The final exam for CHEM 169/269 has two options. You will choose one and complete it fully.
Option 1: Self-Guided Project Final
Build and complete your own project route.
Timeline and deliverables
Deadline 1: Project proposal
Due: Friday, March 6, 2026 at 11:59 PM
➡️ Need a model? View the Proposal Template + Example
Submit one written proposal that clearly states:
- The scientific problem/question you want to tackle (biology, biochemistry, proteins, small molecules, quantum chemistry, molecular dynamics, materials science, or related areas)
- Why you are personally interested in this problem (for example: your research interests, something you discovered through AI/chatbot exploration, or a long-standing personal curiosity)
- The computational approach you plan to use
- One ambitious stretch component you want to attempt (for example: contrastive learning, a stronger comparison model, or a deeper analysis extension)
- The data you expect to use
- What your final route + solution will include
Important: Proposal approval is required to continue with Option 1. The main approval criterion is that your exact dataset(s) are clearly identified and feasible for your planned route + solution.
Deadline 2: Final project submission
Due: Tuesday, March 17, 2026 at 11:59 PM (exam day)
Submit:
- Your custom climb route prompt (the route itself)
- Your full route solution/submission
- A GitHub repository for the project
- Optional: one approved bonus extension for extra credit
GitHub repository requirements (Option 1)
Your repository must include a polished README.md with:
- Project title and one-paragraph summary
- Biological problem and motivation
- Data source(s) and what was used
- Computational approach and model/workflow overview
- Your route design and what was completed
- Results summary with key figures/tables
- Interpretation, limitations, and next steps
- Reproducibility instructions (how to run your analysis)
Your notebook(s), code, and final artifacts should be clearly linked from the README.
Expected route themes (examples)
- Biochemical prediction task
- Representation-based analysis
- Model comparison and interpretation on a biological dataset
Option 2: Standard Exam Routes
Complete one instructor-released route on exam day for full credit.
What you do
- Complete Route A released on the exam date (required for full credit).
- Show intermediate reasoning, calculations, and model outputs.
- Submit Route A by the exam deadline.
- Optional: complete Route B for extra credit.
Route themes
- Residue-level PLM embeddings
- Protein-protein interactions with AlphaFold 3 scoring (pairwise and pooled calculations)
Required deliverables
- Completed submission for Route A (required)
- Completed submission for Route B (optional extra credit)
Baseline and Extra Credit Policy
- One complete route is the full-credit baseline for the final exam.
- Option 1: one custom route + full solution + required project repo.
- Option 2: one standard exam route (Route A).
- Extra credit is available through:
- Option 1: one approved bonus extension
- Option 2: completion of Route B
Selection and Logistics (Prototype Draft)
The policy below is being finalized and will be confirmed in a follow-up post:
- Option declaration + proposal deadline (Option 1): Friday, March 6, 2026 at 11:59 PM
- Switching options after declaration: TBD
- Exact exam-day release/submission times: TBD
- Submission location and file format: TBD
- Collaboration/tools policy for each option: TBD
If you already know you are pursuing Option 1, start by scoping a project that is feasible and well-defined.
If you are leaning Option 2, keep progressing through current routes; the standard final routes will draw on the same style of reasoning and execution.
More concrete logistics will be posted next.