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pLDDT for the housing market

Anyone know the state of the art for how to pool embeddings from LLMs in natural language? Are we still doing mean pooling?

That concludes my list of favourite papers 2001-2023. I plan to do another one in a couple of decades... The list is collected for convenience at jgreener64.github.io/posts/favourit…. (1/3)

Joe Greener The silliest thing is that even though the sequence is only 58% similar to closest training set sequence, almost half of the "novelty" (the unaligned 42%) is from one other sequence. Much less novel than advertised! Can't find original tweet but IIRC Brian Naughton saw this first

The underlying premise here is already wrong - scientific publications are generally (unfortunately) not a high-signal resource. - The graph of biomedical entities (symptoms, diseases, conditions, biomarkers, ...) is highly interconnected. Literature basically connects any

Andrew White 🐦‍⬛ I find that this graphical abstract communicates the key finding quite effectively (DOI: 10.1021/acs.jcim.4c00049)

We also assess protein fitness prediction in ProteinGym comparing a couple existing models with structure-based models and ensembles that combine structure with other modalities. That builds on the StructSeq idea (openreview.net/forum?id=8PbTU…). Simple ensembles do quite well. 4/

Pretty good slides from a recent presentation on this: De novo prediction of protein structural dynamics Diego del Alamo, PhD Principal Scientist, Protein Design & Informatics, GSK delalamo.xyz/assets/post_im…

Anyone have a good reference or review for what current reinforcement learning techniques are being used for stuff like fine-tuning PLMs for predicting variant effects, function, etc?

Does anyone know if there are any published examples of a head-to-head comparison of SE(3) transformer/structure module vs diffusion for protein structure prediction?

PSA: If you're trying to run the Boltz ColabFold notebook and finding that it's crashing with this error, it's because you need to switch to an A100 GPU; the notebook no longer works with T4/L4 GPUs

Onlookers mooing

Long shot but does anyone have either a web server for alphaflow, a colab notebook for alphaflow, or some spare compute they'd be willing to share? I'm GPU-poor for the next two months and want to try something for a personal project