How well can deep learning models predict the effect of modifying chromatin on gene expression???
Our work -- led by Sanjit Batra and Alan Cabrera when they were in @yun-s-song.bsky.social ’s and Isaac Hilton’s labs -- tries to answer this.
🧵🧬🧪
elifesciences.org/reviewed-pre...
Congrats to Nathaniel and Sri for their exciting work teaching protein language models to generate beyond what evolution has explored. They introduce Reinforcement Learning from eXperimental Feedback (RLXF) to steer generation toward enhanced and non-natural functions
www.biorxiv.org/content/10.1...
Relationship between perplexity and zero shot performance.
Protein language model likelihood are better zero shot mutation effect predictions when they have perplexity 3-6 on the wildtype sequence.
www.biorxiv.org/content/10.1...
One of the toughest parts of the field of massively parallel reporter assays to measure >~thousands of elements is that there are hundreds of pubs using them, but no central repo to easily locate the results....until now! Great collab w/ Jingjing Zhao, Ilias G-S, and @nadavahituv.bsky.social!!
@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...
Really enjoyed this creative paper using "DNA prompts" to guide Evo in designing genomic sequences. Curious to see how this research evolves.
www.biorxiv.org/content/10.1...
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
Can we bypass the resource bottleneck of pretraining genomic Foundation Models? Our work L2G repurposes language LLMs for genomics via cross-modal transfer, matching fine-tuned genomic FMs. Kudos to Wenduo & fantastic collab w/ @atalwalkar.bsky.social. L2G, language to genome; L2G, life’s too good!
Screenshot of the paper.
Even as an interpretable ML researcher, I wasn't sure what to make of Mechanistic Interpretability, which seemed to come out of nowhere not too long ago.
But then I found the paper "Mechanistic?" by
@nsaphra.bsky.social and @sarah-nlp.bsky.social, which clarified things.
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4
arxiv.org/abs/2411.11158
