Ava Amini

@avapamini

principal researcher @MSFTResearch | AI for biomedicine | instructor @MITDeepLearning | alumna @MIT @Harvard

avaamini.com

Joined September 2014

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Ava Amini
@avapamini
Jul 26, 2025
thrilled to share The Dayhoff Atlas of protein language data and models 🚀 protein biology in the age of AI! aka.ms/dayhoff/prepri… we built + open source the largest natural protein dataset, w/ 3.3 billion seqs & a first-in-class dataset of structure-based synthetic proteins
Microsoft Research and 4 others
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Ava Amini
@avapamini
Apr 16
The Hallmarks of Cancer brought clarity through abstraction - but cancer is more complex than we can reduce. honored to build on their legacy in our @CellCellPress perspective on generative models as unified, multimodal systems for cancer discovery 📄 msft.it/6013QhkUS !
Microsoft Research and 2 others
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Ava Amini
@avapamini
Apr 7
excited to release a new benchmark for protein fitness prediction: FLIP2 FLIP2 has 7 new datasets spanning enzymes, PPIs, and light-sensitive proteins, + splits designed to test generalization in realistic protein engineering settings paper, data, code: flip.protein.properties
Microsoft Research and 4 others
Kevin K. Yang 楊凱筌
@KevinKaichuang
Feb 25
We made FLIP2, a protein fitness benchmark spanning seven new datasets, including enzymes, protein-protein interactions, and light-sensitive proteins, as well as splits that measure generalization relevant to real-world protein engineering campaigns.
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Ava Amini
@avapamini
Mar 31
protein language models capture rich structural signals, but where that knowledge lives in the network is still unclear we show that small subnetworks inside PLMs encode structural concepts, from residues to folds journals.plos.org/ploscompbiol/a… @PLOSCompBiol work led by @riavinod_!
Microsoft Research and 5 others
Ava Amini
@avapamini
Mar 25
cell types are hierarchical, but single-cell models ignore this we introduced hierarchical cross-entropy: a simple loss to align models with biological ontologies to improve cell type annotation nature.com/articles/s4358… @NatComputSci great work @sebacultrera @davide_dascenzo!
Microsoft Research and 7 others
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