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Amy Lu

@amyxlu.bsky.social
914 followers 198 following 10 posts

AI for drug discovery at Isomorphic Labs. Prev: PhD @ UC Berkeley | 🇨🇦

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Reposted by Amy Lu
Milot Mirdita @milot.bsky.social · 20/01/2026
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
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Reposted by Amy Lu
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/01/2025
Just coincidentally found GenBank Release 84.0 from 1994 in the neighboring lab. Anyone out there with an even older version?
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Amy Lu @amyxlu.bsky.social · 28/12/2024
In case you missed our ML for proteins seminar on CHEAP compression for protein embeddings back in October, here it is -- thanks @megthescientist.bsky.social for doing so much for the MLxProteins community 🫶
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Reposted by Amy Lu
Meg T (she/her/hers) @megthescientist.bsky.social · 16/12/2024
•introduced “zero shot prediction” as a question of guessing a bioassay’s outcome by likelihoods of pLMs •commented on biases in evolutionary signals from Tree of life used to train pLMs (a favorite paper I read in 2024: shorturl.at/fbC7g)
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Amy Lu @amyxlu.bsky.social · 15/12/2024
Thanks @workshopmlsb.bsky.social for letting us share our work! 🔗📄 bit.ly/plaid-proteins
bit.ly
Generating All-Atom Protein Structure from Sequence-Only Training Data
Generative models for protein design are gaining interest for their potential scientific impact. However, protein function is mediated by many modalities, and simultaneously generating multiple modali...
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Reposted by Amy Lu
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 09/12/2024
We trained a model to co-generate protein sequence and structure by working in the ESMFold latent space, which encodes both. PLAID only requires sequences for training but generates all-atom structures! Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
generations from PLAIDThe PLAID model architectureConditional generations from PLAID
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Amy Lu @amyxlu.bsky.social · 06/12/2024
1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations: bit.ly/plaid-proteins 🧵
overview of results for PLAID!
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