Cas
@caswognum.nl
Trying to teach machines (and myself) drug discovery at Valence Labs and Polaris.
www.caswognum.nl
🇳🇱🇨🇦
www.caswognum.nl
🇳🇱🇨🇦
Pinned
Cas
@caswognum.nl
· Nov 18
Polaris
The benchmarking platform for drug discovery
www.polarishub.io
Hey! 🦋
I work at Valence Labs, where I contribute most my time to Polaris. I spend my days thinking about how we can bring innovators and practitioners closer together to develop methods that matter in ML for drug discovery.
Learn more:
- www.polarishub.io
- www.nature.com/articles/s42...
I work at Valence Labs, where I contribute most my time to Polaris. I spend my days thinking about how we can bring innovators and practitioners closer together to develop methods that matter in ML for drug discovery.
Learn more:
- www.polarishub.io
- www.nature.com/articles/s42...
Reposted by Cas
1/ At Valence Labs, @recursionpharma.bsky.social's AI research engine, we’re focused on advancing drug discovery outcomes through cutting-edge computational methods
Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
May 20, 2025 at 3:55 PM
1/ At Valence Labs, @recursionpharma.bsky.social's AI research engine, we’re focused on advancing drug discovery outcomes through cutting-edge computational methods
Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
Reposted by Cas
(1/5) The Molecular Machine Learning Conference (MoML) is back @mila-quebec.bsky.social this June 18th.
Join researchers advancing machine learning, molecular modeling, and therapeutic design.
Tickets are free for students.
Register Today: portal.ml4dd.com/events/molec...
Join researchers advancing machine learning, molecular modeling, and therapeutic design.
Tickets are free for students.
Register Today: portal.ml4dd.com/events/molec...
April 17, 2025 at 1:20 PM
(1/5) The Molecular Machine Learning Conference (MoML) is back @mila-quebec.bsky.social this June 18th.
Join researchers advancing machine learning, molecular modeling, and therapeutic design.
Tickets are free for students.
Register Today: portal.ml4dd.com/events/molec...
Join researchers advancing machine learning, molecular modeling, and therapeutic design.
Tickets are free for students.
Register Today: portal.ml4dd.com/events/molec...
Had a great time at the Ascona 2025 conference on benchmarking in biology! Thanks to @markrobinsonca.bsky.social and all other organizers.
I’m grateful for the opportunity to present our @polarishub.io platform at the historic and beautiful Monte Verità (“Mount Truth”) venue.
Look at that view! 😍
I’m grateful for the opportunity to present our @polarishub.io platform at the historic and beautiful Monte Verità (“Mount Truth”) venue.
Look at that view! 😍
March 27, 2025 at 6:03 PM
Had a great time at the Ascona 2025 conference on benchmarking in biology! Thanks to @markrobinsonca.bsky.social and all other organizers.
I’m grateful for the opportunity to present our @polarishub.io platform at the historic and beautiful Monte Verità (“Mount Truth”) venue.
Look at that view! 😍
I’m grateful for the opportunity to present our @polarishub.io platform at the historic and beautiful Monte Verità (“Mount Truth”) venue.
Look at that view! 😍
Reposted by Cas
🚀 Antiviral Challenge Results! 🚀
After weeks of competition, and nearly 400 submissions, the antiviral challenge has concluded!
Thank you to all of our participants. Each submission came with a report — check out the full leaderboard and find more details 👇
After weeks of competition, and nearly 400 submissions, the antiviral challenge has concluded!
Thank you to all of our participants. Each submission came with a report — check out the full leaderboard and find more details 👇
March 21, 2025 at 4:24 PM
🚀 Antiviral Challenge Results! 🚀
After weeks of competition, and nearly 400 submissions, the antiviral challenge has concluded!
Thank you to all of our participants. Each submission came with a report — check out the full leaderboard and find more details 👇
After weeks of competition, and nearly 400 submissions, the antiviral challenge has concluded!
Thank you to all of our participants. Each submission came with a report — check out the full leaderboard and find more details 👇
Reposted by Cas
✨ Symposium session reveal ✨ AI-assisted Drug Discovery: Benchmarking the Field - Gustavo Stolovitzky and @caswognum.nl will explore how benchmarking can drive better, more reliable AI tools for drug discovery and biomedicine. Learn more and register here: conscience.ca/symposium2025
March 20, 2025 at 6:05 PM
✨ Symposium session reveal ✨ AI-assisted Drug Discovery: Benchmarking the Field - Gustavo Stolovitzky and @caswognum.nl will explore how benchmarking can drive better, more reliable AI tools for drug discovery and biomedicine. Learn more and register here: conscience.ca/symposium2025
Reposted by Cas
In case you missed it!
Thanks to everyone who joined us last week! You can now watch the recording of the webinar: youtu.be/_ykP_tEVrOk
February 24, 2025 at 4:42 PM
In case you missed it!
Reposted by Cas
Join us tomorrow to hear @peterskrinjar.bsky.social talk about 🌹 Runs N' Poses 🌹! Curious to hear your thoughts on how to keep up with benchmarking in this field.
We’re hosting @peterskrinjar.bsky.social for a webinar to discuss his latest paper “Have protein co-folding methods moved beyond memorization?”!
Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi...
Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...
Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi...
Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...
February 20, 2025 at 12:34 PM
Join us tomorrow to hear @peterskrinjar.bsky.social talk about 🌹 Runs N' Poses 🌹! Curious to hear your thoughts on how to keep up with benchmarking in this field.
Reposted by Cas
⚡ The intermediate leaderboard for the antiviral challenge is now live!
👀 See how you placed: antiviral.polarishub.io
The challenge officially ends on March 10th, but there's one last leaderboard update before the final results.
Submit before midnight on Feb 26th! polarishub.io/competitions
👀 See how you placed: antiviral.polarishub.io
The challenge officially ends on March 10th, but there's one last leaderboard update before the final results.
Submit before midnight on Feb 26th! polarishub.io/competitions
February 17, 2025 at 6:40 PM
⚡ The intermediate leaderboard for the antiviral challenge is now live!
👀 See how you placed: antiviral.polarishub.io
The challenge officially ends on March 10th, but there's one last leaderboard update before the final results.
Submit before midnight on Feb 26th! polarishub.io/competitions
👀 See how you placed: antiviral.polarishub.io
The challenge officially ends on March 10th, but there's one last leaderboard update before the final results.
Submit before midnight on Feb 26th! polarishub.io/competitions
Reposted by Cas
We’re hosting @peterskrinjar.bsky.social for a webinar to discuss his latest paper “Have protein co-folding methods moved beyond memorization?”!
Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi...
Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...
Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi...
Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...
February 13, 2025 at 3:37 PM
We’re hosting @peterskrinjar.bsky.social for a webinar to discuss his latest paper “Have protein co-folding methods moved beyond memorization?”!
Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi...
Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...
Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi...
Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...
February 11, 2025 at 1:57 PM
Reposted by Cas
We’re extremely excited to host Runs N’ Poses on Polaris!
The authors show how current co-folding methods struggle to generalize beyond ligand poses in their training data.
Explore the benchmark: polarishub.io/benchmarks/p...
Explore the dataset: polarishub.io/datasets/pli...
The authors show how current co-folding methods struggle to generalize beyond ligand poses in their training data.
Explore the benchmark: polarishub.io/benchmarks/p...
Explore the dataset: polarishub.io/datasets/pli...
February 10, 2025 at 1:43 PM
We’re extremely excited to host Runs N’ Poses on Polaris!
The authors show how current co-folding methods struggle to generalize beyond ligand poses in their training data.
Explore the benchmark: polarishub.io/benchmarks/p...
Explore the dataset: polarishub.io/datasets/pli...
The authors show how current co-folding methods struggle to generalize beyond ligand poses in their training data.
Explore the benchmark: polarishub.io/benchmarks/p...
Explore the dataset: polarishub.io/datasets/pli...
New leaderboard on @polarishub.io for Runs 'N Poses! 🎸
Anyone has any protein-ligand co-folding methods laying around they would like to put to the test?
polarishub.io/benchmarks/p...
Great work @peterskrinjar.bsky.social @jeeberhardt.bsky.social @torstenschwede.bsky.social @ninjani.bsky.social
Anyone has any protein-ligand co-folding methods laying around they would like to put to the test?
polarishub.io/benchmarks/p...
Great work @peterskrinjar.bsky.social @jeeberhardt.bsky.social @torstenschwede.bsky.social @ninjani.bsky.social
February 8, 2025 at 1:35 PM
New leaderboard on @polarishub.io for Runs 'N Poses! 🎸
Anyone has any protein-ligand co-folding methods laying around they would like to put to the test?
polarishub.io/benchmarks/p...
Great work @peterskrinjar.bsky.social @jeeberhardt.bsky.social @torstenschwede.bsky.social @ninjani.bsky.social
Anyone has any protein-ligand co-folding methods laying around they would like to put to the test?
polarishub.io/benchmarks/p...
Great work @peterskrinjar.bsky.social @jeeberhardt.bsky.social @torstenschwede.bsky.social @ninjani.bsky.social
Reposted by Cas
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:02 AM
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Big milestone for @polarishub.io. We merged our first external contribution, thanks to @fastprop.bsky.social! 🎉
github.com/polaris-hub/...
#opensource #benchmarking #ml #drugdiscovery
github.com/polaris-hub/...
#opensource #benchmarking #ml #drugdiscovery
`Subset.as_dataframe()` hides targets instead of raising an error by JacksonBurns · Pull Request #258 · polaris-hub/polaris
Changelogs
Subset.as_dataframe() would raise an error when called on a test set (which hides its targets), this PR allows method to work, just doesn't return targest
Checklist:
Was this PR...
github.com
February 4, 2025 at 5:37 PM
Big milestone for @polarishub.io. We merged our first external contribution, thanks to @fastprop.bsky.social! 🎉
github.com/polaris-hub/...
#opensource #benchmarking #ml #drugdiscovery
github.com/polaris-hub/...
#opensource #benchmarking #ml #drugdiscovery
Reposted by Cas
🚨 Extension Alert: The intermediate leaderboard submission deadline for the antiviral challenge has been extended to midnight on February 7th!
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
January 31, 2025 at 2:04 PM
🚨 Extension Alert: The intermediate leaderboard submission deadline for the antiviral challenge has been extended to midnight on February 7th!
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
With @polarishub.io we early on decided to purposefully restrict the flexibility of our datasets and benchmarks.
We understand that this can be frustrating at times, but we believe it’s an important step to improve reproducibility.
Our team is here to help if you need support! Reach out on Github.
We understand that this can be frustrating at times, but we believe it’s an important step to improve reproducibility.
Our team is here to help if you need support! Reach out on Github.
You’ve heard us talk about our mission to be the source of truth for the ML community in drug discovery. But what does that really mean, and how does it shape the way Polaris is built?
In the latest blog, we break down the key design choices that make this possible: polarishub.io/blog/reprodu...
In the latest blog, we break down the key design choices that make this possible: polarishub.io/blog/reprodu...
January 30, 2025 at 8:14 PM
With @polarishub.io we early on decided to purposefully restrict the flexibility of our datasets and benchmarks.
We understand that this can be frustrating at times, but we believe it’s an important step to improve reproducibility.
Our team is here to help if you need support! Reach out on Github.
We understand that this can be frustrating at times, but we believe it’s an important step to improve reproducibility.
Our team is here to help if you need support! Reach out on Github.
Reposted by Cas
💡Have questions about the data behind the antiviral challenge?💡
This week, @asapdiscovery.bsky.social and @omsf.io are hosting 3 virtual office hour sessions with the experimentalists behind the data!
RSVP here: docs.google.com/forms/d/e/1F...
This week, @asapdiscovery.bsky.social and @omsf.io are hosting 3 virtual office hour sessions with the experimentalists behind the data!
RSVP here: docs.google.com/forms/d/e/1F...
January 27, 2025 at 3:58 PM
💡Have questions about the data behind the antiviral challenge?💡
This week, @asapdiscovery.bsky.social and @omsf.io are hosting 3 virtual office hour sessions with the experimentalists behind the data!
RSVP here: docs.google.com/forms/d/e/1F...
This week, @asapdiscovery.bsky.social and @omsf.io are hosting 3 virtual office hour sessions with the experimentalists behind the data!
RSVP here: docs.google.com/forms/d/e/1F...
Only a few days left to submit your predictions for the first, intermediate leaderboard.
We’ve got an incredibly passionate team on standby to help solve any issues you may run into and we’d love to hear your feedback.
🧑💻 Github: github.com/polaris-hub/...
💬 Discord: discord.gg/vBFd8p6H7u
We’ve got an incredibly passionate team on standby to help solve any issues you may run into and we’d love to hear your feedback.
🧑💻 Github: github.com/polaris-hub/...
💬 Discord: discord.gg/vBFd8p6H7u
January 28, 2025 at 12:20 AM
Only a few days left to submit your predictions for the first, intermediate leaderboard.
We’ve got an incredibly passionate team on standby to help solve any issues you may run into and we’d love to hear your feedback.
🧑💻 Github: github.com/polaris-hub/...
💬 Discord: discord.gg/vBFd8p6H7u
We’ve got an incredibly passionate team on standby to help solve any issues you may run into and we’d love to hear your feedback.
🧑💻 Github: github.com/polaris-hub/...
💬 Discord: discord.gg/vBFd8p6H7u
If you have been waiting for the right time to start working on the ASAP Discovery challenge, this is it! 🏆
For all results submitted up until January 31st, we will publish an intermediate leaderboard. Get your first set of results in now and see how you stack up against your peers.
For all results submitted up until January 31st, we will publish an intermediate leaderboard. Get your first set of results in now and see how you stack up against your peers.
📣 We heard your feedback! We’ll be putting all results submitted by Jan 31st on an intermediate leaderboard so you can see how you rank across other participants in the antiviral challenge.
Ready to put your predictions to the test?
📨 Submit your results today: polarishub.io/competitions
Ready to put your predictions to the test?
📨 Submit your results today: polarishub.io/competitions
January 23, 2025 at 4:36 PM
If you have been waiting for the right time to start working on the ASAP Discovery challenge, this is it! 🏆
For all results submitted up until January 31st, we will publish an intermediate leaderboard. Get your first set of results in now and see how you stack up against your peers.
For all results submitted up until January 31st, we will publish an intermediate leaderboard. Get your first set of results in now and see how you stack up against your peers.
The @polarishub.io discord is feeling very lively right now. I love learning with and from all of you!💡
If you haven't yet, join us and put your methods to the test to learn what is working and what's not in ADMET, potency and pose prediction.
Get started in a few lines of code. Great video by Lu!
If you haven't yet, join us and put your methods to the test to learn what is working and what's not in ADMET, potency and pose prediction.
Get started in a few lines of code. Great video by Lu!
It only takes a few lines of code to get started with the @asapdiscovery.bsky.social x @omsf.io antiviral challenge!
In this short tutorial, we’ll show you how easy it is to login, load the challenge data, train a simple baseline model, and submit your predictions 🧵
youtu.be/KBZJFA_arAg
In this short tutorial, we’ll show you how easy it is to login, load the challenge data, train a simple baseline model, and submit your predictions 🧵
youtu.be/KBZJFA_arAg
Tutorial: Getting Started with the Antiviral Challenge
YouTube video by PolarisHQ
youtu.be
January 21, 2025 at 3:48 PM
The @polarishub.io discord is feeling very lively right now. I love learning with and from all of you!💡
If you haven't yet, join us and put your methods to the test to learn what is working and what's not in ADMET, potency and pose prediction.
Get started in a few lines of code. Great video by Lu!
If you haven't yet, join us and put your methods to the test to learn what is working and what's not in ADMET, potency and pose prediction.
Get started in a few lines of code. Great video by Lu!
Reposted by Cas
Incredibly excited to see how well ADMET, affinity, and pose prediction models *actually* perform in the ASAP x OpenADMET x PolarisHub blind challenge:
polarishub.io/competitions
polarishub.io/competitions
Polaris
The benchmarking platform for drug discovery
polarishub.io
January 17, 2025 at 6:25 PM
Incredibly excited to see how well ADMET, affinity, and pose prediction models *actually* perform in the ASAP x OpenADMET x PolarisHub blind challenge:
polarishub.io/competitions
polarishub.io/competitions
Reposted by Cas
Working on predictive models for drug discovery? Here's your chance to see how well your models actually work!
Together with @polarishub.io and OpenADMET, we've launched a blind prospective challenge to see how well predictive models for drug discovery can actually predict real drug discovery data!
Together with @polarishub.io and OpenADMET, we've launched a blind prospective challenge to see how well predictive models for drug discovery can actually predict real drug discovery data!
🏁 The antiviral challenge is live! 🏁
Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑💻
Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑💻
January 15, 2025 at 3:44 PM
Working on predictive models for drug discovery? Here's your chance to see how well your models actually work!
Together with @polarishub.io and OpenADMET, we've launched a blind prospective challenge to see how well predictive models for drug discovery can actually predict real drug discovery data!
Together with @polarishub.io and OpenADMET, we've launched a blind prospective challenge to see how well predictive models for drug discovery can actually predict real drug discovery data!
The @asapdiscovery.bsky.social x OpenADMET (@omsf.io) blind challenge is live! 🚀
You're free to use any publicly available training data, but the challenge provides 770 ligand poses, 1031 potency datapoints and 434 ADMET datapoints as a consistently generated training set.
Come learn with us! 🏆
You're free to use any publicly available training data, but the challenge provides 770 ligand poses, 1031 potency datapoints and 434 ADMET datapoints as a consistently generated training set.
Come learn with us! 🏆
🏁 The antiviral challenge is live! 🏁
Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑💻
Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑💻
January 14, 2025 at 3:27 PM
The @asapdiscovery.bsky.social x OpenADMET (@omsf.io) blind challenge is live! 🚀
You're free to use any publicly available training data, but the challenge provides 770 ligand poses, 1031 potency datapoints and 434 ADMET datapoints as a consistently generated training set.
Come learn with us! 🏆
You're free to use any publicly available training data, but the challenge provides 770 ligand poses, 1031 potency datapoints and 434 ADMET datapoints as a consistently generated training set.
Come learn with us! 🏆
Reposted by Cas
🎥 At NeurIPS, we had the opportunity to chat with the authors of several dataset and benchmarking papers that are relevant to machine learning for drug discovery. First up—a quick interview with the team behind WelQrate! 🧵
youtu.be/pbatKLphJAE
youtu.be/pbatKLphJAE
NeurIPS 2024 Series - A Chat with the WelQrate Team
YouTube video by PolarisHQ
youtu.be
January 10, 2025 at 5:53 PM
🎥 At NeurIPS, we had the opportunity to chat with the authors of several dataset and benchmarking papers that are relevant to machine learning for drug discovery. First up—a quick interview with the team behind WelQrate! 🧵
youtu.be/pbatKLphJAE
youtu.be/pbatKLphJAE
Reposted by Cas
🎉 Zarr-Python 3 is here! 🎉
- Full support for Zarr v3 spec
- Chunk-sharding for more efficient data storage
- Major performance boosts with async I/O & parallel compression
💻 pip install --upgrade zarr
💻 conda install --channel conda-forge zarr
Blog post: https://buff.ly/3C3OwYw
- Full support for Zarr v3 spec
- Chunk-sharding for more efficient data storage
- Major performance boosts with async I/O & parallel compression
💻 pip install --upgrade zarr
💻 conda install --channel conda-forge zarr
Blog post: https://buff.ly/3C3OwYw
January 9, 2025 at 4:28 PM
🎉 Zarr-Python 3 is here! 🎉
- Full support for Zarr v3 spec
- Chunk-sharding for more efficient data storage
- Major performance boosts with async I/O & parallel compression
💻 pip install --upgrade zarr
💻 conda install --channel conda-forge zarr
Blog post: https://buff.ly/3C3OwYw
- Full support for Zarr v3 spec
- Chunk-sharding for more efficient data storage
- Major performance boosts with async I/O & parallel compression
💻 pip install --upgrade zarr
💻 conda install --channel conda-forge zarr
Blog post: https://buff.ly/3C3OwYw