Halfway Through GSoC: My Experience and Progress

Thu, 17 Jul 2025 00:00:00 +0000

As part of the RAG-ST project, my proposal under the mentorship of Ziheng Duan aims to build a retrieval-augmented generation framework to predict spatial gene expression from histology images.

🚀 Achievements

✅ Ran the HEST-1K Pipeline

I successfully ran gene expression prediction models on the HEST-1K dataset, reproducing baseline image-to-expression workflows and setting up data loaders, evaluation metrics, and visual inspection of outputs.

✅ Explored Tangram’s Alignment Code

I studied and ran Tangram, a well-known scRNA-seq to ST alignment method, gaining key insights into cross-modality mapping. These ideas will inform our strategy to align histology images to scRNA-seq data.

✅ Designed the RAG-ST Architecture

I drafted the architecture for the RAG-ST pipeline, including:

Vision encoder to process image patches.
Retrieval module to find relevant examples from a curated database.
Generation head that conditions predictions on the retrieved examples — allowing transparency and context-aware outputs.

🧠 Challenges

Data Alignment: Spatial transcriptomics datasets often lack perfect alignment between histology, gene expression, and scRNA-seq, requiring custom preprocessing and normalization.
Trade-off Between Interpretability and Accuracy: Retrieval-augmented designs allow us to trace the origin of predictions but require care to avoid overfitting or performance drops.
Computation: High-resolution images and large-scale retrieval can be computationally expensive. I’ve begun exploring downsampling and vector database indexing strategies.

🔜 What’s Next

🔧 Build the end-to-end retrieval-generation pipeline
🧬 Prototype histology-to-scRNA-seq alignment using adapted Tangram ideas
📊 Benchmark RAG-ST vs. MLP baselines
👁️ Develop interpretability visualizations to show which samples were retrieved for each prediction

🧾 Deliverables Progress

Deliverable	Status
HEST-1K Baseline Pipeline	✅ Completed
Tangram Exploration	✅ Completed
Data Curation	🟡 In Progress
RAG-ST Architecture	✅ Drafted
Full Pipeline	⏳ Planned
Evaluation & Comparison	⏳ Planned

🙌 Closing Thoughts

It’s been a rewarding first half of GSoC. I’ve gained hands-on experience with spatial transcriptomics datasets, explored state-of-the-art tools like Tangram, and laid the groundwork for a new interpretable gene prediction model.

I’m excited to continue building RAG-ST and look forward to sharing more results soon. Huge thanks to my mentor Ziheng Duan for the guidance and support throughout!

If you have questions or want to discuss spatial modeling, feel free to reach out.

zeyuzou | UCSC OSPO