EnhancAR: Use evolution and deep learning to design enhancers with desired expression profiles! Had a lot of fun working with Andrew Duncan, Micaela Consens @alexijie.bsky.social @lcrawford.bsky.social Jennifer Mitchell and Alan Moses! www.biorxiv.org/content/10.6...

Check out how we exploit observations of homology from evolution to design enhancers, even when we don't have prior knowledge or ability to specify function!

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 5mo ago

EnhancAR: Use evolution and deep learning to design enhancers with desired expression profiles! Had a lot of fun working with Andrew Duncan, Micaela Consens @alexijie.bsky.social @lcrawford.bsky.social Jennifer Mitchell and Alan Moses! www.biorxiv.org/content/10.6...

Five years ago, we released FLIP. The core question was: can ML models for protein fitness prediction generalize in the ways that actually matter for protein engineering, i.e. low data, extrapolation to more mutations, out-of-distribution sequences?

We made FLIP2, a protein fitness benchmark spanning seven new datasets, including enzymes, protein-protein interactions, and light-sensitive proteins, as well as splits that measure generalization relevant to real-world protein engineering campaigns.

Come do a PhD internship with me!

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 10mo ago

You have until Dec 1 to apply to the bioml PhD research internship! This is where you apply to work with me, @alexijie.bsky.social @avapamini.bsky.social @lcrawford.bsky.social or Kristen Severson! (new) link and some instructions below apply.careers.microsoft.com/careers/job/...

Was incredible to work with Arushi during her summer internship - check out her preprint showing that single cell representation learning methods for microscopy can be confounded by cells in the background of their inputs!

Arushi Gupta@arushigupta.bsky.social · last yr.

This work began from a summer internship at ‪@msftresearch.bsky.social‬ New England. Incredibly thankful to mentors @alexijie.bsky.social and Alan Moses, whose deep involvement and guidance made this possible! 📄: www.biorxiv.org/content/10.1... 💻: tinyurl.com/microscopy-c...

Read our preprint that demonstrates a growing bias in medical imaging datasets against pediatrics, and how it impacts downstream AI development! Props to our first author @stanhua.bsky.social, who among many other feats, filtered hundreds of datasets/papers to establish this trend.

@stanhua.bsky.social · last yr.

The release of public datasets is driving innovations in healthcare AI, but are children seeing the benefit? Our systematic dataset review reveals that children account for less than 1% of patients across 181 public medical imaging datasets. #HealthEquity #SafePediatricAI

At NeurIPS and interested in talking about BioML? Catch me at the Microsoft booth in the expo hall between 2:00-2:30p and 3:30-4:30p today!