Data Analysis with TDA Mapper
Spring 2017 Section 0001: 11:00A - 12:15P TTh 113 MLH
Instructor: Dr. Isabel K. Darcy,
Department of Mathematics and AMCS,
University of Iowa
Office:B1H MLH
Phone: 335- 0778
Email: isabel-darcy AT uiowa.edu
Office hours: Tuesdays/Thursday 8:50 - 9:15am, 12:30 - 1:35pm and by appointment.
TA: Maria GommelTDA 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):
| Tentative Schedule | HW/Announcements | ||
| Week 1 | |||
|---|---|---|---|
| 1/17 | Professor Gunnar Carlsson Introduces Topological Data Analysis, Mapper slides, worksheet |
Icon Quiz 1 (Due 1/19 at 7:00 AM) over
Voronoi (6:06 min)
and
k-means (9:10 min)
HW 1(Due 1/19) --10 points | |
| 1/19 | Meet in B5 MLH: Lab 1 files , slides | ||
| FYI: scikit-learn clustering | |||
| Week 2 | |||
| 1/24 | More TDA mapper |
HW 2 (Due 1/24) -- 5 points : Start writing code to create your own TDA mapper. Note, you only need to outline the algorithm using commenting.
Project HW 1 (Due 1/26) -- 5 points
HW 3 (due Thursday 1/26, 10 points):
Project HW 2 (Due 1/26) -- 10 points
| |
| 1/26 | Meet in B5 MLH: Lab 2 | ||
| FYI: | |||
| Week 3 | |||
| 1/31 | Mapper Examples |
Icon
Quiz 2 (Due 2/2 at 7am) over TDA Mapper videos: Intro, slides Examples, slides Summary, slides
Project HW 3 (Due 2/2) -- 10 points | |
| 2/2 | Mapper applied to cancer data | ||
| Week 4 | |||
| 2/7 |
Project HW 4 (Due 2/7) -- 10 points Slides describing a clustering method or poster introducing the TDA mapper algorithm. | ||
| 2/9 | Mini-presentations on clustering or TDA mapper(50 points) | ||
| Week 5 | |||
| 2/14 | Lab files |
Project HW (Due 2/17) Intro draft including 2, 8, 10 | |
| 2/16 | Github (optional) | ||
| Week 6 | |||
| 2/21 | slides, Ayasdi resources, Patient Stratification, Iris data set, databasics.r, flaresTransformed.r | Icon Quiz 3 (10 points; Due 2/23 at 7:00 AM) over first 20 minutes of Applications of TDA to the Understanding of Disease and Drug Discovery, Pek Lum, Ayasdi | |
| 2/23 | slides, Identification of type 2 diabetes subgroups through topological analysis of patient similarity, Science Translational Medicine, 2015, Precision Medicine Using Topological Data Analysis, | ||
| Week 7 | |||
| 2/28 | slides, |
Project HW 5 (Due 2/28) -- 10 points: Analyze dataset as described here Icon Quiz 4 (10 points; Due 2/28 at 7:00 AM) over first 40 minutes of Applications of TDA to the Understanding of Disease and Drug Discovery, Pek Lum, Ayasdi Icon Quiz 5 (10 points; Due 3/2 at 7:00 AM) over Applications of TDA to the Understanding of Disease and Drug Discovery, Pek Lum, Ayasdi Icon Quiz 6 Review (50 points; Due 3/2 at 7:00 AM)
Project HW 6 (Due 3/4) -- 20 points:
| |
| 3/2 | slides | ||
| Week 8 | |||
| 3/7 | Midterm (100 points) | Project HW (Due Sunday 3/5) Intro draft including 2, 3 8, 10. Focus on description of TDA mapper algorithm. | |
| 3/9 | slides | ||
| Week 9 | |||
| 3/21 | Exploring data with topological tools, Marinka Zitnik, XRDS: Crossroads, The ACM Magazine for Students, 2014, slides |
Icon Quiz 7 Reading (10 points; Due 3/21 at 7:00 AM) Icon Quiz 8 Reading (10 points; Due 3/23 at 7:00 AM) | |
| 3/23 | A Topological Data Analysis Approach to Visualizing Ebola Tweets, Herchel Thaddeus Machacon, 2016, slides | ||
| Week 10 | |||
| 3/28 | KS statistics, ks.r | Project HW (Due Monday, 3/27) Polished draft including 2, 3 4, 7 - 10.
| |
| 3/30 | LAB: meet in B5 MLH (basement computer lab) | ||
| Week 11 | |||
| 4/4 | slides Topological Methods for the Analysis of High Dimensional Data Sets and 3D Object Recognition. G. Singh, F. Memoli and G. Carlsson. Symposium on Point Based Graphics 2007, Prague, September 2007 |
Project HW (due 4/5) Draft of your project which should be at least 50% done. Icon Quiz 9 Reading (10 points; Due 4/6 at 7:00 AM)
| |
| 4/6 | Simplicial complex and Topology | ||
| Week 12 | |||
| 4/11 | Multi-resolution/multi-scale |
Icon Quiz 10 Reading (10 points; Due 4/11 at 7:00 AM) Icon Quiz 11 Reading (10 points; Due 4/13 at 7:00 AM)
| |
| 4/13 | Mini-presentations | ||
| Week 13 | |||
| 4/18 | Clustering and Multi-dimensional Mapper | Project HW (due 4/17) Draft of your project which should be at least 80% done. Icon Quiz 12 Reading (10 points; Due 4/20 at 7:00 AM)
| |
| 4/20 | Mapper on 3D Shape Database | ||
| Week 14 | |||
| 4/25 | meet in computer lab B5 MLH |
Finished Project due 4/26 Project slides due 4/30 | |
| 4/27 | Guest Lecturer Wako Bungulo: Grad School/Mapper PCA , Euler characteristic | ||
| Week 15 | |||
| 5/2 | Student presentations (200 pts) Big Data |
HW 9 (due 5/2)
Summarize May 2th presentations (0 points) HW 10 (due 5/4) Summarize May 4th presentations(0 points) Project HW (due 5/4) Outside presentations, etc (300 pts) |
|
| 5/4 |
Student presentations (200 pts) Cleaning Data | ||
Topology
and data, G Carlsson (2009) (Mapper: p. 281 - 289)
Topological methods for exploring
low-density
states in biomolecular folding pathways (2009)
Nov 22
video,
pptx,
pdf
An eQTL biological data visualization challenge and approaches
from the
visualization community (2011)
Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival M. Nicolau, A. J. Levine, G. Carlsson (2011) video, pptx, pdf
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
DNA
MICROARRAY VIRTUAL LAB,
youtube
video
How to Analyze DNA Microarray Data,
Howard Hughes Medical Institute
Pearson
Product-Moment Correlation
Nov 20
video,
pptx,
pdf
Intro to RNA & Topological Landscapes for Visualization of Scalar-Valued Functions.
Generating and exploring a collection of topological landscapes
for visualization of scalar-valued functions.
by W. Harvey and Y. Wang, Comput. Graphics Forum (Special issue from EuroVis) 2010
Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils (Sept 2014)
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