Jose Jimenez-Luna
@jjimenezluna.bsky.social
📤 1274
📥 564
📝 59
Senior researcher
@msftresearch.bsky.social
- views my own | ∇⌬ | De sevillanas manners 💃
pinned post!
BioEmu is now on
@science.org
! The revised version includes an upgraded model and makes a lot of MD simulation data internally generated at MSR available to the public. This took a lot of firepower from us in the last two years.
www.science.org/doi/10.1126/...
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Scalable emulation of protein equilibrium ensembles with generative deep learning
Following the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu, a deep learning system that...
https://www.science.org/doi/10.1126/science.adv9817
3 months ago
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Want to join the BioEmu team at MSR AI for Science? We have multiple intern (
jobs.careers.microsoft.com/global/en/jo...
) and one fixed-term postdoc (
jobs.careers.microsoft.com/global/en/jo...
positions available! Please share with potential candidates :)
3 days ago
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We have multiple senior scientist / engineer positions available across several geos in MSR AI for Science. Ping me or any of my colleagues if you have any questions!
www.microsoft.com/en-us/resear...
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Microsoft Research AI for Science - Microsoft Research
“Over the coming decade, deep learning looks set to have a transformational impact on the natural sciences. The consequences are potentially far-reaching and could dramatically improve our ability to ...
https://www.microsoft.com/en-us/research/lab/microsoft-research-ai-for-science/opportunities/
23 days ago
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well you don't hit the cover of a journal like this often
about 1 month ago
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"Solar panels are useless in Britain"
about 2 months ago
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Jose Jimenez-Luna
Tian Xie
about 2 months ago
Want to join our efforts
@msftresearch.bsky.social
AI for Science to push the frontier of AI for materials? We are the team behind MatterGen & MatterSim and we have 2 job openings! Each can be in Amsterdam, NL, Berlin, DE, or Cambridge, UK.
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Search Jobs | Microsoft Careers
https://jobs.careers.microsoft.com/global/en/job/1850507/Senior-Researcher-in-Materials---AI-for-Science
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To whomever decided to include this track into the new Tony Hawk's 3+4 remake... I salute you.
open.spotify.com/track/4GPne3...
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Precious Stones
Mastodon · Emperor of Sand · Song · 2017
https://open.spotify.com/track/4GPne3vf5okCDszbmeCUZz?si=hT4AtVIBTOeSb4SjZmovZQ&context=spotify%3Aplaylist%3A37i9dQZF1DWU4xkATYcbh7
2 months ago
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Summer's behaving beautifully 😍
3 months ago
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reposted by
Jose Jimenez-Luna
Microsoft Research
3 months ago
Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale.
www.science.org/doi/10.1126/...
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reposted by
Jose Jimenez-Luna
Frank Noe
3 months ago
BioEmu now published in
@science.org
!! What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
add a skeleton here at some point
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BioEmu is now on
@science.org
! The revised version includes an upgraded model and makes a lot of MD simulation data internally generated at MSR available to the public. This took a lot of firepower from us in the last two years.
www.science.org/doi/10.1126/...
loading . . .
Scalable emulation of protein equilibrium ensembles with generative deep learning
Following the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu, a deep learning system that...
https://www.science.org/doi/10.1126/science.adv9817
3 months ago
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reposted by
Jose Jimenez-Luna
Merriam-Webster
3 months ago
'Vacations.' The word is 'vacations.'
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Jose Jimenez-Luna
Frank Noe
3 months ago
@msftresearch.bsky.social
AI for science presents Orbformer, a foundation model for high accuracy quantum Chemistry. Strongly correlated states such as bond dissociation can be accurately computed without manually selecting active spaces or basis sets.
add a skeleton here at some point
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reposted by
Jose Jimenez-Luna
Microsoft Research
3 months ago
Microsoft researchers achieved a breakthrough in the accuracy of DFT, a method for predicting the properties of molecules and materials, by using deep learning. This work can lead to better batteries, green fertilizers, precision drug discovery, and more.
www.microsoft.com/en-us/resear...
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Jose Jimenez-Luna
Molondrongo 🐹💾 Retro Capibara Extraordinaire
3 months ago
As a native Spanish speaker, it baffles me the dissonance between written and oral languages in English. For instance, you write "BlueSky is a dead echo chamber for libs", but it reads "I want to post slurs without being blocked".
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time for summer!
youtu.be/yMyJKJAyakM?...
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Los Delinquentes - A La Luz Del Lorenzo
YouTube video by Los Delinqüentes Catálogo
https://youtu.be/yMyJKJAyakM?si=xEA1Y7IjxVGB0OIG
3 months ago
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'Tis but a scratch. Cambridge beer festival gives out the nicest glasses every year
4 months ago
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Media recommendation of the week:
petespans.co
It's the best YouTube/Instagram cooking channel re. Catalan/French cuisine out there. By far. And it's made by an American 🤯
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Home - Pete's Pans
Cook like a local What is Pete’s Pans? Pete’s Pans is a reverential journey around traditional Spanish, French & Portuguese cookery. We steer clear of personal interpretations and additional touches, ...
https://petespans.co/
4 months ago
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reposted by
Jose Jimenez-Luna
M A Osborne
5 months ago
I moved to the UK during "Britain's failed experiment in open borders". The company I co-founded has created >100 jobs, and my wife and I are raising two British kids. If the UK is becoming an "island of strangers", it's because the country is demonising and isolating immigrants like me
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Keir have you been to Benidorm
5 months ago
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What the heck Keir. Now I need to wait another 6 years?
5 months ago
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oh dear council elections
youtu.be/Lu0lAFbCqGU?...
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Seb Lowe - Ode to Britannia (Official Music Video)
YouTube video by Seb Lowe
https://youtu.be/Lu0lAFbCqGU?si=fAEwIlw6F9zcu-WD
5 months ago
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reposted by
Jose Jimenez-Luna
Frank Noe
5 months ago
BioEmu can now be run on Azure foundry. You can really scale up inference there if you don't have your own cluster.
@msftresearch.bsky.social
ai.azure.com/explore/mode...
add a skeleton here at some point
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reposted by
Jose Jimenez-Luna
Technology Connections
5 months ago
Pleading for a world where the reaction to this is a return to standard operating paradigms which don't require a smartphone or an app.
add a skeleton here at some point
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OK so who went full DOGE on the Spanish grid system
5 months ago
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reposted by
Jose Jimenez-Luna
Arne Elofsson
5 months ago
Sign of the time
xkcd.com/3081/
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PhD Timeline
https://xkcd.com/3081/
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Rooting for Arsenal. Arguably more Spanish than Madrid
5 months ago
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reposted by
Jose Jimenez-Luna
NY Times Pitchbot
6 months ago
It’s been a full week, and not a single penguin has backed down or sold out. Could there be a lesson here for America’s law firms and universities?
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I've just put an offer for a house here in the UK. It's the first time I do something like this - is there anything I should know, fellow blueskyers?
6 months ago
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reposted by
Jose Jimenez-Luna
TimOfLegend
6 months ago
Sometimes in this fast-moving and complex modern world, it’s hard to know what’s right and what’s wrong. But here’s a handy rule of thumb: If you are ever on one side of an issue, and Sesame Street is on the other, YOU’RE the bad guy.
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Jose Jimenez-Luna
Martin Steinegger 🇺🇦
6 months ago
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations. Thanks
@jjimenezluna.bsky.social
for the help! 🌐
colab.research.google.com/github/sokry...
📄
www.biorxiv.org/content/10.1...
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Google Colab
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/BioEmu.ipynb
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reposted by
Jose Jimenez-Luna
Natalie Wynn
6 months ago
new video
youtu.be/teqkK0RLNkI?...
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CONSPIRACY | contrapoints
YouTube video by ContraPoints
https://youtu.be/teqkK0RLNkI?si=C7KXisKWPEb_ylPN
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little new toy
6 months ago
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reposted by
Jose Jimenez-Luna
Frank Noe
6 months ago
Just arrived at APS. Please reach out if you want to chat. I'll open the foundation models session at 3pm, talking about BioEmu:
summit.aps.org/events/MAR-J37
#MachineLearning
#AI
#Physics
#Proteins
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Foundational Models for Physics Research
3:00 pm – 5:48 pm, Tuesday March 18, Session MAR-J37, Anaheim Convention Center, 258B (Level 2)
https://summit.aps.org/events/MAR-J37
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confirms all my suspicions about cod
7 months ago
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reposted by
Jose Jimenez-Luna
The Guardian
7 months ago
Canada goose fights off bald eagle in rare, symbolism-laden battle on ice
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Canada goose fights off bald eagle in rare, symbolism-laden battle on ice
Photographer captures 20-minute clash between birds emblematic of Canada and US amid high political tensions For the second time in weeks, a Canadian icon has emerged as the unlikely victor in an existential battle on the ice. Mervyn Sequeira, an…
https://www.theguardian.com/environment/2025/mar/05/canada-goose-bald-eagle-political-symbolism?utm_source=dlvr.it&utm_medium=bluesky&CMP=bsky_gu
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can't wait for those new exciting clock features
7 months ago
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With all that's happening at the moment, for Spaniards it's particularly relevant to remember what happened to the Maine.
en.wikipedia.org/wiki/USS_Mai...
. Stand with the EU.
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USS Maine (1889) - Wikipedia
https://en.wikipedia.org/wiki/USS_Maine_(1889)
7 months ago
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Feliz día de Andalucía 🫒
open.spotify.com/track/7HhjCh...
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Verde, blanca y verde
Carlos Cano, Coro de Triana · Que Naveguen Los Suenos · Song · 2009
https://open.spotify.com/track/7HhjChZx1QD6s7MBF5uTd6?si=82a19dd150ac417a
7 months ago
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Movie you've watched more than 6 times, gifs only
add a skeleton here at some point
7 months ago
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Jose Jimenez-Luna
The Onion
7 months ago
DOGE By The Numbers
theonion.com/doge-by...
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Jose Jimenez-Luna
Frank Noe
7 months ago
Today we have published BioEmu-Benchmarks (MIT license): a code to evaluate the multi-conformation sampling benchmarks, MD free energy landscape benchmarks, and folding free energy benchmarks shown in the BioEmu-1 paper with BioEmu or your own model. Some details below 🧵
github.com/microsoft/bi...
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GitHub - microsoft/bioemu-benchmarks: Benchmarking code accompanying the release of `bioemu`
Benchmarking code accompanying the release of `bioemu` - microsoft/bioemu-benchmarks
https://github.com/microsoft/bioemu-benchmarks
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Jose Jimenez-Luna
Microsoft Research
7 months ago
Meet BioEmu-1 from Microsoft Research. This deep learning model can generate thousands of protein structures per hour, unlocking new possibilities for protein scientists and drug discovery and research.
www.microsoft.com/en-us/resear...
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Jose Jimenez-Luna
Cecilia Clementi
7 months ago
Our new preprint is out: Extending the RANGE of Graph Neural Networks: Relaying Attention Nodes for Global Encoding.
arxiv.org/abs/2502.13797
We present a new architecture to address the problem of "short-sightedness" of MLFF based on GNN, which outperform in speed and accuracy Ewald-based GNN.
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Extending the RANGE of Graph Neural Networks: Relaying Attention Nodes for Global Encoding
Graph Neural Networks (GNNs) are routinely used in molecular physics, social sciences, and economics to model many-body interactions in graph-like systems. However, GNNs are inherently local and can s...
http://arxiv.org/abs/2502.13797
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reposted by
Jose Jimenez-Luna
Frank Noe
7 months ago
The BioEmu-1 model and inference code are now public under MIT license!!! Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
add a skeleton here at some point
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Jose Jimenez-Luna
Frank Noe
7 months ago
Check out this great BioEmu talk by
@jjimenezluna.bsky.social
and
@yuxie.bsky.social
in the VantAI lecture series. Thank you for hosting
@mmbronstein.bsky.social
@lucanaef.bsky.social
www.youtube.com/watch?v=8vsT...
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Emulation of protein equilibrium ensembles with generative deep learning | José Jiménez Luna, Yu Xie
YouTube video by VantAI
https://www.youtube.com/watch?v=8vsTsb-m7u4
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Jose Jimenez-Luna
The Guardian
7 months ago
In an NHS ward I saw how Britain relies on immigrants. Yet still we tell them they’re not wanted | John Harris
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In an NHS ward I saw how Britain relies on immigrants. Yet still we tell them they’re not wanted | John Harris
My dad’s journey through the health and social care systems proves what politicians secretly know: we’ll be lost if they succeed in ‘sending them home’, says Guardian columnist John Harris
https://www.theguardian.com/commentisfree/2025/feb/16/nhs-britain-immigrants-dad?utm_term=Autofeed&CMP=bsky_gu&utm_medium=&utm_source=Bluesky#Echobox=1739712809
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Bundt walnut chocolate cake
#statswhocook
?
7 months ago
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www.theguardian.com/commentisfre...
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Trump is willing to wreck the world economy. The global fightback must start now | Gaby Hinsliff
Britain is less vulnerable to US tariffs than other nations, but shares a historic responsibility. A recession would mean dark days for everyone, says Guardian columnist Gaby Hinsliff
https://www.theguardian.com/commentisfree/2025/feb/03/donald-trump-world-economy-britain-us-tariffs
8 months ago
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😆
add a skeleton here at some point
8 months ago
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Ads over scaffolding? No, this is Seville, how about a weeping Virgin Mary?
8 months ago
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