Sameer Soi
@sameersoi
Dropping science like Galileo dropped the orange. VP DS & AI @AbaloneBio, ex-DS/ML @Atomwise @Zymergen, @grandroundsinc, PhD @UPennGCB
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Multiple hypothesis testing strikes again: cureus.com/articles/19627…
This is a great way to encode inductive biases through pretraining tasks in biological datasets -- simulations! Important that they are non-trivial simulations. I have seen that simple tasks that amount to counting provide no benefit.
Compute Rosetta energies for protein variants and use them as pretraining targets to improve generalization on difficult protein property prediction tasks. @romerolab1 @anthonygitter
I love my statistics peeps but while they are still gatekeeping semantics around _p-values_, ML folks are building the future. I guess it was inevitable but the gap is so much starker in 2024.
I'm late to the party because I use vim and just got @codeiumdev set up but it is clear to me that coding assistants are the (first) killer app of LLM's. I've used LLM's in other contexts but this is like it's reading my mind. I don't even have GPT4 with my free tier. Mind blow!
Scoop: Atomwise has hired a CMO w/ 25-plus years experience in the drug industry, as the AI biotech pivots from partnerships to pipeline CEO Abe Heifets talked with me about the new focus, starting with TYK2, and why faster isn't necessarily better endpts.com/atomwise-ceo-o…
Just updated my Zoom client for Ubuntu and see that both background blur and the whiteboard work. This really is the Year of Linux on the Desktop. Praise be!!
If this tweet gets 1k likes I'll waste my weekend benchmarking all the vector dbs to figure out what is real and what isn't. I'll throw `np.array` in the mix as well, and will use some "big data."
Omnigenic epistasis regulates complex trait heritability biorxiv.org/cgi/content/sh… #biorxiv_genetic
New pre-print alert 🚨 Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale. See 🧵below: biorxiv.org/content/10.110…
Impact of phylogeny on structural contact inference from protein sequence data biorxiv.org/cgi/content/sh… #biorxiv_bioinfo
Excited to share our findings training GPN, a DNA language model for Arabidopsis thaliana, with @sanjitsbatra and @yun_s_song: DNA language models are powerful predictors of non-coding variant effects, without the need for any labeled data. doi.org/10.1101/2022.0… 1/n
Excited for the future of computational drug discovery!
@NucleateHQ's Activator is now OPEN for biotech company builders. Accepting applications from academics worldwide. Bring your own idea or join a team. apply.nucleate.xyz
Another heuristic from @michelebusby: "if your programmers are swearing at you in five years about your terrible code, that’s a win! You lasted five years and grew enough to hire judgmental programmers! Congratulations!" (from this wonderful blog post: michelebusby.tumblr.com/post/643211974…)
The process of “spinning out” science from universities is broken. Why?👇🏾🧵
Dear @ucla treating applicants and prospective and current employees with respect and dignity, and paying them a living wage, is the bare minimum. BARE MINIMUM. Signed, The Universe
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