Everything you could
study, filtered.

3Blue1Brown · Essence of Linear Algebra

Thursday · M1 · Thursday, first

Produce: notes/ml/M1.md: what a matrix does to a vector; one example redone in NumPy

In: LABLOOP-W01 Notebook

Crash Course Biology #7 · "ATP & Respiration"

Tuesday · B2 · Tuesday, first

Produce: Three lines in notes/bio/B2.md: why DO falls when biomass grows

In: LABLOOP-W02 Notebook

3Blue1Brown · Essence of Calculus

Thursday · M2 · Thursday

Produce: notes/ml/M2.md: what a derivative is, in your own words

In: LABLOOP-W02 Notebook

StatQuest · "Principal Component Analysis (PCA), Step-by-Step"

Thursday · M2 · after 3Blue1Brown · Essence of Calculus · Before Friday's PCA code

Produce: The 3-line explanation of scores vs loadings you will paste into Sunday's post

In: LABLOOP-W02 Notebook

3Blue1Brown · "Eigenvectors and eigenvalues"

Thursday · M3 · Thursday, first

Produce: One sentence in notes/ml/M3.md: what last Friday's principal components actually are

StatQuest · "Machine Learning Fundamentals: Bias and Variance"

Thursday · M3 · after 3Blue1Brown · "Eigenvectors and eigenvalues" · Thursday, after V4

Produce: The bias-variance sentence in notes/ml/M3.md

In: LABLOOP-W03 Notebook

StatQuest · "Linear Regression, Clearly Explained!!!"

Thursday · M3 · after StatQuest · "Machine Learning Fundamentals: Bias and Variance" · Thursday, after V2

Produce: One regression fitted on two IndPenSim variables and read aloud: slope, intercept, what it means

In: LABLOOP-W03 Notebook

Khan Academy · "Fermentation and anaerobic respiration"

Tuesday · B4 · Tuesday, first

Produce: One paragraph in notes/bio/B4.md: "what is a fermentation, really"

In: LABLOOP-W04 Notebook

StatQuest · "Machine Learning Fundamentals: Cross Validation"

Thursday · M4 · Thursday, first

Produce: The sentence "why random k-fold is wrong for batch data" in notes/ml/M4.md

In: LABLOOP-W04 Notebook

Crash Course Biology #11 "DNA, Hot Pockets, & The Longest Word Ever"

Tuesday · after OpenStax Biology 2e

Crash Course Biology #11 "DNA, Hot Pockets, & The Longest Word Ever" (YouTube, 13 min)

In: LABLOOP-W05 Notebook

StatQuest "Regularization Part 1: Ridge (L2) Regression"

StatQuest "Regularization Part 1: Ridge (L2) Regression" and "Gradient Boost Part 1: Regression Main Ideas" (YouTube, 25 min)

In: LABLOOP-W05 Notebook

MIT OCW 7.016 lectures on protein structure and enzymes

MIT OCW 7.016 lectures on protein structure and enzymes (ocw.mit.edu/courses/7-016-introductory-biology-fall-2018), ~50 min

In: LABLOOP-W07 Notebook

Khan Academy "Steady states and the Michaelis Menten equation"

Tuesday · after MIT OCW 7.016 lectures on protein structure and enzymes

Khan Academy "Steady states and the Michaelis Menten equation" (MCAT section) (15 min)

In: LABLOOP-W07 Notebook

Brunton & Kutz, Data-Driven Science and Engineering (2nd ed.), ch. 7 on SINDy — databookuw.com (…

Brunton & Kutz, Data-Driven Science and Engineering (2nd ed.), ch. 7 on SINDy — databookuw.com (free PDF) (40 min) + Steve Brunton "Sparse Identification of Nonlinear Dynamics (SINDy)" (YouTube, 30 min)

In: LABLOOP-W12 Notebook

StatQuest "False Discovery Rates, FDR, clearly explained" and "p-hacking: What it is and how to…

Tuesday · after Modern Statistics for Modern Biology ch. 6 "Testing"

StatQuest "False Discovery Rates, FDR, clearly explained" and "p-hacking: What it is and how to avoid it!" (YouTube, 20 min)

In: LABLOOP-W14 Notebook

Stanford CS336 lecture on evaluation

Stanford CS336 lecture on evaluation (cs336.stanford.edu, videos on Stanford Online YouTube) (60 min); your week 7 notes on Zheng et al. 2023 judge biases (15 min)

In: LABLOOP-W14 Notebook

S. Keshav (2007), "How to Read a Paper"

S. Keshav (2007), "How to Read a Paper", ACM SIGCOMM Computer Communication Review 37(3):83-84 (2 pages, 15 min); then three FermLit papers with P11 and IMRaD noted (60 min)

In: LABLOOP-W15 Notebook

MIT 6.874 Deep Learning in the Life Sciences

Tuesday · after Lin et al. (2023), "Evolutionary-scale prediction of atomic-level protein structure with a langu…

MIT 6.874 Deep Learning in the Life Sciences (Manolis Kellis, 2021, YouTube playlist), protein lecture (first 40 min)

In: LABLOOP-W16 Notebook

Hugging Face model card facebook/esm2_t33_650M_UR50D

Hugging Face model card facebook/esm2_t33_650M_UR50D (10 min) + MIT 6.874 protein lecture second half (40 min); code block with ridge head

In: LABLOOP-W17 Notebook

StatQuest "Ridge vs Lasso Regression, Visualized!!!"

StatQuest "Ridge vs Lasso Regression, Visualized!!!" (YouTube) for the head you fit

In: LABLOOP-W17 Notebook

Simon Peyton Jones, "How to write a great research paper"

Simon Peyton Jones, "How to write a great research paper" (YouTube, Microsoft Research, ~1 h) + NeurIPS Paper Checklist (neurips.cc, current year's author guidelines) (30 min)

In: LABLOOP-W18 Notebook

StatQuest "PCA main ideas", "t-SNE, Clearly Explained" and "UMAP Dimension Reduction, Main Ideas…

StatQuest "PCA main ideas", "t-SNE, Clearly Explained" and "UMAP Dimension Reduction, Main Ideas!!!" (YouTube, 30 min) — the three plots every single-cell talk shows

In: LABLOOP-W19 Notebook

Patrick Winston, "How to Speak"

Patrick Winston, "How to Speak" (MIT OCW / YouTube, ~1 h) — watch Saturday; it prepares both the mock sessions and the talk proposal

In: LABLOOP-W20 Notebook

iBiology, "Uri Alon: How to Choose a Good Scientific Problem"

iBiology, "Uri Alon: How to Choose a Good Scientific Problem" (verify; talk version)

In: LABLOOP-W21 Notebook

StatQuest "Spearman's Rank Correlation" if needed

StatQuest "Spearman's Rank Correlation" if needed (search; verify) and "Bootstrapping Main Ideas" (carry over)

In: LABLOOP-W22 Notebook

Khan Academy / Crash Course refresh on protein folding and denaturation ("why heat unfolds prote…

Khan Academy / Crash Course refresh on protein folding and denaturation ("why heat unfolds proteins") (15 min)

In: LABLOOP-W23 Notebook

Y Combinator Startup School, "How to Talk to Users"

Y Combinator Startup School, "How to Talk to Users" (Eric Migicovsky, YouTube, ~20 min)

In: LABLOOP-W27 Notebook

Coursera Process Mining: Data Science in Action

Coursera Process Mining: Data Science in Action (Eindhoven), week 1 lecture on event logs (30 min) — cycle time from timestamps is process mining in miniature

In: LABLOOP-W29 Notebook

StatQuest "Statistical Power"

Tuesday · after Cumming (2014) "The new statistics"

StatQuest "Statistical Power" (carry over)

In: LABLOOP-W30 Notebook

Lewis et al. (2020), "Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks"

Lewis et al. (2020), "Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks", NeurIPS, abstract + figure 1 (15 min)

In: LABLOOP-W34 Notebook

Es et al. (2023), "RAGAS: Automated Evaluation of Retrieval Augmented Generation"

Tuesday · after Lewis et al. (2020), "Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks"

Es et al. (2023), "RAGAS: Automated Evaluation of Retrieval Augmented Generation", arXiv:2309.15217 (30 min)

In: LABLOOP-W34 Notebook

Stanford CS224N lecture on retrieval/RAG

Tuesday · after Es et al. (2023), "RAGAS: Automated Evaluation of Retrieval Augmented Generation"

Stanford CS224N lecture on retrieval/RAG (web.stanford.edu/class/cs224n; verify current lecture list) (30 min)

In: LABLOOP-W34 Notebook

Patrick Winston, "How to Speak"

Patrick Winston, "How to Speak" (MIT OCW / YouTube, ~1 h; re-watch the first 30 min)

In: LABLOOP-W38 Notebook

Simon Peyton Jones, "How to give a great research talk"

Simon Peyton Jones, "How to give a great research talk" (Microsoft Research, YouTube)

In: LABLOOP-W38 Notebook

Bill Burnett & Dave Evans, Designing Your Life (book, paid) — chapters on "odyssey plans"

Bill Burnett & Dave Evans, Designing Your Life (book, paid) — chapters on "odyssey plans" and "choosing well"; or Bill Burnett's TEDx talk "Designing Your Life" (YouTube, free) (30 min)

In: LABLOOP-W40 Notebook