You: please act normal, you need these people to like you Me: ok! People: hi Me: there is a parasite on salmon called Henneguya zschokkei which started as a jellyfish cancer before *budding off into its own species*.

parafilm is cool dot com@parafilmm.bsky.social · 3mo ago

You: please act normal, you need these people to like you Me: ok! People: hi Me: Parafilm is a semi-transparent, flexible film composed of a blend of waxes and polyolefins. It is a non-toxic, tasteless, odorless, and self-sealing thermoplastic, which can be stretched up to 200%

Alright chaps, I am in Boston for PEGS, here to chat all things AI + antibody engineering. Send me a message if you're around! 🧬 (PS I'm hiring! Pharma x AI startup, come make drugs with us.)

🚀 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!

Automated ML-guided lead optimization: surpassing human-level performance at protein engineering

YouTube video by Patrick Kidger

youtube.com

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✨!

MLSB (in San Diego + Copenhagen)@workshopmlsb.bsky.social · 11mo ago

🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE. Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.

💥 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 🚀

MLSB (in San Diego + Copenhagen)@workshopmlsb.bsky.social · 11mo ago

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉 Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

🚀 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...

GitHub - patrick-kidger/tinyio: Ever used asyncio and wished you hadn't? A tiny (~300 lines) event loop for Python.

Ever used asyncio and wished you hadn't? A tiny (~300 lines) event loop for Python. - patrick-kidger/tinyio

github.com

Patrick Kidger@patrickkidger.bsky.social · last yr.

✨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. 🔥

✨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...

GitHub - patrick-kidger/typst_pyimage: Typst extension, adding support for generating figures using inline Python code

Typst extension, adding support for generating figures using inline Python code - patrick-kidger/typst_pyimage

github.com

✨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. 🔥

GitHub - patrick-kidger/tinyio: Ever used asyncio and wished you hadn't? A tiny (~200 lines) event loop for Python.

Ever used asyncio and wished you hadn't? A tiny (~200 lines) event loop for Python. - patrick-kidger/tinyio

github.com

✨ 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!

🚀 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]

Cradle – Optimizing Cetuximab

News, updates, tutorials, and more from the makers of Cradle

cradle.bio

Patrick Kidger@patrickkidger.bsky.social · 2y ago

🔥 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 ! ✨

🌟 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]

GitHub - patrick-kidger/esm2quinox: An implementation of ESM2 in Equinox+JAX

An implementation of ESM2 in Equinox+JAX. Contribute to patrick-kidger/esm2quinox development by creating an account on GitHub.

github.com

✨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...

Real Semantic Versioning

Semantic version (SemVer) is possibly the most widely used software versioning scheme. We all know how SemVer works: MAJOR.MINOR.PATCH. The first number is for backward-incompatible changes, the middl...

kidger.site

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 ! ✨

Cradle – 8x improvement in EGFR binding affinity: winning the Adaptyv Bio protein design competition

News, updates, tutorials, and more from the makers of Cradle

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

Cradle – Cradle raises $73M Series B to Put AI-Powered Protein Engineering in Every Lab

News, updates, tutorials, and more from the makers of Cradle

cradle.bio

*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. 🤓

GitHub - patrick-kidger/equinox: Elegant easy-to-use neural networks + scientific computing in JAX. https://docs.kidger.site/equinox/

Elegant easy-to-use neural networks + scientific computing in JAX. https://docs.kidger.site/equinox/ - patrick-kidger/equinox

github.com

Ashley Ringer McDonald@aringermcdonald.bsky.social · 2y ago

If you want to help your students move from just writing code and scripts to actually developing scientific software that is useable and maintainable in the long-term, check out our latest paper in JCE. pubs.acs.org/doi/10.1021/...

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

Gabriele Corso@gcorso.bsky.social · 2y ago

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!