455 CARDS · 41 WEEKS · EVERY SOURCE THE PLAN NAMES
Every video, chapter, paper and repository in the programme, as one card each, with the time it costs and why it is there. Filter by how long you have.
11 cards shown. Stashes: LABLOOP-W00 Notebook (15) LABLOOP-W01 Notebook (18) LABLOOP-W02 Notebook (15) LABLOOP-W03 Notebook (19) LABLOOP-W04 Notebook (17) LABLOOP-W05 Notebook (16) LABLOOP-W06 Notebook (12) LABLOOP-W07 Notebook (12) LABLOOP-W08 Notebook (15) LABLOOP-W09 Notebook (10) LABLOOP-W10 Notebook (11) LABLOOP-W11 Notebook (12) LABLOOP-W12 Notebook (12) LABLOOP-W13 Notebook (13) LABLOOP-W14 Notebook (12) LABLOOP-W15 Notebook (10) LABLOOP-W16 Notebook (14) LABLOOP-W17 Notebook (13) LABLOOP-W18 Notebook (10) LABLOOP-W19 Notebook (10) LABLOOP-W20 Notebook (10) LABLOOP-W21 Notebook (13) LABLOOP-W22 Notebook (10) LABLOOP-W23 Notebook (9) LABLOOP-W24 Notebook (9) LABLOOP-W25 Notebook (12) LABLOOP-W26 Notebook (11) LABLOOP-W27 Notebook (10) LABLOOP-W28 Notebook (6) LABLOOP-W29 Notebook (7) LABLOOP-W30 Notebook (10) LABLOOP-W31 Notebook (8) LABLOOP-W32 Notebook (5) LABLOOP-W33 Notebook (13) LABLOOP-W34 Notebook (12) LABLOOP-W35 Notebook (10) LABLOOP-W36 Notebook (8) LABLOOP-W37 Notebook (7) LABLOOP-W38 Notebook (6) LABLOOP-W39 Notebook (6) LABLOOP-W40 Notebook (6)
Tuesday · after Dallago et al. (2021), "FLIP: Benchmark tasks in fitness landscape inference for proteins"
Jarzab et al. (2020), "Meltome atlas — thermal proteome stability across the tree of life", Nature Methods 17:495-503 — abstract and figure 1 (20 min)
In: LABLOOP-W17 Notebook
Saturday sandbox
Yang, Wu & Arnold (2019), "Machine-learning-guided directed evolution for protein engineering", Nature Methods 16:687-694. The classic review; read it before week 21
In: LABLOOP-W17 Notebook
Saturday sandbox · after Yang, Wu & Arnold (2019), "Machine-learning-guided directed evolution for protein engineering"
Frances Arnold, Nobel Lecture 2018 "Innovation by Evolution: Bringing New Chemistry to Life" (nobelprize.org)
In: LABLOOP-W17 Notebook
Saturday sandbox · after Frances Arnold, Nobel Lecture 2018 "Innovation by Evolution: Bringing New Chemistry to Life"
Notin et al. (2023), "ProteinGym: large-scale benchmarks for protein fitness prediction and design", NeurIPS Datasets and Benchmarks
In: LABLOOP-W17 Notebook
Saturday sandbox · after Notin et al. (2023), "ProteinGym: large-scale benchmarks for protein fitness prediction and desi…
Andrew White, Deep Learning for Molecules and Materials — dmol.pub, chapter on "Deep learning on sequences" (with Colab buttons)
In: LABLOOP-W17 Notebook
StatQuest "Ridge vs Lasso Regression, Visualized!!!" (YouTube) for the head you fit
In: LABLOOP-W17 Notebook
Download the meltome splits; read the README on "mixed", "human" and "human_cell" splits; load them with pandas
In: LABLOOP-W17 Notebook
Browse the leaderboard page and the baselines list; note where ESM-2 sits
In: LABLOOP-W17 Notebook
Reuse protein_language_modeling.ipynb to cache mean-pooled embeddings to disk
In: LABLOOP-W17 Notebook
The curated reading list by Kevin Yang; pick 2 papers for PARKING.md, not more
In: LABLOOP-W17 Notebook
RidgeCV on embeddings → melting temperature; report Spearman correlation with a bootstrap interval
In: LABLOOP-W17 Notebook