Writing

Notes on Biology & Computation

Technical posts and research notes on AIVC, single-cell biology, and computational herbology.

AIVC

Decoder Virtual Instruments as Epistemic Tools: What Uncertainty Tells Us About the Tumor Microenvironment

When TME-VI declines to make a prediction, it's not failing — it's communicating genuine biological ambiguity. Here's what high-entropy cell neighborhoods reveal about immune escape.

12 min read
AIVC

Zero-shot Transfer Across Cancer Types: Promise and Pitfalls

Extending a melanoma-trained model to NSCLC via CELLxGENE Census — what transfers, what doesn't, and what that tells us about the universality of immune cell representations.

8 min read
Comp. Herbology

From Field to Perturbation: A Pipeline for Computational Ethnobotany

How do you turn a medicinal herb into a Virtual Cell experiment? A walkthrough of the full pipeline from LC-MS profiling to LINCS L1000 mapping to perturbation prediction.

10 min read
AIVC

Why Knowledge Graphs Beat Flat RAG for Scientific Literature

Vector search retrieves relevant chunks. Knowledge graphs answer relational questions. Here's why CellScout uses both, and when each one wins.

7 min read
Comp. Herbology

Ligand-receptor Priors Meet Traditional Medicine

CellChatDB and NicheNet encode known signaling relationships. Can the same prior knowledge infrastructure validate traditional herbal hypotheses computationally?

6 min read