Jason Yim
@jyim.bsky.social
PhD candidate at MIT CSAIL. Generative models, protein design.
Ex: DeepMind, Microsoft, Instagram, Johns Hopkins University.
Website: https://people.csail.mit.edu/jyim/
X: https://x.com/json_yim
Ex: DeepMind, Microsoft, Instagram, Johns Hopkins University.
Website: https://people.csail.mit.edu/jyim/
X: https://x.com/json_yim
I'll be at ICLR. Come check out our generative modeling work! Reach out if you want to chat.
Proteina: openreview.net/forum?id=TVQ...
Protcomposer: openreview.net/forum?id=0ct...
Generator matching: openreview.net/forum?id=RuP...
Proteina: openreview.net/forum?id=TVQ...
Protcomposer: openreview.net/forum?id=0ct...
Generator matching: openreview.net/forum?id=RuP...
Proteina: Scaling Flow-based Protein Structure Generative Models
Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop *Proteina*, a new large-scale flow-based...
openreview.net
April 20, 2025 at 4:07 PM
I'll be at ICLR. Come check out our generative modeling work! Reach out if you want to chat.
Proteina: openreview.net/forum?id=TVQ...
Protcomposer: openreview.net/forum?id=0ct...
Generator matching: openreview.net/forum?id=RuP...
Proteina: openreview.net/forum?id=TVQ...
Protcomposer: openreview.net/forum?id=0ct...
Generator matching: openreview.net/forum?id=RuP...
I really enjoyed seeing how protein generation models scale with more data and weights. Congrats to Nvidia and the core contributors for this amazing work!
📢📢 "Proteina: Scaling Flow-based Protein Structure Generative Models"
#ICLR2025 (Oral Presentation)
🔥 Project page: research.nvidia.com/labs/genair/...
📜 Paper: arxiv.org/abs/2503.00710
🛠️ Code and weights: github.com/NVIDIA-Digit...
🧵Details in thread...
(1/n)
#ICLR2025 (Oral Presentation)
🔥 Project page: research.nvidia.com/labs/genair/...
📜 Paper: arxiv.org/abs/2503.00710
🛠️ Code and weights: github.com/NVIDIA-Digit...
🧵Details in thread...
(1/n)
March 5, 2025 at 5:51 AM
I really enjoyed seeing how protein generation models scale with more data and weights. Congrats to Nvidia and the core contributors for this amazing work!
See our preprint on a new computational protein design benchmark!
🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding.
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
February 19, 2025 at 9:09 PM
See our preprint on a new computational protein design benchmark!
Congrats Simon! I enjoyed our time together while starting protein design at DeepMind. Excited to see what you build. Consider joining latent labs if you're interested in ML and bio!
Latent Labs comes out of stealth today with $50M funding. Our goal? To push the frontiers of generative biology, giving partners instant access to tools capable of accelerating drug design
February 13, 2025 at 3:15 PM
Congrats Simon! I enjoyed our time together while starting protein design at DeepMind. Excited to see what you build. Consider joining latent labs if you're interested in ML and bio!
Reposted by Jason Yim
new preprint on chemical synthesis ML models
- showing how to combine multiple models in a principled way
- modern Transformers + GNN to featurize chemical reaction:
- new insights in where the models shine
+ bonus: find the quirky named reaction!
Feedback welcome!
arxiv.org/abs/2412.05269
- showing how to combine multiple models in a principled way
- modern Transformers + GNN to featurize chemical reaction:
- new insights in where the models shine
+ bonus: find the quirky named reaction!
Feedback welcome!
arxiv.org/abs/2412.05269
Chimera: Accurate retrosynthesis prediction by ensembling models with diverse inductive biases
Planning and conducting chemical syntheses remains a major bottleneck in the discovery of functional small molecules, and prevents fully leveraging generative AI for molecular inverse design. While ea...
arxiv.org
December 9, 2024 at 2:19 AM
new preprint on chemical synthesis ML models
- showing how to combine multiple models in a principled way
- modern Transformers + GNN to featurize chemical reaction:
- new insights in where the models shine
+ bonus: find the quirky named reaction!
Feedback welcome!
arxiv.org/abs/2412.05269
- showing how to combine multiple models in a principled way
- modern Transformers + GNN to featurize chemical reaction:
- new insights in where the models shine
+ bonus: find the quirky named reaction!
Feedback welcome!
arxiv.org/abs/2412.05269
Reposted by Jason Yim
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Structure-based drug design with equivariant diffusion models - Nature Computational Science
This work applies diffusion models to conditional molecule generation and shows how they can be used to tackle various structure-based drug design problems
www.nature.com
December 9, 2024 at 2:00 PM
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Excited this is out! I learned a lot interning with Andrew Foong, @franknoe.bsky.social, and the team. Check out Frank's thread and the preprint to learn more.
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 6, 2024 at 1:26 PM
Excited this is out! I learned a lot interning with Andrew Foong, @franknoe.bsky.social, and the team. Check out Frank's thread and the preprint to learn more.
Reposted by Jason Yim
🚨Our Machine Learning Force Field Mattersim is now available! 🚨
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
GitHub - microsoft/mattersim: MatterSim: A deep learning atomistic model across elements, temperatures and pressures.
MatterSim: A deep learning atomistic model across elements, temperatures and pressures. - microsoft/mattersim
msft.it
December 3, 2024 at 5:11 PM
🚨Our Machine Learning Force Field Mattersim is now available! 🚨
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
Reposted by Jason Yim
In a gratuitous attempt to acquire more followers myself 😁, I've made a start on a "starter pack". Hopefully as more people from 🐦 make it over to 🦋, we can extend this a bit. Suggestions welcome!
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
November 15, 2024 at 8:04 PM
In a gratuitous attempt to acquire more followers myself 😁, I've made a start on a "starter pack". Hopefully as more people from 🐦 make it over to 🦋, we can extend this a bit. Suggestions welcome!
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔