iiinova — where your digital self keeps evolving

Reposted by Clay Kosonocky

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 24/08/2026

Curate a molecule <-> text dataset, train a model, and use it to discover molecules that fight antibiotic resistance by deactivating beta-lactamase enzymes. @kosonocky.bsky.social www.biorxiv.org/content/10.6...

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Clay Kosonocky @kosonocky.bsky.social · 18/08/2026

One part of this project I'm very excited about is the website we made to explore the PubCheF-1 predictions over 13.2 million molecules! 🧵

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Clay Kosonocky @kosonocky.bsky.social · 17/08/2026

Can we use human language to predict novel bioactive molecules that work in vivo? In our new paper, we trained a deep learning model on a dataset derived from PubMed text and used it to discover novel antibiotic co-inhibitors that reduced infection burden, even in mouse models!

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Reposted by Clay Kosonocky

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 14/08/2026

Learning from human and chemical languages to predict biological function www.biorxiv.org/content/10.64898/20…

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Clay Kosonocky @kosonocky.bsky.social · 02/07/2026

I'll be in Seoul next week for ICML 2026! 🇰🇷 Message me if you'd like to meet up for food, coffee, or drinks! Would love to talk all things proteins, small molecules, and biology in general 🧬

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Clay Kosonocky @kosonocky.bsky.social · 19/05/2026

I also recently discussed the Bits to Binders competition with my co-organizers and Ron Green on the KUNGFU.AI Hidden Layers podcast! It was a very fun conversation 🤠🧬 (links below)

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Clay Kosonocky @kosonocky.bsky.social · 19/05/2026

I’ve been asked a few times how I got started running a worldwide protein design competition. The short answer is that I never intended to start this project at all: it just sort of happened. The more correct answer requires me to tell the origin story of the BioML Society [1/2]

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Clay Kosonocky @kosonocky.bsky.social · 21/04/2026

Have you wondered what the wet lab success rates are for current AI-driven protein design models? Look no further! In our new review, @kevinkaichuang.bsky.social @avapamini.bsky.social, @sarahalamdari.bsky.social, and I report wet lab success rates for *over 200* different protein design tasks 🧬💻

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Clay Kosonocky @kosonocky.bsky.social · 09/03/2026

Huge shoutout to Twist for making the competition possible!

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Reposted by Clay Kosonocky

Edward Marcotte @edwardmarcotte.bsky.social · 05/03/2026

Amazing work from Clay @kosonocky.bsky.social, Alex Abel and LEAH labs, and all the collaborators and participants in the Bits2Binders AI CAR-T therapy protein design competition. The results are in! bsky.app/profile/koso...

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Reposted by Clay Kosonocky

Claus Wilke @clauswilke.com · 04/03/2026

Results from an impressive world-wide binder design competition.

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Clay Kosonocky @kosonocky.bsky.social · 04/03/2026

The results are finally in! 🏆💻🧬 I'm thrilled to announce that the manuscript for the Bits to Binders protein design competition is out on bioRxiv! Here's a summary of our findings, including some simple criteria that nearly *double* success rates when applied as a filter 🧵

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Clay Kosonocky @kosonocky.bsky.social · 02/09/2025

🚨The Bits to Binders Competition has concluded!🧬 One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors Spoiler: They work!

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Clay Kosonocky @kosonocky.bsky.social · 17/05/2025

For better or worse, I've subconsciously adopted a policy of "AI/fake/bot unless proven innocent" w/ regards to internet content from anyone I don't know personally

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Clay Kosonocky @kosonocky.bsky.social · 17/05/2025

Some recent used bookstore acquisitions of mine Part of a few themes I'm trying to understand: - cultures & life via classic lit - basics of philosophy & history - modern political climate & trajectory - how can we make cities better? - what will the future look like?

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Clay Kosonocky @kosonocky.bsky.social · 12/02/2025

Effect of SMILES representation on structure prediction, now with a large sample size!

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Clay Kosonocky @kosonocky.bsky.social · 04/02/2025

PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used May also be the case with AF3 & Boltz-1, but haven't verified As to what this means... see the rest of the thread 🧵

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Clay Kosonocky @kosonocky.bsky.social · 30/01/2025

The DNA for the Bits to Binders competition has just arrived from @twistbio.bsky.social! It is now being handed off to LEAH Labs where they will begin testing the 12,000 binders in a few days 👀 Stay tuned!

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Clay Kosonocky @kosonocky.bsky.social · 22/12/2024

This year I've read 30 books so far. Here are the ~10 that I found the most valuable 🧵 1) One Hundred Years of Solitude (1967) by Gabriel Garcia Marquez Fantastic novel that I think everybody should read once. Captures the feeling of human life that feels instinctually correct

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Clay Kosonocky @kosonocky.bsky.social · 20/12/2024

Unparalleled levels of productivity this week

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Clay Kosonocky @kosonocky.bsky.social · 03/12/2024

@ddelalamo.bsky.social Just looked at the data. We fine-tuned ProteinMPNN on AlphaFold structures from each class of temperature in the HotProtein dataset. We found no change in performance on FireProtDB ddG or dTM. Work done w/ Phillip Woolley at UT Austin

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Clay Kosonocky @kosonocky.bsky.social · 22/11/2024

Last year I made an intro Protein + ML project to teach BioML Society members about protein embeddings. Here it is! Hope you all enjoy Should get you familiar extracting embeddings for proteins, visualizing them, and using them for property prediction

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Clay Kosonocky @kosonocky.bsky.social · 18/11/2024

"open-source and commercially available" 😎

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Clay Kosonocky @kosonocky.bsky.social · 12/11/2024

Has anybody been curating a list of the most seminal papers in the BioML space? Mainly interested in work that expands our ability to do and understand new things rather than improve upon benchmarks

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Reposted by Clay Kosonocky

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 11/11/2024

I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd

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