iiinova — where your digital self keeps evolving

Patrick Kidger @patrickkidger.bsky.social · 15/05/2026

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*.

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Patrick Kidger @patrickkidger.bsky.social · 11/05/2026

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.)

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Patrick Kidger @patrickkidger.bsky.social · 07/10/2025

🚀 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!

youtube.com

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

YouTube video by Patrick Kidger

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Patrick Kidger @patrickkidger.bsky.social · 25/09/2025

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✨!

Machine Learning in Structural Biology

Join leading researchers at the intersection of machine learning and structural biology and explore cutting-edge advances in predictive modelling and design of biological macromolecules.

US, December 7, 2025, Close to San Diego Convention Center
EU, December 6/7, 2025, Bella Center, Copenhagen

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Patrick Kidger @patrickkidger.bsky.social · 12/09/2025

💥 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 🚀

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Patrick Kidger @patrickkidger.bsky.social · 04/08/2025

🚀 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.com

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

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Patrick Kidger @patrickkidger.bsky.social · 01/08/2025

✨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.com

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

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Patrick Kidger @patrickkidger.bsky.social · 22/07/2025

✨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.com

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

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Patrick Kidger @patrickkidger.bsky.social · 18/06/2025

✨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!

jobs.ashbyhq.com

Machine Learning Researcher in Protein Design (f/m/*)

Join a scaleup researching and operating ML-guided lead optimization of proteins. This means developing a combination of protein language models, and multi-property prediction and generation.

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Patrick Kidger @patrickkidger.bsky.social · 04/06/2025

🚀 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

A snapshot of the top of the GitHub README, describing its features.

A snapshot of the debugger's interface, showing an error and a view of the stack.

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Patrick Kidger @patrickkidger.bsky.social · 20/05/2025

🔥 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

A screenshot of the start of the blog post. Entirely text.

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Patrick Kidger @patrickkidger.bsky.social · 19/05/2025

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

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Patrick Kidger @patrickkidger.bsky.social · 08/05/2025

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

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Patrick Kidger @patrickkidger.bsky.social · 03/05/2025

🚀 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...)

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Patrick Kidger @patrickkidger.bsky.social · 31/03/2025

✨ 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.bio

Cradle – Optimizing Cetuximab

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

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Reposted by Patrick Kidger

Patrick Kidger @patrickkidger.bsky.social · 26/02/2025

🌟 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! 🚀

jobs.ashbyhq.com

Software Engineering/Machine Learning Intern (f/m/*)

Machine Learning Eningeer - Internship

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Patrick Kidger @patrickkidger.bsky.social · 26/02/2025

jobs.ashbyhq.com

Software Engineering/Machine Learning Intern (f/m/*)

Machine Learning Eningeer - Internship

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Patrick Kidger @patrickkidger.bsky.social · 11/02/2025

🚀 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.com

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.

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Patrick Kidger @patrickkidger.bsky.social · 21/01/2025

✨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]

jobs.ashbyhq.com

Bioinformatician - Protein Science

THIS IS CRADLE Proteins are the molecular machines of life, used for many therapeutic, diagnostic, chemical, agricultural and food applications. Designing and optimizing proteins takes a lot of exper...

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Reposted by Patrick Kidger

c0nc0rdance @c0nc0rdance.bsky.social · 30/12/2024

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'...

A diagram showing what ploidy states look like
Taken from Donne et al (2020) "Polyploidy in liver development, homeostasis and disease" Nature Reviews Gastroenterology & Hepatology

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Reposted by Patrick Kidger

Sam Rodriques @sgrodriques.bsky.social · 19/12/2024

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/

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Patrick Kidger @patrickkidger.bsky.social · 11/12/2024

🔥 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.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

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Patrick Kidger @patrickkidger.bsky.social · 10/12/2024

🎉 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 🌟

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Patrick Kidger @patrickkidger.bsky.social · 26/11/2024

✨ 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.bio

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

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Reposted by Patrick Kidger

Simone Scardapane @sscardapane.bsky.social · 22/11/2024

*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...

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Patrick Kidger @patrickkidger.bsky.social · 18/11/2024

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.com

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

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Patrick Kidger @patrickkidger.bsky.social · 17/11/2024

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

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Patrick Kidger @patrickkidger.bsky.social · 13/11/2024

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 :)

nature.com

AIntibody: an experimentally validated in silico antibody discovery design challenge - Nature Biotechnology

Nature Biotechnology - AIntibody: an experimentally validated in silico antibody discovery design challenge

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Patrick Kidger @patrickkidger.bsky.social · 17/10/2023

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

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