Projects

Description

Students will collaborate in groups of 1 or 2 persons to complete a project on Generative AI for Biomedicine. These projects should have some AI and Biomedical applications.

Key Dates:

• Project Proposal Deadline: Oct 21, 2025 (11.59 PM)

• Project Mid Report : Nov 13, 2025 Nov 20, 2025 (11.59PM)

• Poster Presentation : Dec 8, 2025 (2.00 PM to 6.00 PM) @ 4th Floor Lobby (4400)

  Poster Printing

  • Poster Specs: 42" (width) x 31.5" (height). PDF only.
    • Note: You must leave 0.5 inch margins on all sides (the printer does not print to the edge).
  • Printing Options:
    • Students WITH an SCS account:
      • Submit a Poster Request via SCS Computing.
      • Deadline: We strongly recommend submitting by Dec 4th by 5:00 PM due to high printing volume at the end of the semester
    • Students WITHOUT an SCS account:
      • Submit your poster through this Google Form. We will submit the printing requests on your behalf.
      • Deadline: Dec 4th by 11:00 AM.

• Project Final Report : Dec 7, 2025 Dec 10, 2025 (11.59PM)

  • Use this LaTeX template, and modify it accordingly.

Project Proposal

You proposal should describe:

• What Biomedical problem are you planning to address? -- what are the technical challenges?
• What are the existing state-of-art methods on this problem? Is the source code/model available? 
• Possible directions for going forward. 
• How do you evaluate the performance?
• Who is your team and how are you planning to split the workload between team members?
• A rough timeline/milestones
• What CPU, GPU and storage infrastructure do need for this project? Please estimate the amount of computation time required.  

Project Report (midterm/final)

• Introduction/Motivation: This essentially lays out the problem definition, motivation, talks about why we need to work on it, the key contributions expected/presented in the work. 
• Related Work/Background: This talks about key papers/works that provide context to your current work. Instead of listing down multiple past works, talk about the ones that minimally differ from your work, and how. 
• Methodology: This section talks about your method, raises research questions and how you are going to address them.
• Experiments: This section can describe your experiments and the results you obtain. For mid-term report, please list preliminary results.
• Analysis/Ablations: Typically, you would have multiple factors involved in your experimental setting. Analysis sections help you probe deeper into the results and help piece out contributions from individual modeling decisions made. 
• (Mid-term report) list a timeline plan for remaining work.
• (Final report) Conclusion/Discussion: This would list the main takeaways from your work, discuss some future ideas (if any) and engage in discussion. 
• Limitations: This section lays out some known limitations of your work. 
• [final report only] Team Member Contributions List out each individual's contributions in this section.

Suggested Directions for Projects

• Proposing an improvement for an existing method

• Applying generative ai methods to solve a question in biology

• Re-implementing a method proposed in the literature, while providing more insights about the design choices (e.g. https://iclr-blog-track.github.io/2022/03/25/conformation-generation/)

• Providing a highly accessible guide on a complex method (E.g. https://d2jud02ci9yv69.cloudfront.net/2025-04-28-the-illustrated-alphafold-55/blog/the-illustrated-alphafold/)

• Benchmarking several recent methods and analyzing their performances on a task (e.g. https://ramith.fyi/assets/pdf/2025_struct_poster.pdf, https://static.ramith.io/genomics_poster_ramith_final.pdf, )

• Have more ideas? Discuss with us during office hours!