Patrick Kidger
@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
🧪 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
🚀 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"
▶️ 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
October 7, 2025 at 1:26 PM
🚀 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"
▶️ 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✨!
Send in your 🧪bio+🤖ML papers, for either
🇺🇸San Diego,
🇩🇰Copenhagen, or
✨both✨!
September 25, 2025 at 3:03 PM
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✨!
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 🚀
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 🚀
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💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
September 12, 2025 at 1:44 PM
💥 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 🚀
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...
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...
August 4, 2025 at 10:59 AM
🚀 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...
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...
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
August 1, 2025 at 12:47 PM
✨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...
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. 🔥
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
July 22, 2025 at 11:35 AM
✨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. 🔥
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. 🔥
✨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 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
June 18, 2025 at 1:55 PM
✨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 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!
Reposted by Patrick Kidger
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
June 12, 2025 at 8:52 PM
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
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
June 4, 2025 at 1:13 PM
🚀 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 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
✨ "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
May 20, 2025 at 1:42 PM
🔥 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
✨ "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 🚀
May 19, 2025 at 10:20 AM
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!
Want to try ESMC but don't want to switch from #JAX to pytorch?
Here’s a super barebones translation to @patrickkidger.bsky.social's excellent equinox: github.com/escalante-bi...
Here’s a super barebones translation to @patrickkidger.bsky.social's excellent equinox: github.com/escalante-bi...
GitHub - escalante-bio/esmj: jax translation of esmc
jax translation of esmc. Contribute to escalante-bio/esmj development by creating an account on GitHub.
github.com
May 8, 2025 at 8:03 PM
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...)
*And* we actually also just passed 1k commits as well.🎉
(github.com/patrick-kidg...)
May 3, 2025 at 8:21 AM
🚀 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...)
*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]
🚀 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]
March 31, 2025 at 11:03 AM
✨ 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]
🚀 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]
Reposted by Patrick Kidger
🌟 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/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!
🚀
Software Engineering/Machine Learning Intern (f/m/*)
Machine Learning Eningeer - Internship
jobs.ashbyhq.com
February 26, 2025 at 9:10 PM
🌟 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/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!
🚀
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!
🚀
Software Engineering/Machine Learning Intern (f/m/*)
Machine Learning Eningeer - Internship
jobs.ashbyhq.com
February 26, 2025 at 9:10 PM
🌟 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/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]
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
February 11, 2025 at 2:40 PM
🚀 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]
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]
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]
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...
jobs.ashbyhq.com
January 21, 2025 at 10:33 AM
✨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]
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...
🤖 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
January 15, 2025 at 1:32 PM
✨ I wrote a new blog post!
🤖 RealSemVer: or, how Semantic Versioning _really_ gets used.
kidger.site/thoughts/rea...
🤖 RealSemVer: or, how Semantic Versioning _really_ gets used.
kidger.site/thoughts/rea...
Reposted by Patrick Kidger
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'...
But there are other 'ploidies' in your cells.
To start with, 80+% of your cells have NO chromosomes: red blood cells or 'erythrocytes'...
December 30, 2024 at 1:52 PM
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'...
But there are other 'ploidies' in your cells.
To start with, 80+% of your cells have NO chromosomes: red blood cells or 'erythrocytes'...
Reposted by Patrick Kidger
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/
December 19, 2024 at 3:29 PM
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 ! ✨
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
www.cradle.bio
December 11, 2024 at 4:09 PM
🔥 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 ! ✨
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 🌟
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 🌟
December 10, 2024 at 12:33 AM
🎉 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 🌟
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
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
www.cradle.bio
November 26, 2024 at 8:50 AM
✨ 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
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