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CSCI2370: Interdisciplinary Scientific Visualization (fall 2024)
Calendar

How to Hand Stuff In

How to: We use a shared Google Drive folder to manage homeworks and some other shared resources.
Inside the folder, you will deliver your assignments to the subfolder the_due_date/yourBrownShortID.ext.
For example, David could upload his first assignment to foler 09-14 as file dhl.txt.

Due: All handins are due by 9AM the same day of class to allow for review before class. Please get your reviews and readings done in time. A significant aspect of the class is to get different points of view for interdisciplinary research problems. It’ll make classes much more fun and valuable if everybody participates and expresses an opinion. It’s not fair to others to make them always carry the weight of leading the discussions. Prepare for a dynamic and open discussion in almost every class.

How to Read Papers and Proposals

Some of the readings needed for the class are password protected due to copyright and privacy issues. These links will appear styled like this, as opposed to the public links. The user/pwd is specific to the Vis group website (VisWeb); it is not the same as your CS account. Make sure to contact the instructors to get the username and password if you forget it (we’ll give it out the first day of class).

Almost all of the readings we will do are online. Printing them for your own use is fine.

Finally, please respect the grant proposals you will be reading. They are not published documents and should not be circulated outside of class. Please make sure that you destroy any copies of those documents when you are finished with them for class.

Calendar


Week 1 (back to top)

Date & Topic Assignment

Thu 9/5, 2024

Introduction

Logistics

  • Make sure the course is in your Courses@Brown (CAB) shopping cart before Friday!!!

Week 2 (back to top)

Date & Topic Assignment (due before this class)

Tue 9/10, 2024

  • Open problems in Visualization
  • What makes a good problem?
  • Meeting with collaborators

Logistics

  • Send David (David_Laidlaw at brown.edu) a small photo of yourself to include on the website.
  • Make sure you can use the shared google drive. Email David if you need help.

Reading

Read, with an eye toward your essay (below) and also to discuss in class:

Deliverables (9am)

  • Personal background handed in as yourBrownShortID.txt
  • A fictional essay, 250-500 words, set 5-20 years in the future. Imagine a scenario where you, using your unique skills, experiences, and resources, have contributed to solving or addressing one or more of the visualization research challenges discussed in the readings. Reference at least one of the specific applications from the project ideas page. Focus on a plausible and innovative approach that reflects your own insights and creativity.

    Rather than referencing the course directly, ground your story in detailed, realistic elements that demonstrate how you envision tackling these challenges in the real world. Avoid generic solutions—I'm interested in seeing how you personally might contribute to the field. Please submit your essay as yourBrownShortID-2.txt, following the same format used for the personal background hand-in.

    I know that chatGPT could produce a fine essay. I am not interested in what chatGPT can do. I want to know about your ideas. I am fine with chatGPT helping you with writing, but not with doing all of it or with providing all of the creativity, at least for this essay. I will endeavor to grade accordingly. As we move forward, you will be welcome to use chatGPT to help more broadly, e.g., with divergent thinking. You will be responsible for the accuraacy of what you hand in and will need to watch out for hallucinations and other inaccuracies!

Thu 9/12, 2024

  • Collaborator Peter Bajcsy visit. You can find the slides and recording of this visit here.
  • Review and discuss NSF ITR proposal: Understanding Unsteady Bioflows through Simulation, Modeling, Visualization, Art, and Psychology (Laidlaw et al.)
  • Evaluating project possibilities

Reading

These readings will give you a feel for what goes into a research grant proposal:

Deliverables (9am)

  • Hand in your own review for the ITR grant as yourBrownShortID.txt
  • Hand in a list of at least three possible collaborators for your class project as yourBrownShortID-2.txt. The RFP for class projects will help you understand more about the criteria for judging a project idea. Possible collaborators should mostly be from the list of project ideas suggested by various researchers around campus and beyond. They could also be other established researchers, but in that case you should include a project idea writeup like the ones on the list. Describe the discipline of each possible collaborator and how it is distinct from your area. At least two must be contributors to the list of project ideas.
  • If Peter Bajcsy is one of the possible collaborators on your list, be prepared to ask him questions. He will be visiting at the start of class to introduce his ideas and to answer any questions. Make sure that you will have the answers you need to prepare a proposal. He will not be available from 9/16-9/27.

Collaborator’s list - You will need to meet with at least three possible collaborators and report on those meetings on 9/24/2024. These meetings will help you develop the interdisciplinary part of the project. Get started scheduling these meetings and look at what you’ll need to hand in as a report. Coordinate with other class members and David for interviewing to avoid duplicating collaborator effort. David would like to be present at the first meeting with each collaborator as a mostly-silent facilitator. Don't delay!


Week 3 (back to top)

Date & Topic Assignment

Tue 9/17, 2024

  • Review of NSF CAREER proposal Shape Capture and Modeling for Wrist Dynamics and Ancient Pottery Analysis using Manifold Surfaces and Signed-Distance Volume Images (Laidlaw)
  • Evaluating project possibilities, research contributions

Reading

Deliverables (9am)

  • Write your own review ( using this form) of the CAREER proposal and hand it in as yourBrownShortID.txt. Do the review before reading the NSF report.
  • Continue interviewing possible collaborators.

Thu 9/19, 2024

  • Discuss project ideas

Reading

Deliverables (9am)

  • Three possible proposal titles and summaries as yourBrownShortID.txt. For each, include a brief description, a list of participants, and your evaluation of the proposal you imagine. Use the RFP to guide your project ideas and to self-evaluate them. Clearly identify the research contributions.

Week 4 (back to top)

Date & Topic Assignment

Tue 9/24, 2024

  • Review and discuss NIH proposal Quantitative Inverse Electrocardiography (Johnson)
  • Discuss interviews
  • Proposal needs?
  • Scoring second proposal idea

Reading

  • Read NIH guide to proposals, skimming over the structure of a submission (pg. 1-15), then focusing on the research plan details (pg. 15-18), review criteria (pg. 34), and other interesting and relevant parts you find.
  • Read this PowerPoint presentation about the NIH proposal review process
  • Read Quantitative inverse electrocardiography (Johnson). This proposal is more than 25 years old, so the work is not current. It does show an excellent example of a successful non-clinical NIH grant proposal. Non-clinical work is often quite difficult to get funded by NIH. Note the structure of the proposal, with well-formulated hypotheses to test. Skim the whole thing and read the four sections starting with Specific Aims.
  • Read partial list of resulting papers
  • Read Visualizing bioelectric fields, MacLeod et al. (sorry about the pictures...)

Deliverables (9am)

Thu 9/26, 2024

  • Comparing project ideas
  • Searching literature for related work
  • Review and discuss additional NSF proposals
  • Visualizing multi-dimensional data

Reading

Deliverables (9am)

  • A list of at least five interesting and reaonably rich sharable observations for the class. Hand in as usual. Do not duplicate observations already handed in. I suggest editing your observations in the handin directory to avoid duplication. If you have less rich observations, include more of them.

Week 5 (back to top)

Date & Topic Assignment

Tue 10/1/2024

  • Visualization tools
  • Paraview volume rendering
  • Proposal challenges

Reading

  • Read Visualization Handbook's table of contents. For the class, see if the topics in the book suggest some readings related to your project. Are there any new ideas in there for a different project? Google for the authors' web pages and see what other stuff they are working on. If you're interested in reading more, the book may be available at the Sciences Library (SciLi) -- it was at some point :-) and there is a link below. Some chapters are likely available online. Many topics will have Wikipedia pages or other tutorial-level pages that will help you become visualization experts.
  • Here is the entire Visualization Handbook for your perusing/skimming pleasure (you are not expected to read it for class except as it is relevant to your project).
  • Read The Value of Visualization, and The Value of Infovis. Look for ways to understand and motivate the contributions of your proposed projects. Can you find papers that cite these that are helpful? This could lead to some things for your literature review and related work sections.

    • Deliverables (9am)

    • Hand in results from literature search as yourBrownShortID.txt

      • You should do this search on the project you are most seriously considering doing out of all the ideas you have. Google Scholar is the main place to search for research papers, but there is a list of other options, some of which may be outdated. here (Question 3 Where do I search for research papers?). Continue developing your project proposal, filling in any weaknesses, fleshing out the related work section, etc. Be prepared to briefly describe the project idea you are most seriously considering and any issues, concerns, problems, etc. that we can discuss in class.

    • The first item in your literature search should be the paper you think would be most valuable for the class to all read and discuss. Clearly label it as such.
    • Install Paraview on your computer from the first step in the tutorial. Also download the tutorial.vtk file. Bring to class.

    Thu 10/3/2024

    • Contributions and related work
    • Proposal challenges
    • Discuss Value of *Vis
    • Paraview volume rendering

    Deliverables (9am)

    • Preliminary proposal handed in as yourBrownShortID.pdf. This should be a full draft, ready for comments by peer reviewers.
    • An overleaf template for your proposal can be accessed here.
    • Be sure to follow the instructions in the RFP

      • Make sure your proposal is saved as a pdf.


    Week 6 (back to top)

    Date & Topic Assignment

    Tue 10/8/2024

    • Proposal presentations, 5 minutes each + 5 discussion, randomized:
    • Kevin, Matthew, Byron, Richard, Jasmine, Yang, Eric

    Reading

    • Read proposals from the shared Google Drive folder

    Deliverables (9am)

    • Presentation slides handed in as yourBrownShortID_slides.pptx. These must be pptx, and should not have external links like youtube videos, which google slides often use. Everything must be embedded in the pptx. One way to ensure that is to make sure that your pptx works on a computer that is off the network.
    • Review the first-draft proposals assigned to you. You are assigned four proposals, the two following you in the alphabetical list that do not have you as a co-pi and the two preceeding you. Wrap around the beginning or end of the list as necessary. Use a separate form for each review you write, and name the file proposer_by_reviewer.txt when you hand it in. For instance, if David reviews Ugur's proposal, he should hand in a file called ugur_by_dhl.txt. Review assignments and roles are made explicit in "this spreadsheet". Each proposal is listed with the PI and Co-PI under the "Role" column. That column also shows a "1" for the primary reviewer, a "2" for the secondary reviewer, and a "3" for any tertiary reviewers. At the study section the primary reviewer will summarize the proposal and the factors that influence their scores. The other reviewers will add any additional factors that influenced them.

    Thu 10/10/2024

    • Proposal presentations, 5 minutes each + 5 discussion, randomized:
    • Aalok, Arjun, Musa, Thais, Sam, Kei, Brendan
    • be prepared to share your screen in zoom for your presentation

    Reading and Revising

    Deliverables (9am)

    • Your response to reviewers document. It should be the first part of the final proposal that you hand in next week, and the handin today should also include the preliminary proposal. The response should include all the reviews, with each review point responded to following the point. Distinguish the review text from the response text -- indent one or italicize one, etc. Numbering the individual responses or the comments can help in referring back to something that was commented on and addressed in an earlier part of the response. The response should not debate the comment, it should explain how the final proposal has been changed to address the comment. (Or how it will be changed -- the changes don't have to be made yet.) You can include the reviews by David and chatGPT if you wish, but do not have to.

      Please refer to this example of a response-to-reviewers document. It is for a paper rather than a proposal, but it should give some idea of what to aim for.


    Week 7 (back to top)

    Date & Topic Assignment

    Mon 10/14/2024

      Not a class; stuff due MONDAY!!

    Deliverables (9am)

    • Final proposal handed in as yourBrownShortID.pdf
    Date & Topic Assignment

    Tue 10/15/2024

    • Study section 1 of 2 (evaluate, score, “fund” proposals)
    • IEEE Visualization Conference online (David remote in zoom "laidlaw")

    Link for in-class activity:

    • Table of linked reviews and NIH-style proposal scores: Score sheet

    Reading

    • Read final proposals from the shared Google folder

    Deliverables (9am)

    • Review the final proposals assigned to you. Hand in reviews for the proposals where you are primary, secondary, or tertiary. The primary reviewer should be prepared to summarize the proposals contributions in class, then go through each sub-score and the overall score justifying them. The secondary and tertiary reviewers will then comment on any additions to or disagreements with what has been said. Everyone will score every proposal based on that discussion. Use a separate form for each review you write, and name the file proposer_by_reviewer.txt when you hand it in. For instance, if David reviews Ugur's proposal, he should hand in a file called ugur_by_dhl.txt.
    • Respond to the quick questions in this form as yourBrownShortID.txt

    Thu 10/17/2024

    • Study section 2 of 2 (evaluate, score, “fund” proposals)

    Week 8 (back to top)

    Date & Topic Assignment

    Tue 10/22/2024

    • IEEE Visualization Conference review

    • Work on projects
    • Primary reviewers: augment your one primary review with a panel summary section capturing the outcome of the review session discussion.

    Thu 10/24/2024

    • Week 1 project updates

      Deliverables (9am)

    • Be ready to explain and discuss your project progress with others in class. A Gantt chart can be a good way to show/explain progress.

    Week 9 (back to top)

    Date & Topic Assignment

    Tue 10/29/2024

    • Where would your project fit at the conference?
    • Review VIS 2024 program
    • Relate your project to the VIS conference
    • Work on projects.

    Thu 10/31/2024

    • Week 2 project progress reports.
    • Paper contributions.
    • Prepare week 2 project progress reports.

    Week 10 (back to top)

    Date & Topic Assignment

    Tue 11/5, 2024

    Election Day, No Class.
    Vote!

    Thu 11/7, 2024

    • Week 3 project progress reports.
    • Prepare week 3 project progress reports. Be sure to include a list of the research contributions that your final paper will have and the evidence of those contributions accessible to a new audience member. These should be similar to the research contributions from Vis Conference papers that we listed on the board in class. Images of the board and notes from earlier class are in the shared google doc https://tinyurl.com/mr3y5uby
      Course alum Lucas Brito will be new guest audience member today.

    Week 11 (back to top)

    Date & Topic Assignment

    Tue 11/12/2024

    • More Vis 2024 paper evaluations, including 2-minute flash talks of example papers. no prep needed.
    • Volume Rendering (another try...)

    Thu 11/14/2024

    • Week 4 project progress reports.

    • Prepare week 4 project progress reports.

    Week 12 (back to top)

    Date & Topic Assignment

    Tue 11/19/2024

    • User Study Design Practice

    Thu 11/21/2024

    • Week 5 project progress reports

    Deliverables (9am)

      Hand in your slides. Name the file login1_login2.pptx or .pdf.

    Week 13 (back to top)

    Date & Topic Assignment

    Tue 11/26/2024

    • No class. Happy Thanksgiving!

    Thu 11/28/2024

    • No class. Happy Thanksgiving!

    Week 14 (back to top)

    Date & Topic Assignment

    Tue 12/3/2024

    • Week 6 project progress reports

  • Prepare week 6 project progress reports.
  • Include a "cartoon" version of your results section. That includes sketches of visuals, graphs, and any other results that will make the contributions clearer. Each of these is a "panel" for your cartoon results. These should all be placeholder visuals or graphs where you make up some plausible results. Label axes, include legends, and make each panel as complete as you can. At the same time, don't fuss about visual perfection. Bonus points for sketchiness, hand-drawn, quickly produced versions. Content over format! Make sure that the captions for those make clear what the audience should be able to see (eventually) in each panel. And make sure that all contributions are represented in the set of panels.

    • Thu 12/5/2024

    • Ultimate class
    • Presentation Dress Rehearsal!

    In class, each project group will deliver a 6 minute presentation about their project. This is a dress rehearsal for the final presentation.

    • The audience will have 5-10 minutes to ask questions after each talk. You should practice your presentation before class at least three times; remember to focus on contributions and results, and don’t go over time. We will critique presentations as a class in preparation for the public final presentations.
    • Use the feedback you receive in and after class to revise your final presentation.

    Deliverables (9am)

    • Hand in a pptx of your slideshow (one per group). Name the file login1_login2.pptx corresponding to the group members.

    Feedback on other reports (11:59pm)

  • Provide provide a handin with feedback about the the four projects following yours. Name it pi_copi_by_you.txt Aim for suggestions that could be handled in the remaining few days, thoughts on what worked, or lessons that the authors could take with them for future projects.

    • Weeks 15-16 (back to top)

    Date & Topic Assignment

    Thu 12/12/2024, 11:59pm

    • Final Project Draft Reports

    Hand in Final Report (11:59pm EST)

    • By midnight, hand in a draft two-page extended abstract (pdf) for your project as login1_login2.pdf. References do not count toward the page limit. Each project should have one report, but each student should also include a single page describing their intellectual and practical contributions to the project. Describe those contributions in separate, labelled sections.
    • Your abstract must match the formatting requirements for our class proceedings. Latex template for final report can be accessed here. Reference may continue onto a third page.

    Thu 12/19/2024, 10:30am

    • Final Project Presentation

    Present your Final Project (10:30am)

    • Before the presentation slot, hand in a pptx of your slideshow (one per group). Name the file login1_login2.pptx corresponding to the group members.
    • Plan for a maximum of 6 minutes of presentation. Each group member should present some part of the work. You will have a few minutes after your talk to answer questions from the audience.

    Fri 12/20/2024

    • Final Reports Due

    Hand in Final Report and Self-evaluation (11:59pm EST)

    • By the end of the day, hand in a revised two-page extended abstract (pdf) for your project as described above.
    • Your abstract must match the formatting requirements for our class proceedings. Latex template for final report can be accessed here. References may continue onto a third page.
      P.S. the link here is the same as the link for your draft submission.
      P.P.S don't forget the extra page describing the individual contributions (possibly updated) from your 12/12 handin
    • Hand in a short self-evaluation. Copy the table of expertise levels you set out for yourself for the course learning goals in your first handin. Those had a column for pre-course expertise and predicted post-course expertise. Add a new column for actual post-course expertise and fill those numbers in. Be honest -- there is no penalty for having predicted too high or too low, just an opportunity to learn. Also, write your expected grade and justification, keeping in mind the course goals and the following grading rubric:
      25% written research proposal
      20% 3-4 presentations in class
      30% final research extended abstract and presentation
      15% homeworks
      10% class participation
    If you're wondering, here's what we did last time: (2022 calendar)