Youtube: https://youtu.be/w6L9-ySnxZI?si=7RBusTAyy0Ums6Oh
Spotify: https://open.spotify.com/episode/2EgnV9Y1Mm9JV5m9KAY6yL?si=GcZR80aFS26uO88lpmadBQ
Apple Podcast: https://apple.co/4pu4TRB
Transcript: https://www.owlposting.com/p/we-dont-know-what-most-microbial
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This is an interview with Yunha Hwang, an assistant professor at MIT (and co-founder of the non-profit Tatta Bio). She is working on building and applying genomic language models to help annotate the function of the (mostly unknown) universe of microbial genomes.
There are two reasons I filmed this (and think its worth watching):
One, Yunha is working on an absurdly difficult and interesting problem: microbial genome function annotation. Even for E. coli, one of the most studied organisms on Earth, we don’t know what half to two-thirds of its genes actually do. For a random microbe from soil, that number jumps to 80-90%. Her lab is one of the leading groups working to apply deep learning to solving the problem, and last year, released a paper that increasingly feels foundational within it (with prior podcast guest Sergey Ovchinnikov an author on it!). We talk about that paper, its implications, and where the future of machine learning in metagenomics may go.
And two, I was especially excited to film this so I could help bring some light to a platform that she and her team at Tatta Bio has developed: SeqHub. There’s been a lot of discussion online about AI co-scientists in the biology space, but I have increasingly felt a vague suspicion that people are trying to be too broad with them. It feels like the value of these tools are not with general scientific reasoning, but rather from deep integration with how a specific domain of research engages with their open problems. SeqHub feels like one of the few systems that mirrors this viewpoint, and while it isn’t something I can personally use—since its use-case is primarily in annotating and sharing microbial genomes, neither of which I work on!—I would still love for it to succeed. If you’re in the metagenomics space, you should try it out at seqhub.org!