bioRxiv submission guide
Monday build block · Read it inside Monday's build block
Build-block reading · bioRxiv submission guide (biorxiv.org/submit-a-manuscript)
In: LABLOOP-W16 Notebook
455 CARDS · 41 WEEKS · EVERY SOURCE THE PLAN NAMES
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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.
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Lin et al. (2023), "Evolutionary-scale prediction of atomic-level protein structure with a langu…
Lin et al. (2023), "Evolutionary-scale prediction of atomic-level protein structure with a language model", Science 379(6637):1123-1130 — abstract, introduction and figures (40 min)
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In: LABLOOP-W16 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)
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In: LABLOOP-W16 Notebook
Angelopoulos & Bates
Angelopoulos & Bates (2021), "A Gentle Introduction to Conformal Prediction and Distribution-Free Uncertainty Quantification", arXiv:2107.07511, sections 1-2 (60 min)
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Rives et al. (2021), "Biological structure and function emerge from scaling unsupervised learnin…
Saturday sandbox
Rives et al. (2021), "Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences", PNAS 118(15) — the ESM-1b paper, for the "why it works" story
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DeepMind, "AlphaFold: The making of a scientific breakthrough"
Saturday sandbox · after Rives et al. (2021), "Biological structure and function emerge from scaling unsupervised learnin…
DeepMind, "AlphaFold: The making of a scientific breakthrough" (YouTube, 8 min) — the emotional context of protein AI
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In: LABLOOP-W16 Notebook
Nobel Prize in Chemistry 2024 lectures
Saturday sandbox · after DeepMind, "AlphaFold: The making of a scientific breakthrough"
Nobel Prize in Chemistry 2024 lectures (Baker, Hassabis, Jumper) — nobelprize.org
In: LABLOOP-W16 Notebook
Anastasios Angelopoulos' conformal prediction tutorial videos
Saturday sandbox · after Nobel Prize in Chemistry 2024 lectures
Anastasios Angelopoulos' conformal prediction tutorial videos (YouTube; verify)
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Valence Labs (YouTube), search "ESM" or "protein language models"
Saturday sandbox · after Anastasios Angelopoulos' conformal prediction tutorial videos
Valence Labs (YouTube), search "ESM" or "protein language models" in the M2D2 reading group
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In: LABLOOP-W16 Notebook
huggingface/notebooks
Colab: examples/protein_language_modeling.ipynb — fine-tune/embed with ESM-2 through transformers; switch the model to facebook/esm2_t33_650M_UR50D in fp16 on your 3050
In: LABLOOP-W16 Notebook
facebookresearch/esm
Read the README's "ESM-2" and embedding extraction sections; the original reference
In: LABLOOP-W16 Notebook
evolutionaryscale/esm (now redirects to Biohub/esm)
Read only; the newer ESM C/ESM3 family. Parked for Half 2
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aangelopoulos/conformal-prediction
Colab: notebooks/meps-cqr.ipynb (conformalized quantile regression on tabular data); map it onto your soft sensor
In: LABLOOP-W16 Notebook
scikit-learn-contrib/MAPIE
Regression example with SplitConformalRegressor (or the current API); get coverage on held-out batches in 20 lines
In: LABLOOP-W16 Notebook