Weekend project: Comparing ESM3 from EvolutionaryScale to ESM2 and inv_cov. The ultimate test of a protein language models is how well the pairwise dependencies it learns correlate to structure. (1/8)

biorxiv.org/content/10.110… We're live!

After we trained ESM3, we were excited to see it could respond to complex prompts, which greatly improved with scale. While scaling has been driving advances across AI—in biology it has been largely underestimated. Article by Ewen Callaway for nature: nature.com/articles/d4158…

Great application of ESM-2: Accurately resolving the evolutionary trajectories of SARS-CoV-2, all starting from a single sequence! In the near-term future, viral genomic surveillance could look very different...

The Machine Learning in Structural Biology workshop will be back at #NeurIPS for its 5th edition in December! Stay tuned as we will soon share details about the stellar lineup of speakers 🌟, the call for papers 🧬, and a very exciting innovation for this year's workshop 🥁🚀!!

As promised, the next 3 weeks of speakers for Machine learning for protein engineering seminar : 07/23, Roshan Rao with ESM3 07/30, Jason Yang with CARE 08/06, Alex Tong with Sequence-Augmented SE(3)-Flow Matching Visit our website to sign up for slack and our g-group newsletter!

The ESM3 package was updated on pip. We fixed an issue with iterative structure prediction. Expect to see major improvements after doing: pip install -U esm

To provide real value, generative molecular methods really do need a litany of features and control modalities which each deserve their own models and attention. At Terray we use latent diffusion to build up a suite of models that build towards that. biorxiv.org/content/10.110…

Incredible to see the field recognized by the Nobel committee!! Congratulations to David, Demis, and John, and to everyone who contributed to the success of Rosetta/AlphaFold!

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy Wohlwend, Saro and an amazing team at MIT and Genesis Therapeutics. A thread!

Introducing ESM Cambrian. Unsupervised learning can invert biology at scale to reveal the hidden structure of the natural world. We’ve scaled up compute and data to train a new generation of protein language models. ESM C defines a new state of the art for protein

i love this plot

1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations: bit.ly/plaid-proteins 🧵

We're thrilled to present ESM3 in Science Magazine. ESM3 is a generative language model that reasons over the three fundamental properties of proteins: sequence, structure, and function. Today we're making ESM3 available free to researchers worldwide via the public beta of an API

Founders who were PhD or post-doc in my lab at Berkeley, **largely funded by NSF / DoD grants**, start-up, market cap (collected by OpenAI Deep Research)

📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs. 💻 github.com/Bitbol-Lab/rag… 🔗 doi.org/10.1101/2025.0… 1/7

Very excited to share my PhD project, out today in Neuron! Check out the thread below for my best attempt at a high-level summary. cell.com/neuron/fulltex…

The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬 Stay tuned MLSB (in San Diego) as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

MLSB this year will be hosted, co-located with NeurIPS in its own location! Stay tuned for more updates, but it's happening 🧬🧬 Always looking for sponsors too, please reach out if you're able to help.