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...

Boltz v0.4.0 is here! Today, we’re releasing our full data processing pipeline, making it easier than ever to build on top of Boltz. This release also includes our evaluation code and new results. Oh, and also pocket conditioning :)

Bonus: you can now watch on YouTube the recording of the seminar we gave on Boltz-1 with @mmbronstein.bsky.social and VantAI! www.youtube.com/watch?v=mN5p...

Yes they appear to be having server problems, here is a link to the paper PDF: evodesign.org/Semantic_Min...

Are all of bioRxiv's paper pdfs unavailable right now? e.g. www.biorxiv.org/content/10.1... Want to send over a pdf @brianhie.bsky.social ? :D

New Title Alert: Boltz-1- an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands & glycans. Learn more here: https://buff.ly/3ZAPowA #SBGridSoftware #SBGrid