ROC, Paper, Scissor, Shoe

📊 Working through ROC-AUC from scratch, then poking at its blind spots — low prevalence, calibration, and finally Decision Curve Analysis. Mostly notes to myself on what I learned (and got confused by) along the way. 🤔📈

Cross-Validation From Scratch and a Surprise at n=100

Textbooks say LOOCV has the lowest bias but highest variance compared to 10 and 5-fold. Coded a K-Fold CV from scratch for learning to test that on simulated data 🔍📊 — and at n=1000 it holds up. At n=100? Not so much. 🤔

Learning Amino Acids Part 1: Non-Polar Amino Acids, Rodrigues Rotation, and Lennard-Jones Potential

🧬 Back to basics! Learning non-polar amino acids, what zwitterions actually are, and dipping into the applied math — Rodrigues rotation and Lennard-Jones potential. Slowly building toward optimal phi/psi!

Exploring the CovR/S Two-Component System in Streptococcus pyogenes

Exploring the CovR/S two-component system in Group A Strep 🧫 — from genome annotation with Bakta & BaktFold, to AlphaFold confidence metrics, and a first attempt at protein docking with Haddock3. Learning as we go! 🙌

Learning & Exploring Survival Analysis Part 1 - A Note To Myself

A note to myself on survival analysis — KM curves, log-rank tests & Cox models 🧮 If I wrote it the way I understood it, maybe I’ll actually remember it 🤞