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Seyone Chithrananda

@seyonec.bsky.social
263 followers 156 following 3 posts

phd student @stanford | undergrad @berkeleyeecs

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Seyone Chithrananda @seyonec.bsky.social · 06/01/2025
Post-preprint, we’ve added guidance on how to check for exchangeability (i.e.: does a given similarity threshold’s guarantee hold on your test proteins of interest?) prior to calibration, refined code usability and notation. It was awesome working on this with Ron, Anastasios, & crew! (3/3)
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Seyone Chithrananda @seyonec.bsky.social · 06/01/2025
Our work provides steps for how to do calibrated annotation for domains of unknown function, enzyme search, and to conduct proteome-scale structural searches in a fraction of the time through pre-filtering. Think of it as a “model-free pLDDT”-style confidence for embedding-based search! (2/3)
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Seyone Chithrananda @seyonec.bsky.social · 06/01/2025
Excited to share our work on calibrated protein search and genome mining with conformal prediction, now in @naturecomms.bsky.social! 📎 rdcu.be/d5pJG 💻 github.com/ronboger/confo… (1/3)
rdcu.be
Functional protein mining with conformal guarantees
Nature Communications - This study presents a protein search framework with conformal prediction, enabling statistically reliable annotation of protein function. The method improves homology...
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Reposted by Seyone Chithrananda
Yun S. Song @yun-s-song.bsky.social · 16/11/2024
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...
openreview.net
Ultrafast classical phylogenetic method beats large protein...
Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned...
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