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CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction

Emaad Khwaja, View ORCID ProfileYun S. Song, View ORCID ProfileBo Huang
doi: https://doi.org/10.1101/2022.05.27.493774
Emaad Khwaja
*UC Berkeley - UCSF Joint Bioengineering Graduate Program
‡Computer Science Division, UC Berkeley, CA 94720
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Yun S. Song
†Department of Statistics, UC Berkeley, CA 94720
‡Computer Science Division, UC Berkeley, CA 94720
§Chan Zuckerberg Biohub, San Francisco, CA 94158
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Bo Huang
§Chan Zuckerberg Biohub, San Francisco, CA 94158
¶Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA 94143
‖Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94143
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  • For correspondence: bo.huang@ucsf.edu
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Abstract

Predicting the cellular activities of proteins from their primary amino acid sequences is a highly desirable capability that could greatly enhance our functional understanding of the proteome. Here, we demonstrate CELL-E, a text-to-image transformer architecture, which given a protein sequence and a reference image for cell (or nucleus) morphology, can generate a 2D probability density map of the protein distribution within cells. Unlike previous in silico methods, which rely on existing, discrete class annotation of protein localization to predefined subcellular compartments, CELL-E uses imaging data directly, thus relying on a native description of protein localization relative to the cellular context.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • emaad{at}berkeley.edu, yss{at}berkeley.edu, bo.huang{at}ucsf.edu

  • https://github.com/BoHuangLab/Protein-Localization-Transformer

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 29, 2022.
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CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction
Emaad Khwaja, Yun S. Song, Bo Huang
bioRxiv 2022.05.27.493774; doi: https://doi.org/10.1101/2022.05.27.493774
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CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction
Emaad Khwaja, Yun S. Song, Bo Huang
bioRxiv 2022.05.27.493774; doi: https://doi.org/10.1101/2022.05.27.493774

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