Our structural core gene pipeline Unicode is now published at GBE
📄 doi.org/10.1093/gbe/...

Please also check out @dongwookkim.bsky.social’s
🧵 bsky.app/profile/dong...

Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109

Can't wait for when I can vibe code a production recommender system.

Until then, here's some system designs:

• Retrieval vs. Ranking: eugeneyan.com/writing/syst...
• Real-time retrieval: eugeneyan.com/writing/real...
• Personalization: eugeneyan.com/writing/patt...

What industrial recsys papers have you enjoyed or found useful in the past year or two? Sharing my list:

# 1. Integrating LLMs into recsys

1.1. LLM-augmented recommenders
• Better Generalization with Semantic IDs: A Case Study in Ranking for Recommendations
- arxiv.org/abs/2306.08121

SNU Profs Woon Ju Song & Martin Steinegger (Biology) developed the AI-based SeekRank algorithm to discover enzymes for cancer immunotherapy. doi.org/10.1093/nar/...

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...

Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1

And if you're looking for more learning over the long thanksgiving weekend, this could be a good place to start: eugeneyan.com/start-here/

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...