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...

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...

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...

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...

📢 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...

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...

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...

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

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

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

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!

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)

🚨 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

🔥 ProtComposer (ICLR'25 Oral) is a Swiss Army knife: (i) Manually create new protein structure layouts? ✅ (ii) Generation with favorable designability/diversity/novelty trade-offs? ✅ (iii) Spatially edit given proteins? ✅ Very original work by the amazing @hannes-stark.bsky.social and Bowen Jing!🔥

New paper (and #ICLR2025 Oral :)): ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025 Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs. 1/6

The Evo 2 authors join us tomorrow in the reading group to discuss their paper: "Genome modeling and design across all domains of life with Evo 2" www.biorxiv.org/content/10.1... Join on zoom (Monday) at 9am PT / 12pm ET / 6pm CET: www.biorxiv.org/content/10.1...

📢📢 "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)

Excited to share my #ICLR2025 paper, with JC Hütter and friends! Genetic perturbation screens allow biologists to manipulate and measure the genes in cells = discover causal relationships! BUT they are expensive to run, expensive to interpret. ... We use LLMs to help!

Feeling mostly very relieved to share that gRNAde was accepted at @iclr-conf.bsky.social as a Spotlight! What started as a side project over 2 years ago has lead to a spotlight paper and a new scientific journey for me -- Here I am learning how to pipette :D

reading group session tomorrow: "The Importance of Being Scalable: Improving the Speed and Accuracy of Neural Network Interatomic Potentials Across Chemical Domains" arxiv.org/abs/2410.241... with the authors Join on zoom 9am PT / 12pm ET: portal.valencelabs.com/logg

In our reading group session tomorrow, we discuss "Inference-Time Scaling for Diffusion Models beyond Scaling Denoising Steps" arxiv.org/abs/2501.09732 with the authors! Join us on Zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

Tomorrow's reading group: "The Superposition of Diffusion Models Using the Itô Density Estimator" arxiv.org/abs/2412.17762 with the authors! Join on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

Next Tues (2/18) at **5PM ET** we will have @hannes-stark.bsky.social and Bowen Jing present "ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids" Paper: openreview.net/forum?id=0ct... Sign up on our website for zoom links!

A protein language model trained to predict subcellular localization for human proteins can generate de novo sequences with the desired localization and identify pathological mutations. @itamarchinn.bsky.social @pgmikhael.bsky.social www.science.org/doi/10.1126/...

For the reading group session tomorrow we have another @Nature paper: "Targeting protein–ligand neosurfaces with a generalizable deep learning tool" www.nature.com/articles/s41... With three of the authors tomorrow (Mon) on Zoom at 12pm ET / 6pm CET: portal.valencelabs.com/logg

Tomorrows reading group session is delayed by 30 min! Valentin De Bortoli joins us for his paper "Accelerated Diffusion Models via Speculative Sampling" arxiv.org/abs/2501.05370 On zoom at 9:30am PT / 12:30pm ET / 6:30pm CET: portal.valencelabs.com/logg

Reading group session on Monday: Valentin De Bortoli joins us for his paper "Accelerated Diffusion Models via Speculative Sampling" arxiv.org/abs/2501.05370 On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

On monday in our reading group we discuss "Flow Matching with General Discrete Paths: A Kinetic-Optimal Perspective" arxiv.org/abs/2412.03487 With Neta Shaul. Join on zoom on Monday at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

Tomorrow in the reading group, we will discuss "PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion" with Sophia Tang! Join us on Zoom at 9pm / 12pm / 6pm CET: portal.valencelabs.com/logg

Awesome paper! BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1... Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

Tomorrow, in the reading group, Johannes Brehmer will present his paper "Does equivariance matter at scale?" arxiv.org/abs/2410.23179 Join us on zoom at 12pm ET / 6pm CET: portal.valencelabs.com/logg

🧵(1/7) Have you ever wanted to combine different pre-trained diffusion models but don't have time or data to retrain a new, bigger model? 🚀 Introducing SuperDiff 🦹‍♀️ – a principled method for efficiently combining multiple pre-trained diffusion models solely during inference!

🧵(3/7)This is all due to an amazing team: @martaowesyou.bsky.social @lazaratan.bsky.social @joeybose.bsky.social @alextong.bsky.social 📄Paper: arxiv.org/abs/2412.17762 💻Code: github.com/necludov/sup... 🤗HuggingFace: huggingface.co/superdiff

This is the kind of benchmarking work the field needs!

Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving. Happy holidays everyone! www.plinder.sh/blog/updates

Two major life updates: - I'm moving to Senior Applied Research Scientist in Digital Biology at NVIDIA (Jan '25) - I'm starting a new lab at Duke as Visiting Assistant Prof (early '25) Both roles focus on tackling hard problems in biological machine learning through collaborative research. Long 🧵

MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly www.eurekalert.org/news-release...