Chloe Hsu

 

This was my academic website. I completed my PhD at the University of California, Berkeley, advised by Jennifer Listgarten and Moritz Hardt.

Research

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Generative models for protein structures and sequences


Chloe Hsu, Clara Fannjiang, and Jennifer Listgarten
Nature Biotechnology, 2024
paper

(Published as a primer) How can generative models be useful for protein engineering?

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Learning inverse folding from millions of predicted structures


Chloe Hsu, Robert Verkuil, Jason Liu, Zeming Lin, Brian Hie, Tom Sercu, Adam Lerer*, Alexander Rives*
ICML (Outstanding Paper Runner Up Award), 2022
paper | code | slides | colab notebook

Inverse folding aims to design sequences to fold into desired structures. With 12M new predicted structures as additional training data, ESM-IF1 is more accurate at structure-based sequence design, while also generalizing to more sophisticated design tasks.

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Learning protein fitness models from evolutionary and assay-labeled data


Chloe Hsu, Hunter Nisonoff, Clara Fannjiang, and Jennifer Listgarten
Nature Biotechnology, 2022
paper | talk | code

A simple yet highly effective hybrid approach to protein fitness prediction. Also a comparative analysis to highlight the importance of systematic evaluations and sufficient baselines.

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Nanopore callers for epigenetics from limited supervised data


Brian Yao, Chloe Hsu, Gal Goldner, Yael Michaeli, Yuval Ebenstein, and Jennifer Listgarten
bioRxiv, 2021
paper

Calling epigenetic modifications on nanopore sequencing platforms when the training data is incomplete.


Design and source code from Jon Barron's website and Leonid Keselman's Jekyll fork.