RJ Honicky @honicky
BioTech - AI - Host of Latent Space AI for Science podcast Mostly SF Bay Area Joined April 2009-
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Our paper on ESMC, ESMFold2, and mechanistic interpretability for proteins is up on @biorxivpreprint! We've made a few changes since the initial version went online last week. 1. We found an issue in the way we provided MSAs to OpenFold3. This led us to report lower performance of OpenFold3 on some benchmarks. This issue does not affect any of the other models evaluated. 2. We updated how we report results on Runs N' Poses to more closely match the original paper (counting only ligands with valid SuCOS similarity score). We also add a bar plot to the supplement that stratifies performance by similarity. This mostly changes the absolute values of the pass rate, not the relative performance of models. 3. Added some more BLI data to the supplement. 4. Added some missing citations, fixed typos, etc. Check out the preprint here: biorxiv.org/content/10.648…
Paper Club Video: youtube.com/watch?v=4g1bUR… ESM Episode: youtube.com/watch?v=XdevS0…
Thanks 1M to BioHub team for their awesome presentation of ESMC/ESMFold2/ESM Atlas paper at Latent Space Paper Club. @proteinrosh @THayes427 @awfderry @biohub YT link in the comments 👇
@axiommathai and @CarinaLHong are getting a lot of well deserved hype right now. Carina makes the case the Axiom sits squarely on the path to AGI... and foundation labs do not (right now). Check it out, loved recording this!
🆕Scaling Past Informal AI latent.space/p/axiom @axiommathai founder & CEO @CarinaLHong explains why math may be the missing path from code agents to AGI, why verified AI is about scaling brilliance not just fixing hallucinations, how Lean and formal proofs turn reasoning
ESMC/ESMFold2 authors to present at Latent Space Paper Club tomorrow! Links in the comments. @alexrives @THayes427 @proteinrosh @biohub
event: luma.com/ls?e=evt-UV7RZ… paper: biohub.org/news/world-mod…
I love it when a plan comes together! Congrats Ron, this is a huge milestone.
This weekend at ASCO, we shared first results using @NOETIK_ai TARIO-2 foundation models to predict patients likely to benefit using pre-treatment H&E alone (from actual clinical trial data with @Agenus_Bio!). Some highlights below!
@andremillet @biohub I guess I left out genes: maybe like low level functions, or even single instructures. I explained my thinking a bit more here: latent.space/p/esmfold2
"genes are code" is always vague I like: cell nucleus → storage device / storage controller ribosome → JIT-compiler and runtime features from a world model (use a SAE) → functions Proteins → processes signaling pathways → workflows Phenotypes → behaviors / outputs @biohub
The ESMC/ESMFold2 release also includes ESM Atlas, which makes me very happy :). @biohub team delivers the data!
🆕Biohub’s Protein World Model: ESMC-6B, ESMFold2, 6.8B proteins, 1.1B structures, antibody design, SAEs, & the bitter lesson for biology latent.space/p/esmfold2 @biohub Head of Science @alexrives explains why biology may scale like language modeling, how metagenomics unlocked
@alexrives Alex, loved sitting down together, and look forward to what you all have in store for us next!
@proteinrosh The paper is a tour-de-force! Well done to you and the whole team!
Love this summary of the paper. The paper is definitely worth the read!
I'm so excited to show the world what we've been working on the for the past months!! I'm going to highlight some of the fun results from this paper that I find particularly exciting.
@alexrives What a huge contribution to science!
@latentspacepod @biohub @alexrives Really enjoyed the paper, and really enjoyed sitting down with @alexrives !
@andrewwhite01 Yeah, paper's really good. Hopefully good guidance for fast iteration with automated labs! Keep it coming sir!
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