Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with Martin Pacesa, Zhidian Zhang , Bruno E. Correia, and Sergey Ovchinnikov. 🧬 Code will be released in a couple weeks

The 2nd Generative AI and Biology workshop will collocate with ICML 2025 in Vancouver this year (July 18/19, 2025). CFP: genbio-workshop.github.io/2025/ We have a fantastic lineup of speakers. Mengdi Wang Eric Xing Marinka Zitnik Stefano Ermon Minkai Xu Zhenqiao Song

If you want to know more about how Google Flights works, airline tickets, and why it is super complicated to deal with all the constraints and the combinatorial combinations, I highly recommend this set of slides by Carl de Marcken, one of the co-founders of ITA software, which

Proteins on the move— no literally! Think about it: What if missing NMR assignments = hidden protein dynamics? Super excited to host Gina & Hannah, where they turned that idea into Dyna-1. Intrigued? Catch them at next week’s ML4ProteinEngineering talk!! ml4proteinengineering.com/apr-30

🚨 Thrilled to share one of my main PhD projects! We built an in silico evolution platform that couples a solenoid discriminator network with AlphaFold2 as an oracle, using a genetic algorithm for sequence update. 🧬✨ (1/9)

Noticing myself adopting a certain rhythm in AI-assisted coding (i.e. code I actually and professionally care about, contrast to vibe code). 1. Stuff everything relevant into context (this can take a while in big projects. If the project is small enough just stuff everything

Sergey is an incredible researcher and mentor. I wouldn't be working on biology if it wasn't for him — and his style of working in the open (few folks push to github before they publish!). You should listen to this podcast, and if you have $, fund his ideas!

TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision biorxiv.org/content/10.110…

We are organizing Generative AI for Biology workshop at #ICML2025. Welcome to submit any relevant work on AI for biomolecule, AI model for bio systems, AI and experiments, Agent for bio discovery, new datasets and tools, etc. The deadline is May 25th. genbio-workshop.github.io/2025/

The W-S lab is seeking to hire a research scientist! This person will lead wet-lab innovations in our team as we combine AI and experiments to understand and design dynamics! Thanks for sharing/RTs! jobs.wisc.edu/jobs/scientist…

It's so over

Starlink now available in Sri Lanka! 🇱🇰

Sad to miss #ICML2025 due to visa issue this year, but it's a great time to share our new paper PPDiff, a diffusion model for protein-protein complex sequence-structure co-design with my great collaborators Lei Li Tianxiao Li Martin Renqiang Min.

Incredible to see how fast the field moves since we worked on masked diffusion arxiv.org/abs/2406.04329. Huge congratulations to Jaeyeon (Jay) Kim Sitan Chen for the award!

"I use AI in a separate window. I don't enjoy Cursor or Windsurf, I can literally feel competence draining out of my fingers." DHH, the legendary programmer and creator of Ruby on Rails has the most beautiful and philosophical idea about what AI takes away from programmers.

🚨 The era of infinite internet data is ending, So we ask: 👉 What’s the right generative modelling objective when data—not compute—is the bottleneck? TL;DR: ▶️Compute-constrained? Train Autoregressive models ▶️Data-constrained? Train Diffusion models Get ready for 🤿 1/n

Wrote an annotated Triton implementation of Flash Attention 2. (Links in reply) This is based on the flash attention implementation by the Triton team. Changed it to support GQA and cleaned up a little bit. Check it out to read the code for forward and backward passes along

Seems like a cool paper. Glad that our ICML '23 paper on retrieval for diffusion has conceptually inspired their deep research agent framework.

Saw this on my feed today. Worth sharing! #noloneheroes #mentoringmatters #takesavillage

time to time, it's good to take some time off and just reflect on those who had a big impact on your life, and send a quick note updating on what you've been up to