Notebook
Short explainers, videos, and working notes. Written for curious scientists, whichever side of the bench they sit on.
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NotePinned
Why this notebook exists
A place for short explainers, working notes, and the occasional video on statistics, machine learning, and immunology.
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Video, 3:35
DESeq2 for bulk TCR-seq: a field guide from read counts to off-target calls
A 3.5-minute narrated video and a complete tutorial on using DESeq2 (PyDESeq2) to compare V-gene usage between CAR-T and control T cells: why raw percentages mislead, the five steps inside DESeq2, a…
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Video, 5:35
What is a survival curve? How to read the most important chart in clinical research
A 5-minute narrated video and an illustrated walkthrough of the Kaplan–Meier survival curve: time to an event, censoring, why counting fails, the step-by-step calculation, medians and confidence bands, the log-rank test, the…
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Video, 9:34
How is GPT trained? From next-token guessing to RLHF, step by step
A 10-minute narrated video and an illustrated walkthrough of the four stages behind GPT and ChatGPT: pretraining, supervised fine-tuning, a reward model trained on human rankings, and RLHF with PPO. Every loss…
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Video, 8:59Paper reading
The Virtual Biotech: an AI drug company made of agents
A 9-minute narrated video and an illustrated reading note on Zhang et al. (Science, 2026): how the multi-agent Virtual Biotech is built (a CSO orchestrator, eight specialist agents, MCP tools and a…
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Video, 5:39Paper reading
AI in drug discovery: where do we really stand?
A 6-minute narrated video and an illustrated guided reading of Bender et al. (Nature Reviews Drug Discovery, 2026): why AI’s clinical impact is still thin, where the value really lies, why data…
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Video, 6:31
What is PCA? A visual guide, told with blood cells
A 6-minute narrated video and an illustrated walkthrough of principal component analysis: variance and the spinning line, covariance, eigenvectors and SVD, loadings and scores, real PBMC single-cell data, choosing the number of…
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Video, 6:37
What a p-value is, and isn’t, in 10 minutes
A hand-drawn 6-minute video and an illustrated walkthrough: one clinical trial, a shuffle test, the t-test, α and power, why significant isn’t important, four classic traps, and what 20,000 genes do to…
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Video, 9:47
What is a Transformer? A visual guide, told with one T-cell receptor
A 10-minute narrated video and an illustrated walkthrough: tokens and positions, query, key and value, the attention formula step by step, multi-head attention, the Transformer block, ESM-2 guessing a hidden residue, and…
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