biods-final

This Github repository contains all models implemented for our CS271 Final Project: Predicting Cell Type from Spatial Transcriptomic Data. In total, we have notebooks for 6 models:

1. A Baseline MLP model
2. A Periphery Score MLP model
3. A Cell Boundary CNN
4. A ResNet Cell Boundary Model
5. A Late Fusion Multimodal Model that linearly combines models 2 and 3
6. An early-fusion Transformer model

We used the MERFISH dataset, specially mouse1sample1.hdf5. Periphery scores were calculated and given to us by our external mentors at the Salzman lab.

Code written by: Ayushi Tandel and Nathaniel Chien