Jason Cui

Work

Projects

Things I've built — production systems, open-source tools, and weekend experiments.

Featured

Honors Thesis

Published

This is my honors thesis for the Biomedical Computation degree in the School of Engineering at Stanford University. Completed under the amazing mentorship of Dr. Laurens van de Wiel and Principal Investigator Professor Matthew Wheeler in the Stanford School of Medicine.

PythonSQLiteSLURMHCPgnomAD v4.1Pfam v37.4 ClinVarHidden Markhov Model
2026View →GitHub →

All projects

Self-Supervised Vision Transformers for High-Recall Malaria Detection in Blood Smear Images

Completed

This paper compares three machine learning approaches — a DINOv2 Vision Transformer, an EfficientNet CNN, and a logistic regression baseline — for classifying parasitized and uninfected blood cell images from the NIH Malaria Cell Images dataset. The key finding is that DINOv2 achieves the highest recall and maintains a sensitivity advantage at low prevalence, while also producing interpretable attention maps that highlight parasite-focused regions with minimal fine-tuning.

PythonPyTorchEfficientNet-B0DINOv2 (ViT-S/14)scikit-learnAttention MapsUMAP
2026View →GitHub →

Text to DNA Encoder

In-Progress

An exploration of encoding digital information into synthetic DNA sequences. Click on the Live Site link to test it out for yourself!

PythonTypeScript
2026View →GitHub →Live →

Open Space at the Street Edge

Completed

Final project for Stanford AMSTUD 33: Architectural Theory of the American City. An interactive comparison of Boulder and Longmont, Colorado through the interface between open space and urban infrastructure.

Next.jsReact LeafletSanityTailwind CSS
2026View →