🚀 New talk! "Automated ML-guided lead optimization: surpassing human-level performance at protein engineering" ▶️ www.youtube.com/watch?v=mEhB... ✨🧪 This was a talk I gave at the recent AIxBIO conference in Cambridge UK. A 10-minute pitch for what we do at Cradle!

A reminder that there is now *1 week* left until the MLSB deadline on October 1st! Send in your 🧪bio+🤖ML papers, for either 🇺🇸San Diego, 🇩🇰Copenhagen, or ✨both✨!

💥 We are *also* organizing Machine Learning for Structural Biology @ EurIPS, Copenhagen!! Topics include anything in the ML+bio intersection. Submit your ML+bio short papers! Authors can even present in both locations if they have people in both locations 🚀

🚀 So `tinyio` hit the front page of Hacker News. Now we're at 487 GitHub stars :D I've also just done a ✨v0.2 release✨. Now comes batteries-included with common operations (locks, yield-as-available, etc.) and with a major performance improvement. GitHub: github.com/patrick-kidg...

✨v0.1 release of typst_pyimage!✨ Do you: - write scientific papers in Typst (boo hiss LaTeX)? - have many matplotlib figures? Would you like the code for those images inlined directly into your Typst file, and autogenerated when you compile it?🔥 github.com/patrick-kidg...

✨Announcing: tinyio! A tiny barebones event loop library for Python. Born out of my frustration with asyncio... GitHub: github.com/patrick-kidg... It's nothing too fancy, just a little library that does one thing well. 🔥

✨ We are hiring to build out our automated wet lab! 🤖🦾🧪 jobs.ashbyhq.com/cradlebio/27...

✨Cradle is hiring protein+ML researchers!✨ We operate ML for lab-in-the-loop lead optimization across all industries (pharma, synbio, ...), modalities (antibodies, enzymes, ...), properties (binding, activity, ...) We're a scaleup and already relied upon by 4 of the top 20 big pharma. Apply here!

We added Boltz-2 to our protein design package! Under the hood this relies on a JAX translation, which, thanks to @jeremywohlwend.bsky.social and @gcorso.bsky.social ’s clean code, was fairly easy to write. We’ve been getting great results -- and we have yet to explore the most exciting new features

🚀 Announcing: ✨`patdb`✨! A fast, pretty, TUI/REPL debugger for Python. (Not a database!😄) Think stdlib pdb, but with... - Syntax highlighting - re-raised+grouped exceptions - robust to async/threading/multiprocessing - ... ! > pip install patdb GitHub: github.com/patrick-kidg... 1/3

🔥 Time for my first bioML blog post! This one is for all the folks getting into ML-for-protein-design. ✨ "Just know stuff, proteinML edition" kidger.site/thoughts/jus... This is intended as a curriculum-with-context, as a starting point for the field. 1/2

At CERN the next couple of days for a workshop. Send me a DM if you're around too 🚀

Oh this is pretty cool 😃 ESM-C protein language model in JAX+Equinox!

🚀 I just spotted that we passed a really cool milestone: Equinox is now used by over 1k projects on GitHub. *And* we actually also just passed 1k commits as well.🎉 (github.com/patrick-kidg...)

✨ We previously took 1st place on the Adaptyv protein binding competition. 🚀 In this update, we now take all of *top 12*! Just one of our entries into the competion was tested at the time. Our prize for winning was to have our other designs be tested... Post: www.cradle.bio/blog/adaptyv2 [1/2]

🌟 We have a proteinML PhD internship at Cradle! jobs.ashbyhq.com/cradlebio/d8... Come see what it's like to work at a frontier bioML lab. This is a unique opportunity to work across the entire stack: 🔬 Automated wet lab data; 🤖 Train your own ~1B parameter ML models; 📚 Publish end result! 🚀

🌟 We have a proteinML PhD internship at Cradle! jobs.ashbyhq.com/cradlebio/d8... Come see what it's like to work at a frontier bioML lab. This is a unique opportunity to work across the entire stack: 🔬 Automated wet lab data; 🤖 Train your own ~1B parameter ML models; 📚 Publish end result! 🚀

🚀 It's time for a new JAX ecosystem library! This time quite a small one: ESM2quinox. A #JAX + Equinox implementation of the ESM2 protein language model. GitHub: github.com/patrick-kidg... SciML is obviously my whole jam. My open source has largely focused on the differential equations ... [1/2]

✨We're hiring for bio roles at Cradle! You can expect to work on a huge variety of problems (antibodies, enzymes, peptides, ...) across all modalities (therapeutics, agtech, biosynthesis, ...), as at this point (post series B) we work with pretty much the whole industry. [1/2]

✨ I wrote a new blog post! 🤖 RealSemVer: or, how Semantic Versioning _really_ gets used. kidger.site/thoughts/rea...

In school, you probably learned that human cells have 46 chromosomes, which is 2 copies of 23 chromosomes, sometimes called 'diploid' or '2n'. But there are other 'ploidies' in your cells. To start with, 80+% of your cells have NO chromosomes: red blood cells or 'erythrocytes'...

FutureHouse is launching an independent postdoctoral fellowship program for exceptional researchers who want to apply our automated science tools to specific problems in biology and biochemistry, in collaboration with world-leading academic labs. 1/

🔥 How we won the Adaptyv Bio competition, designing a 1.21nM binder to EGFR using generative AI :) www.cradle.bio/blog/adaptyv... 🌟 This was a super fun project from four of us at Cradle Bio ! ✨

🎉 Okay folks it's that time of year! Who's at NeurIPS?? Come find me and the rest of the Cradle Bio crew 🧪 Always happy to chat sciML, protein design, open source, and everything in between 🌟

✨ wheeeeee we raised a series B AI-powered automated protein optimization: matches or exceeds human performance, works without human intervention. It's pretty cool :D (PS if you're seriously good at ML eng then we're hiring) www.cradle.bio/blog/series-b

*Building neural networks in Equinox* Third lab for the course, after JAX and Keras we see Equinox (from @patrickkidger.bsky.social) - including callable pytrees, stateful modules, and filtering. Stay tuned for part b with a text classification model. 😎 colab.research.google.com/drive/19NHkb...

Good software is an enabler for good science! 💥🧪 Inspired by the below post, I like to point people at libraries like github.com/patrick-kidg... as a template for what a modern Python library looks like: `pre-commit`, ruff, pyright, pyproject.toml, an open-source license, etc. 🤓

Now this is awesome! I love the way that ML, with its open-source-everything approach, is taking on biology.

We have an AI-designed antibodies challenge! 🔥 Nature: www.nature.com/articles/s41... Website: www.aintibody.org (Co-authored with approximately everyone, haha. 🌟) The challenge is primarily around CDR design, with the submitted sequences tested in vitro. 🧪 Come give it a go :)

Testing testing, 123. Let's find out whether this latest Twitter clone goes anywhere... :D