Hannes Stark
@hannes-stark.bsky.social
MIT PhD Student - ML for biomolecules - https://hannes-stark.com/
Reposted by Hannes Stark
Will it bind? A little worried about all the "TTTTTTT" 🧐 But looks cool 😎
October 27, 2025 at 12:07 AM
Will it bind? A little worried about all the "TTTTTTT" 🧐 But looks cool 😎
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Reading group session on Monday: "Lookup multivariate Kolmogorov-Arnold Networks" arxiv.org/abs/2509.07103 with Sergey Pozdnyakov
On zoom at 9am PT / 12pm ET / 6pm CE(S)T: portal.valencelabs.com/starklyspeak...
On zoom at 9am PT / 12pm ET / 6pm CE(S)T: portal.valencelabs.com/starklyspeak...
October 19, 2025 at 6:34 PM
Reading group session on Monday: "Lookup multivariate Kolmogorov-Arnold Networks" arxiv.org/abs/2509.07103 with Sergey Pozdnyakov
On zoom at 9am PT / 12pm ET / 6pm CE(S)T: portal.valencelabs.com/starklyspeak...
On zoom at 9am PT / 12pm ET / 6pm CE(S)T: portal.valencelabs.com/starklyspeak...
Tomorrow on Zoom we talk with Tobias Kreimann about his "Transformers Discover Molecular Structure Without Graph Priors" arxiv.org/abs/2510.02259
Experiments on the new OMol25 dataset!
On zoom 9am PT / noon ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Experiments on the new OMol25 dataset!
On zoom 9am PT / noon ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
October 12, 2025 at 6:12 PM
Tomorrow on Zoom we talk with Tobias Kreimann about his "Transformers Discover Molecular Structure Without Graph Priors" arxiv.org/abs/2510.02259
Experiments on the new OMol25 dataset!
On zoom 9am PT / noon ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Experiments on the new OMol25 dataset!
On zoom 9am PT / noon ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Tomorrow we have a reading group session with @nscorley and @SimMat20 about "Accelerating Biomolecular Modeling with AtomWorks and RF3" www.biorxiv.org/content/10.1...
We will also discuss how to close the gap between AF3 and its open source replications!
portal.valencelabs.com/starklyspeak...
We will also discuss how to close the gap between AF3 and its open source replications!
portal.valencelabs.com/starklyspeak...
October 5, 2025 at 8:21 PM
Tomorrow we have a reading group session with @nscorley and @SimMat20 about "Accelerating Biomolecular Modeling with AtomWorks and RF3" www.biorxiv.org/content/10.1...
We will also discuss how to close the gap between AF3 and its open source replications!
portal.valencelabs.com/starklyspeak...
We will also discuss how to close the gap between AF3 and its open source replications!
portal.valencelabs.com/starklyspeak...
Tomorrow we discuss diffusion models for sampling unnormalized densities "Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matching"
arxiv.org/abs/2504.11713
Join us on zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
arxiv.org/abs/2504.11713
Join us on zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
August 3, 2025 at 11:49 PM
Tomorrow we discuss diffusion models for sampling unnormalized densities "Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matching"
arxiv.org/abs/2504.11713
Join us on zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
arxiv.org/abs/2504.11713
Join us on zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
In 1h we discuss "Predicting cellular responses to perturbation across diverse contexts with State" in the reading group with the author Abhinav Adduri! www.biorxiv.org/content/10.1...
Join us on zoom at 9am PT / 12pm ET: portal.valencelabs.com/starklyspeak...
Join us on zoom at 9am PT / 12pm ET: portal.valencelabs.com/starklyspeak...
July 21, 2025 at 3:02 PM
In 1h we discuss "Predicting cellular responses to perturbation across diverse contexts with State" in the reading group with the author Abhinav Adduri! www.biorxiv.org/content/10.1...
Join us on zoom at 9am PT / 12pm ET: portal.valencelabs.com/starklyspeak...
Join us on zoom at 9am PT / 12pm ET: portal.valencelabs.com/starklyspeak...
Starkly Speaking tomorrow: @bwood_m will present "UMA: A Family of Universal Models for Atoms" ai.meta.com/research/pub...
Join us on Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Join us on Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
June 29, 2025 at 7:52 PM
Starkly Speaking tomorrow: @bwood_m will present "UMA: A Family of Universal Models for Atoms" ai.meta.com/research/pub...
Join us on Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Join us on Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Monday Starkly Speaking: we understand a core diffusion model ingredient better - classifier free guidance.
Via "Classifier-Free Guidance: From High-Dimensional Analysis to Generalized Guidance Forms" arxiv.org/abs/2502.07849
On Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Via "Classifier-Free Guidance: From High-Dimensional Analysis to Generalized Guidance Forms" arxiv.org/abs/2502.07849
On Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
June 21, 2025 at 11:42 PM
Monday Starkly Speaking: we understand a core diffusion model ingredient better - classifier free guidance.
Via "Classifier-Free Guidance: From High-Dimensional Analysis to Generalized Guidance Forms" arxiv.org/abs/2502.07849
On Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Via "Classifier-Free Guidance: From High-Dimensional Analysis to Generalized Guidance Forms" arxiv.org/abs/2502.07849
On Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Presentation of Boltz-2 by @pas_saro @GabriCorso @jeremyWohlwend!
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
www.youtube.com/watch?v=iHDa...
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
www.youtube.com/watch?v=iHDa...
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction
YouTube video by Valence Labs
www.youtube.com
June 18, 2025 at 10:19 PM
Presentation of Boltz-2 by @pas_saro @GabriCorso @jeremyWohlwend!
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
www.youtube.com/watch?v=iHDa...
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
www.youtube.com/watch?v=iHDa...
Reposted by Hannes Stark
Thank you everyone for attending the Boltz-2 Boston, San Francisco and Paris events this week! Given the success of the in-person seminars and the many requests, we are organizing a virtual seminar on Tuesday at 12pm ET / 6pm CET! Sign up here: lu.ma/4bpuwbsr
June 14, 2025 at 7:46 PM
Thank you everyone for attending the Boltz-2 Boston, San Francisco and Paris events this week! Given the success of the in-person seminars and the many requests, we are organizing a virtual seminar on Tuesday at 12pm ET / 6pm CET! Sign up here: lu.ma/4bpuwbsr
On Tue 12pm ET on Zoom: Saro Passaro, Gabriele Corso, Jeremy Wohlwend will present Boltz-2!
bit.ly/boltz2-pdf
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
Zoom link: portal.valencelabs.com/starklyspeak...
bit.ly/boltz2-pdf
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
Zoom link: portal.valencelabs.com/starklyspeak...
June 14, 2025 at 5:14 PM
On Tue 12pm ET on Zoom: Saro Passaro, Gabriele Corso, Jeremy Wohlwend will present Boltz-2!
bit.ly/boltz2-pdf
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
Zoom link: portal.valencelabs.com/starklyspeak...
bit.ly/boltz2-pdf
Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.
Zoom link: portal.valencelabs.com/starklyspeak...
Tomorrow in our reading group we will discuss "Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional" arxiv.org/abs/2504.18506
On zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
On zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
June 8, 2025 at 7:43 PM
Tomorrow in our reading group we will discuss "Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional" arxiv.org/abs/2504.18506
On zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
On zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Reading group tomorrow: Identifying perturbation targets through causal differential networks arxiv.org/abs/2410.03380
With @menghua_wu!
Join us on Zoom at 9am PT 12pm ET 6pm CEST: portal.valencelabs.com/starklyspeak...
With @menghua_wu!
Join us on Zoom at 9am PT 12pm ET 6pm CEST: portal.valencelabs.com/starklyspeak...
June 1, 2025 at 8:58 PM
Reading group tomorrow: Identifying perturbation targets through causal differential networks arxiv.org/abs/2410.03380
With @menghua_wu!
Join us on Zoom at 9am PT 12pm ET 6pm CEST: portal.valencelabs.com/starklyspeak...
With @menghua_wu!
Join us on Zoom at 9am PT 12pm ET 6pm CEST: portal.valencelabs.com/starklyspeak...
Reposted by Hannes Stark
📢 Thrilled to announce the return of MoML @ MIT on Oct. 22 and that paper submissions are now open! Students & postdocs w/ accepted papers will be granted FREE admission to attend and have the chance at winning the Octavian-Eugen Ganea Prize for Best Paper! 🧵 #AcademicSky #compchem #drugdesign
May 28, 2025 at 8:28 PM
📢 Thrilled to announce the return of MoML @ MIT on Oct. 22 and that paper submissions are now open! Students & postdocs w/ accepted papers will be granted FREE admission to attend and have the chance at winning the Octavian-Eugen Ganea Prize for Best Paper! 🧵 #AcademicSky #compchem #drugdesign
Tomorrow @TimothyDuignan joins us to discuss "Orb-v3: atomistic simulation at scale" arxiv.org/abs/2504.06231 and surrounding models to get our understanding of that field up to date!
On Zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
On Zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
May 25, 2025 at 6:12 PM
Tomorrow @TimothyDuignan joins us to discuss "Orb-v3: atomistic simulation at scale" arxiv.org/abs/2504.06231 and surrounding models to get our understanding of that field up to date!
On Zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
On Zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Tomorrow the authors @YuanqiD and Jiajun He will present their paper "FEAT: Free energy Estimators with Adaptive Transport" arxiv.org/abs/2504.11516
Estimating FED is a strong tool for comparing drug's binding affinities
Join us on zoom at 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Estimating FED is a strong tool for comparing drug's binding affinities
Join us on zoom at 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
May 18, 2025 at 6:40 PM
Tomorrow the authors @YuanqiD and Jiajun He will present their paper "FEAT: Free energy Estimators with Adaptive Transport" arxiv.org/abs/2504.11516
Estimating FED is a strong tool for comparing drug's binding affinities
Join us on zoom at 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Estimating FED is a strong tool for comparing drug's binding affinities
Join us on zoom at 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Reading group tomorrow: @json_yim and @woodyahern present "Atom level enzyme active site scaffolding using RFdiffusion2" www.biorxiv.org/content/10.1...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
May 11, 2025 at 5:11 PM
Reading group tomorrow: @json_yim and @woodyahern present "Atom level enzyme active site scaffolding using RFdiffusion2" www.biorxiv.org/content/10.1...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
In the reading group sessions tomorrow Ezra Erives, I and whoever joins, will discuss "A General Framework for Inference-time Scaling and Steering of Diffusion Models" arxiv.org/abs/2501.06848
On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
April 20, 2025 at 4:47 PM
In the reading group sessions tomorrow Ezra Erives, I and whoever joins, will discuss "A General Framework for Inference-time Scaling and Steering of Diffusion Models" arxiv.org/abs/2501.06848
On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
Reading group session tomorrow, March 24th, is at 3pm PT / 6pm ET / midnight CEST about:
"One-step Diffusion Models with f-Divergence Distribution Matching" arxiv.org/abs/2502.15681
Presented by @xuyilun2
Zoom link: portal.valencelabs.com/logg
"One-step Diffusion Models with f-Divergence Distribution Matching" arxiv.org/abs/2502.15681
Presented by @xuyilun2
Zoom link: portal.valencelabs.com/logg
March 23, 2025 at 9:47 PM
Reading group session tomorrow, March 24th, is at 3pm PT / 6pm ET / midnight CEST about:
"One-step Diffusion Models with f-Divergence Distribution Matching" arxiv.org/abs/2502.15681
Presented by @xuyilun2
Zoom link: portal.valencelabs.com/logg
"One-step Diffusion Models with f-Divergence Distribution Matching" arxiv.org/abs/2502.15681
Presented by @xuyilun2
Zoom link: portal.valencelabs.com/logg
Reposted by Hannes Stark
Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models.
Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp
Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp
March 20, 2025 at 3:02 PM
Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models.
Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp
Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp
Reposted by Hannes Stark
Check out this talk from our own Garyk Brixi talking about Evo 2!
Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
Genome modeling and design across all domains of life with Evo 2 | Garyk Brixi
YouTube video by Valence Labs
youtu.be
March 14, 2025 at 2:35 PM
Check out this talk from our own Garyk Brixi talking about Evo 2!
Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
Genome modeling and design across all domains of life with Evo 2 | Garyk Brixi
YouTube video by Valence Labs
youtu.be
March 13, 2025 at 11:55 PM
Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
Reposted by Hannes Stark
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
March 7, 2025 at 1:38 PM
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
Reposted by Hannes Stark
🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly!
Additional details in thread 🧵
#ICLR2025
Additional details in thread 🧵
#ICLR2025
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
March 11, 2025 at 3:02 PM
🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly!
Additional details in thread 🧵
#ICLR2025
Additional details in thread 🧵
#ICLR2025