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patrickkidger.bsky.social
I do SciML + open source! 🧪 ML+proteins @ http://Cradle.bio 📚 Neural ODEs: http://arxiv.org/abs/2202.02435 🤖 JAX ecosystem: http://github.com/patrick-kidger 🧑‍💻 Prev. Google, Oxford 📍 Zürich, Switzerland
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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

submitted 4 days ago • 1 comment

🚀 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

submitted 12 days ago • 1 comment

🔥 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

submitted 27 days ago • 1 comment

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

submitted 28 days ago • 0 comments

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

submitted 39 days ago • 0 comments

🚀 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...)

submitted 44 days ago • 1 comment

✨ 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]

submitted 77 days ago • 1 comment

🌟 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! 🚀

submitted 110 days ago • 0 comments

🌟 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! 🚀

submitted 110 days ago • 0 comments

🚀 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]

submitted 125 days ago • 2 comments

✨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]

submitted 146 days ago • 1 comment

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

submitted 152 days ago • 0 comments

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'...

submitted 168 days ago • 9 comments

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/

submitted 179 days ago • 1 comment

🔥 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 ! ✨

submitted 187 days ago • 0 comments

🎉 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 🌟

submitted 189 days ago • 0 comments

✨ 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

submitted 202 days ago • 2 comments

*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...

submitted 206 days ago • 0 comments