The final version of our transformer-based model of natural selection has come out in MBE. I hope some molecular evolution researchers find this interesting & useful as a way to express richer models of natural selection. doi.org/10.1093/mol... (short 🧵)

We are looking for an #AIEngineer to help build protein language models that capture evolutionary constraints with @matsen.bsky.social and @jbloomlab.bsky.social at #AI@HHMI @hhmijanelia.bsky.social hhmi.wd1.myworkdayjobs.com/en-US/Extern...

The final version of our "Thrifty" paper is up now: elifesciences.org/articles/10... . We were motivated to fit wide-context mutation models based on previous analyses showing "mesoscale" effects and a position-specific effect. But, how to avoid exploding the number of parameters? 🧵

Is an idea likely to advance the field? Our "preflight check" exercise provides a structured approach for thinking through computational biology research projects. github.com/matsengrp/pr... Thanks to @sdwfrost.bsky.social for the core idea!

Interested in doing a PhD or postdoc in our group? Here is a letter to you: matsen.group/general/202... We are ready to recruit a trainee who can help develop the next generation of our transformer-based models of natural selection. See the "joining" tab of our website for details.

Open bioinformatics position on next-generation protein evolution models! Join HHMI's AI initiative at Janelia Farm, Virginia, (an amazing place) and work closely with our team. Help us build the future! 🧬 + 🤖 = ❤️ hhmi.wd1.myworkdayjobs.com/en-US/Exter...

Why does selection feel so weak relative to mutation in affinity maturation? A new blog post giving three perspectives, including our new transformer-based model of natural selection on antibodies: matsen.group/general/202...

In a new preprint we use deep learning on lineage trees to infer the functional form of the relationship between affinity and fitness that controls antibody evolution in germinal centers: arxiv.org/abs/2508.09871 🧵

Here are some useful subagents we've developed for Claude Code. github.com/matsengrp/c... (description in README if you don't know what I'm talking about) Example uses:

Motivated by wanting Claude Code to read papers, and something to fill PDF forms for kid summer camps, I vibe-coded github.com/matsengrp/p... Perhaps you will find it useful!

Go Maggie! @magdalenarussell.bsky.social gets UW's Distinguished Dissertation Award for her PhD work with @matsen.bsky.social "Inferring mechanisms of V(D)J recombination using statistical inference on high-throughput immune repertoire data". 🏆

Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/ www.biorxiv.org/content/10.1...

Wanted to highlight our latest preprint--a huge effort by multiple people and labs, but led primarily by @wsdewitt.github.io, Tatsuya Araki, and Ashni Vora, in a very close wet-dry collaboration with @matsen.bsky.social’s lab at the Hutch www.biorxiv.org/content/10.1...

Working with Claude Code has been transformative. Yes, it does great on new code and refactoring. VSCode integration is 👍. But the big surprise: it can seamlessly edit notebooks and then view the plots to plan next steps. Time to update my blog post matsen.group/general/202...

Many of my favorite collaborators are immigrants who face double threats of funding cuts and the anti-immigrant political climate. To them and immigrants generally: we need you, and we want you here. I understand if you want to leave but I hope you will stay and reach out.

I'm excited about AI not as a way to get a big black-box model, but as a way to assist development of probabilistic models that get us to biological mechanism. New blog post: matsen.group/general/2025...

New blog post: our recent work to understand the somatic hypermutation process that enables antibodies to incrementally improve. A story of running into the limitations of deep learning, but still gaining biological insight along the way. matsen.group/general/2025...

I'm excited about this talk in a week. Faruck has been doing coevolution -> structure since before it was cool, e.g. www.pnas.org/doi/abs/10.1...

Congratulations to Maggie Russell @magdalenarussell.bsky.social for graduating from @mcbseattle.bsky.social with a phenomenal thesis. I will retell the story of her thesis through images from her papers. 🧵 (Here we are with Phil Bradley, who co-advised Maggie.)

Big news from Sebastien Roch and collabs on phylogenetic likelihood function: "... we show that the expected log-likelihood is strongly concave and smooth in a box around the true parameter whose size is independent of both the tree topology and number of leaves." arxiv.org/abs/2501.17622

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome: [1/N] www.biorxiv.org/content/10.1...

Large protein language models can learn complex epistatic interactions, but how much does that help with predicting variant effects? In this NeurIPS article, we show that classical independent-sites phylogenetic models can outperform pLMs on this task. 1/7 openreview.net/forum?id=H7m...

We are here! All future seminar announcements will be posted here.