TDA Mapper Project

## ICON quizzes (63 points)

Icon Quiz 1 (9 points, Due 1/18 at 7am) over TDA Mapper videos:
Intro (slides): A partial repeat of Sept 16th lecture.
Examples (slides): Answers to worksheet examples. Please try worksheet before viewing this video.
Summary (slides): Summarizes some of the many choices (parameters) that must be made.

Icon Quiz 2 Review (5 points; Due 2/6 at 7:00 AM)

Icon Quiz 3 Review (25 points; Due 3/5)

Icon Quiz 4 (4 points; Due Thursday 3/22 at 7:00 AM) over Voronoi (6:06 min) and k-means (9:10 min)

Icon Quiz 5 Review (10 points; Due 4/10 at 7:00 AM)

Icon Quiz 6 Review (10 points; Due 4/24)

## Homework (37 pts)

HW 1 (Due 1/18) --2 points
Add your info (picture, name, interests) to our course wiki class list

HW 2 (Due 1/18) --5 points
Complete worksheet. Note answers are provided in one of the ICON quiz 1 videos. Please try worksheet before viewing Examples video.

HW 3 (Due 11am 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)
For this assignment, I just want you to demonstrate that you understand the TDA mapper algorithm. Thus, as long as you describe the TDA mapper algorithm in terms that another undergraduate (who has NOT taken this course) would understand, you will earn full credit (even if your poster is really ugly -- you can make it look nice for HW 5). Pictures can help illustrate your point. You can hand draw them for this draft or use the TDA mapper software.

Please turn in a paper copy using normal letter size paper at the beginning of class on 1/23. If you have difficulty printing it, you can also e-mail it.

HW 4 (due 11am Thursday 1/25, 10 points):
Do a few Swirl submodules (1 point each for up to 10 submodules of any combination of Swirl courses). Note you only need to do 10 submodules, not 10 courses -- for example "Looking at Data" is a submodule of course R programming.

You can do all 10 submodules from the same course or sample a few courses. Some nice elementary courses include R programming, Exploratory Data Analysis, and Getting and Cleaning Data.

To get credit for a submodule, on ICON just list the Course name/submodule for each of the submodules that you complete. For example if you finished "Looking at Data" from the course R programming, then your list should include:
R programming/Looking at Data

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).

HW 6 (Due 3/6, beginning of class) -- 10 points : Practice exam (ignore crossed out problems).

## Presentations (150 pts total)

Week 7 Mini-presentations: Choose a topic from Ayasdi resources or other resource related to TDA mapper. You may present individually or in a group. (slides 20 pts, talk 10 pts)

Final Presentation

Slides (40 pts total):
first draft (due 4/19) -- 15 pts,
2nd draft (due 4/26, print 6 slides/page and bring to class) -- 15 pts
final version (due 4/30 noon) -- 10 pts,
Talk (30 pts, given during week 15 or earlier)

Outside Presentation: 50 pts

Researchers present their work at conferences. You should too. Find one that interests you and submit an abstract for either a talk or a poster. Travel funds may be available to cover your travel costs. You may present your work at a research conference, an undergraduate research conference, seminar, record a video podcast etc., either off-campus or on.

Note: the number of points earned on the outside presentation will depend on quality, time required, etc. For example, you may give one 50 point talk at a conference (this includes conferences aimed at undergraduates) including providing a 1 page summary of the conference. Alternatively, you could give 2 shorter/simpler (lower quality?) talks/posters (for example a 10 minute talk in mathbio seminar at UI).

You can also earn points by summarizing a talk/paper, etc.

Some conference at (or related to) UI (note dates are from last year and will be updated):

One can also give a seminar at UI or a public talk.

Computational Psychiatry Symposium, April 12

Some conferences outside of UI:
Funding to travel to conferences is often available by applying to the conference organizers. UI also has funds available:

## Project (250 pts total)

You will turn in your project for both points and feedback multiple times during the semester. The following is the suggested timeline for obtaining feedback and earning points.

25 pts: Project (due 2/13) Draft including 2, 3, 7 - 10

Project (due 2/22): Do not include unfinished sections. Note this version will be reviewed by your writing center fellow. You will revise this version based on comments from your writing center fellow and resubmit, preferably by 3/9.

50 pts: Project (due 3/9) Revision of 2/22 version based on writing fellow comments -- extension may be requested depending on suggested revisions.

30 pts: Project (due 3/27) Polished draft including 2, 3 4, 7 - 10

40 pts: Project (due 4/3) Draft of polished project which should be at least 80% completed.

Polished Final Project (due 4/12): Do not include unfinished sections. Note this version will be reviewed by your writing center fellow. This will be your finished final project (though you may revise based on comments from your writing center fellow and resubmit by 4/28)

50 pts: Project (due 4/17)
Final project including unfinished sections. You will likely have some sections that you have started (possible in one of our labs), but won't have time to finish this semester. You can still earn points for these sections. If you don't have unfinished sections, you have likely already earned these points.

30 pts: Finished Polished Project due 4/28. This is the revision of the polished version you submitted to your writing fellow on April 12th.

If you are collaborating with someone, you should decide as a group how the work will be divided and what you would like to accomplish. I will not require that you finish all (or even most parts), but your collaborators can. The following is one potential project outline, but you may follow any journal format you prefer. Note that while the ideal paper would include all of the following, even published papers do not include all of the following. You and your collaborators will need to decide what to include.

NOTE: Even published papers do not include all (or even most) of the following. You and your collaborators will need to decide what to include.

1. Abstract.
2. Introduction: Briefly introduce the problem, techniques, and outline the paper. Try to use as few technical terms as possible (or reference section where defined).
3. Background
• Problem description:
• Fully describe the problem. Describe how the data is created, what is its format, what are issues that one should consider (for example are their different types of noise), etc. Please keep in mind that people from a variety of backgrounds may be interested in your article, so please help them understand your data. Deeper mathematics can be applied if more people have a better understanding of the problem.
• Mathematical background:
• One can reference appropriate papers that describe the methods used in your paper or you can provide the background yourself. Including motivation specific to your problem would be particularly helpful.
4. Results
• Data analysis.
• In either the results or discussion section, motivate your choice of software. Software often requires one to choose various values for different parameters. Motivate your parameter choices. Are these choices robust (for example, does one get similar results for different choices of parameter values).
5. Discussion
6. Conclusion
7. Acknowledgement
• You should acknowledge anyone who has provided significant feedback. If you publish the results of your project, please acknowledge this course. If I provide you with significant helpful feedback, you are also welcome to acknowledge me.
8. Author contribution
• Summarize who contributed what to the paper (who designed, computed, analyzed, wrote, etc.).
9. Funding sources and conflicts of interest
10. References
• This is a very important part of your paper. It lets the reader know where to find additional information. One is also required to reference other people's ideas, analysis, conclusions, figures, etc (even if modified, reworded, or redrawn). Using other people's work without acknowledgment constitutes plagerism. For figures, one may also need to obtain copyright permission if you submit your paper for publication, and redrawing a figure may be discouraged.

If you prefer to write software, there are many other types of potential projects.