DeepMSI
Predicting microsatellite instability in endometrial cancer from whole-slide histology
The problem
Microsatellite instability (MSI) is a tumor marker. A whole-slide image is gigapixels in size, and the only label is one per slide, MSI or not. There are no pixel annotations to learn from.
What I built
A weakly supervised pipeline. Each slide is cut into 256×256 patches, a ResNet50 turns each patch into a 2048-number feature, and attention-based multiple instance learning (MIL) learns which patches matter. A graph convolutional network (GCN) over the 8 nearest neighbours of each patch adds the spatial context a bag of patches loses. The attention weights double as maps a clinician can inspect.
What I learned
Working with patient data changed my priorities. Accuracy mattered, but so did interpretability and how the model fits into a clinician's workflow.
- AUROC
- 97.13%
- Accuracy
- 92.66%
- Recall
- 96.67%
- F1
- 87.88%
Validation set. Dataset of 542 whole-slide images.