Nobel Prize winner talks about how he works, how to "challenge your brain", and his research. 15 minutes well spent! open.spotify.com/episode/4Cx0...

Episode 37: Mario R. Capecchi (Nobel Prize for Medicine and Physiology): The first knockout-mice and anxiety in pigs

Paper Podcast · Episode

open.spotify.com

If you can make it to Boston on Oct 14th, consider submitting a paper to the MIT Molecular ML conference! 2-4 pages 🤗 www.moml.mit.edu/submit

Monday reading group: a bit of insight in autoregressive protei nstructure generation given a tokenization scheme. "Adaptive Protein Tokenization" with @rohit_dilip_ arxiv.org/abs/2602.06418 On Zoom 12pm ET / 6pm CEST: hannes-stark.com/starkly-spea...

Super fun session today discussing DISCO enzyme design with @jarridrb, @martoskreto, and Chenghao Liu! www.youtube.com/watch?v=btJq...

General Multimodal Protein Design Enables DNA-Encoding of Chemistry

YouTube video by Valence Labs

youtube.com

Reading group tomorrow (Monday) about "Leveraging Discrete Function Decomposability for Scientific Design" arxiv.org/abs/2511.03032 With James Bowden from Jennifer Listgarten lab! Join on Zoom at 9am PT / 12pm ET / 6pm CEST: hannes-stark.com/starkly-spea...

Would be fun to see some of you at my thesis defense on Friday, May 1st, 11:15 am ET :) 🤗 "Generative Models for Biomolecular Structures and Design" www.csail.mit.edu/event/thesis... At MIT, 32 Vassar Street (Stata Center), Room G449 (Kiva)

Reading group tomorrow: One-step Language Modeling via Continuous Denoising arxiv.org/abs/2602.16813 With @nmboffi 🤗 Join us on zoom Monday at 9am PT / 12pm ET / 6pm CEST: hannes-stark.com/starkly-spea...

Join our reading group session with the NVIDIA team about their new Proteina binder design model with the authors Karsten Kreis and Kieran Didi! Paper: research.nvidia.com/labs/genair/... Zoom link for Monday 9am PT / 12pm ET / 5pm CET: portal.valencelabs.com/starklyspeak...

ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷 🤗 Hugging Face Space: huggingface.co/spaces/pimen... ⚙️ Google Colab: colab.research.google.com/drive/1l_h7c... 🧵👇

We have a little new paper at ICLR led by @AntonBushuiev. Test time training for proteins :) arxiv.org/abs/2411.02109 For example, you know the sequence that you want to fold, so fine-tune ESM on it at test time to get a better ESMFold structure prediction!

Video of our discussion with MingYang Deng about his paper "Generative Modeling via Drifting"! A new perspective on generative modeling, admitting a one-step model with performance similar to diffusion/flow models on ImageNet and other tasks: www.youtube.com/watch?v=4eHn...

Generative Modeling via Drifting | MingYang Deng

YouTube video by Valence Labs

youtube.com

Explore BoltzGen, an all-atom generative model for designing proteins and peptides across all modalities, at today’s AI & Scientific Discovery Online Seminar! Featuring @hannes-stark.bsky.social, PhD student at MIT Join us online or at DSI at 11am CT - ai-scientific-discovery.github.io

Join us on Monday to discuss "Generative Modeling via Drifting" with the author MingYang Deng! A one-step generative model trained with an MMD loss. On Zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/starklyspeak...

Tomorrow in the reading group we discuss "SeedFold: Scaling Biomolecular Structure Prediction" arxiv.org/abs/2512.24354 Outperforming AF3 on multiple tasks a little bit. Join us on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/starklyspeak...

In the reading group tomorrow we discuss "SLAE: Strictly Local All-atom Environment for Protein Representation" with Yilin Chen from @PossuHuangLab! www.biorxiv.org/content/10.1... Join us on Zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/starklyspeak...

A video where I present our biomolecular binder design model, BoltzGen! youtu.be/9d_QWUUI1Qo Happy New Year! I am very excited to continue working in our amazing ML for bio community in 2026 - let's continue! 🤗

BoltzGen: Toward Universal Binder Design | Generative AI for Drug Discovery (Hannes Stark, MIT)

YouTube video by Hannes Stärk

youtu.be

Join our online BoltzGen presentation and Q&A on Wed. Dec. 17th at noon ET! A few new results, many new insights, and lots of good discussion, I am sure! Paper: www.biorxiv.org/content/10.1... Presentation sign up + Zoom: luma.com/b24bd37m

BoltzGen Zoom presentation + Q&A · Zoom · Luma

Join us on Zoom on Wednesday, Dec. 17th for details on our new model BoltzGen and discussions on the future of biomolecular design 🧬 There will be a 35 minute…

luma.com

Today in the reading group in 5h we discuss Germinal with the authors! "Efficient generation of epitope-targeted de novo antibodies with Germinal" www.biorxiv.org/content/10.1... On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/starklyspeak...

Efficient generation of epitope-targeted de novo antibodies with Germinal

Obtaining novel antibodies against specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low su...

biorxiv.org

Reading group tomorrow: "How to build a consistency model: Learning flow maps via self-distillation" with Nicholas Boffi! arxiv.org/abs/2505.18825 Join us on zoom at 9am PT, 12pm ET, 6pm CET: portal.valencelabs.com/starklyspeak...

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!

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...

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...

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...

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...

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...

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...

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...

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...

Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

YouTube video by Valence Labs

youtube.com

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