Lightnews — Scholar-powered news

Reposted by Cas

Valence Labs @valenceai.bsky.social · May 20

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 🧵

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Valence Labs @valenceai.bsky.social · Apr 17

(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...

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Cas @caswognum.nl · Mar 27

I’ll write up some more detailed thoughts and takeaways once I’m back in Montréal and have a minute!

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Cas @caswognum.nl · Mar 27

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! 😍

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Polaris @polarishub.io · Mar 21

🚀 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 👇

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Conscience @conscience-network.bsky.social · Mar 20

✨ 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

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Peter Škrinjar @peterskrinjar.bsky.social · Feb 24

In case you missed it!

Polaris @polarishub.io · Feb 24

Thanks to everyone who joined us last week! You can now watch the recording of the webinar: youtu.be/_ykP_tEVrOk

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Reposted by Cas

Janani Durairaj (Jay) @ninjani.bsky.social · Feb 20

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.

Polaris @polarishub.io · Feb 13

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...

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Polaris @polarishub.io · Feb 17

⚡ 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

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Cas @caswognum.nl · Feb 14

Volgens mij ga je hierin voorbij aan het doel om elkaar beter te begrijpen. De nadruk ligt daarmee op het woord, niet de intentie.

Ik ben oprecht benieuwd hoe je hier over denkt als journalist.

Zet mij in ieder geval aan het denken!

Cas @caswognum.nl · Feb 14

Verrijkend gesprek! Leuk!

Ik hoor een interessante tegenstelling: Enerzijds blijkt taal voor interpretatie vatbaar, maar anderszijds discussiëren jullie specifieke woordkeuze.

Taal doet er toe - zeker als journalist - maar ik vraag me hardop af of je woordkeuze zo niet té veel macht geeft…

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Polaris @polarishub.io · Feb 13

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...

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Cas @caswognum.nl · Feb 11

Endless views and impressive cloudscapes!

#photography #lions #kenya #maasaimara #simba

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Polaris @polarishub.io · Feb 10

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...

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Cas @caswognum.nl · Feb 8

Would be cool to see how OpenFold does on this new benchmark! 👀

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Cas @caswognum.nl · Feb 8

(And the science, of course!)

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Cas @caswognum.nl · Feb 8

Love the logo and name! 🎸

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Cas @caswognum.nl · Feb 8

And if you're curious, you can learn more about what we actually mean by "ML-ready" in our recent blog: polarishub.io/blog/reprodu...

Polaris

The benchmarking platform for drug discovery

polarishub.io

Cas @caswognum.nl · Feb 8

A few weeks back I got in touch with @ninjani.bsky.social about creating a "ML-ready" version of a PLINDER dataset. Excited to release a first attempt at this!

💬 Let us know how we did
discord.gg/uGCZB7PXmX

bsky.app/profile/dkoe...

David Ryan Koes @dkoes.compstruct.org · Dec 16

Agree with having all the data available, don’t agree with requiring extra steps to get “good” training set - should require extra steps to get all data (eg like you do with columns). I talked with too many ML researchers who were using molecular data uncritically this week: make default reasonable.

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Cas @caswognum.nl · Feb 8

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

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Cas @caswognum.nl · Feb 8

bsky.app/profile/pola...

Polaris @polarishub.io · Dec 5

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Peter Škrinjar @peterskrinjar.bsky.social · Feb 8

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)

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

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Cas @caswognum.nl · Feb 7

@polarishub.io has a benchmarking API which ensures you use the exact same split and metrics as everyone else. See the screenshot.

We're aiming to serve as a source of truth for machine learning in drug discovery. For context, see: polarishub.io/blog/reprodu...

Would love to hear your feedback!

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Cas @caswognum.nl · Feb 7

Interesting!

This would be a nice “baseline” to have for the associated Polaris benchmark. polarishub.io/benchmarks/b....

adme-fang-reg-v1

biogen

polarishub.io

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Cas @caswognum.nl · Feb 4

With the increased activity on the platform recently, things have been breaking in new ways (sorry Windows users!), but I love it!

It shows that people are actually using Polaris! Our team is fixing issues as soon as we can and it’s helping us improve the overall robustness. Keep ‘m coming! 🏗️

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