Lightnews — Scholar-powered news

Patrick Kidger @patrickkidger.bsky.social · 1d

🚀 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

www.youtube.com

4 8

Patrick Kidger @patrickkidger.bsky.social · 13d

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

1

Patrick Kidger @patrickkidger.bsky.social · 26d

💥 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 · 26d

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💫

2 17

Patrick Kidger @patrickkidger.bsky.social · Aug 4

🚀 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...

1 7

Patrick Kidger @patrickkidger.bsky.social · Aug 1

✨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

1 14

Patrick Kidger @patrickkidger.bsky.social · Jul 22

This would run a tick of our event loop each time the asyncio loop gives control to it.

2/2

Patrick Kidger @patrickkidger.bsky.social · Jul 22

Thanks! I was also particularly happy landing on the list syntax.

Indeed it doesn't work with asyncio atm, but... I reckon doing so might just be as simple as adding an `await asyncio.sleep(0)` inside our `run` function (right before it calls `self._step`).

1/2

1

Patrick Kidger @patrickkidger.bsky.social · Jul 22

Also I really needer error propagation to/from threads running sync code, which trio doesn't support. I could have added it with a custom to_thread.run_sync wrapper but it was another reason to try my hand at my own minimal thing.

2

Patrick Kidger @patrickkidger.bsky.social · Jul 22

Yup, trio is excellent. I even recommend it in the README! 😄 For anything big and serious that is definitely the way to go.

This is one part hobby project to learn something, and one part building the simplest possible thing to support the use case I had in mind.

1/2

2 2

Patrick Kidger @patrickkidger.bsky.social · Jul 22

✨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

3 3 19

Patrick Kidger @patrickkidger.bsky.social · Jul 10

✨
We are hiring to build out our automated wet lab!
🤖🦾🧪

jobs.ashbyhq.com/cradlebio/27...

Integrations Engineer - Lab Automation

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...

jobs.ashbyhq.com

2

Patrick Kidger @patrickkidger.bsky.social · Jun 19

Whoops, wrong link!

Fixed: jobs.ashbyhq.com/cradlebio/49...

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

This is an exceptional opportunity to join a very early stage company reimagining protein design through a computational- and AI-first approach. If you’re an ML Researcher with experience in the field...

jobs.ashbyhq.com

1

Patrick Kidger @patrickkidger.bsky.social · Jun 18

✨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!

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.

jobs.ashbyhq.com

1 6 10

Reposted by Patrick Kidger

Nick Boyd @nboyd.bsky.social · Jun 12

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

1 5 21

Patrick Kidger @patrickkidger.bsky.social · Jun 4

...like `pdb`, but with a snappier interface, fewer commands overall, with a focus on a clean REPL/TUI experience to navigate the stack.

Now used by me... and adopted by a host of my coworkers at Cradle! 3/3

Patrick Kidger @patrickkidger.bsky.social · Jun 4

This library brought to you originally by my need to debug re-raised exceptions in some of the libraries I'm using. Then in my usual fashion I kept adding features, and now we have a whole library 😄

If like me your debugging experience has been a lot of `pdb`, then this library is for you... 2/3

1

Patrick Kidger @patrickkidger.bsky.social · Jun 4

🚀 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.

1 1 6

Patrick Kidger @patrickkidger.bsky.social · May 23

Me please! :) I work on bioML. Google scholar mostly reflecting past work in broader sciML:

scholar.google.co.uk/citations?us...

scholar.google.co.uk

1 1

Patrick Kidger @patrickkidger.bsky.social · May 22

Agreed! I have no idea how that works. Is it a thing I submit to or a thing they pick up?

1

Patrick Kidger @patrickkidger.bsky.social · May 21

Hehe! I originally intended to include the rest of bioML and was then like 'this post is becoming way too long' 😄

1

Patrick Kidger @patrickkidger.bsky.social · May 20

A huge thanks to Owl, Johanna Haffner, and Jonathan Ziegler for their feedback on the article! I think we ended up with something great. (If a little intimidating.)

Also as timing would have it, also check out @ncfrey.bsky.social's post from yesterday!

ncfrey.substack.com/p/getting-st...

2/2

x.com

1 2

Patrick Kidger @patrickkidger.bsky.social · May 20

🔥 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.

1 3 20

Patrick Kidger @patrickkidger.bsky.social · May 19

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

7

Patrick Kidger @patrickkidger.bsky.social · May 9

And merged! 😃

1

Patrick Kidger @patrickkidger.bsky.social · May 9

Shall we add this to the Eqx ecosystem page? I really like it.

docs.kidger.site/equinox/awes...

Awesome list - Equinox

The documentation for the Equinox software library.

docs.kidger.site

1 1