLH: Lab 2 goals , Lab 2 files
FYI: scikit-learn clustering
Week 3
1/30	Filter functions II , Clustering II	HW 5 (Due 2/5) -- 5 points : Poster introducing the TDA mapper algorithm (note poster can be printed on normal letter size paper -- make sure you use a readable font size).
2/1	Meet in B5 MLH: Lab 3
Week 4
2/6	Jupyter, Simplicial complexes, etc. , Distances	Icon Quiz 2 Review (10 points; Due 2/6 at 7:00 AM) Project (Due 2/6) Intro draft including 2, 3, 7-10
2/8	Meet in B5 MLH: Lab 4 , Jupyter lab files
Week 5
2/13	coloring, KS statistics	Project (Due 2/13) Intro draft including 2, 3, 7-10
2/15	Meet in B5 MLH: Lab 5 files , goals	Project (Due 2/13) Intro draft including 2, 3, 7-10
Week 6
2/20	KS statistics, Distances, Talk advice, Github	Project (Due 2/22) Writing fellow version
2/22	Meet in B5 MLH	Project (Due 2/22) Writing fellow version
Week 7
2/27	More TDA mapper examples	Mini-presentation slides first draft due Monday 2/26 at 10am (10 - 20 points) Mini-presentation slides final draft due Wednesday 2/28 at 10am (10 - 0 points) HW 6 (Due 3/6) -- 10 points : Practice exam
3/1	Mini-presentations
Week 8
3/6	Review , (with notes)	Icon Quiz 3 Review (25 points; Due 3/5) Project (due 3/9) Revision of 2/22 version based on writing fellow comments -- extension may be requested depending on suggested revisions.
3/8	Midterm (50 points)
***Spring Break March 12 - 19**
Week 9
3/20	Clustering	Icon Quiz 4 (Due Thursday 3/22 at 7:00 AM) over Voronoi (6:06 min) and k-means (9:10 min)
3/22	LAB meet in B5 MLH (basement computer lab) , goals
Week 10
3/27	Clustering; PCA	Project (Due Tuesday, 3/27) Polished draft including 2, 3 4, 7 - 10.
3/29	Lab Files : meet in B5 MLH (basement computer lab)
Week 11
4/3	PCA; MDS	Project (due 4/3) Draft of your project which should be at least 80% done.
4/5	LAB meet in B5 MLH (basement computer lab) , goals
Week 12
4/10	MDS; other methods	Icon Quiz 5 Review (9 points; Due 4/10 at 7:00 AM) Polished Project (due 4/12): Do not include unfinished sections.
4/12	Meet in B5 MLH: Lab files ,
Week 13
4/17	other methods; ethics	Project (due 4/17) Final project including unfinished sections. Final presentation slides first draft (due 4/19) -- 15 pts,
4/19	Industry Guest Lecturer
Week 14
4/24	Guest Lecturer Wako Bungulo: Grad School/Mapper	Icon Quiz 6 Review (9 points; Due 4/24) Final presentation slides 2nd draft (due 4/26, print 6 slides/page and bring to class) -- 15 pts Finished Project due 4/28.
4/26	Ethics/Data Privacy
Week 15
5/1	Student presentations	Final presentation slides final version (due 4/30 noon) -- 10 pts
5/3	Student presentations