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Autoencoder and Optimal Transport to Infer Single-Cell Trajectories of Biological Processes

Karren Dai Yang, Karthik Damodaran, Saradha Venkatchalapathy, Ali C. Soylemezoglu, G.V. Shivashankar, Caroline Uhler
doi: https://doi.org/10.1101/455469
Karren Dai Yang
1Department of Electrical Engineering & Computer Science, and Institute for Data, Systems and Society, Massachusetts Institute of Technology, Cambridge, USA
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Karthik Damodaran
2Mechanobiology Institute, National University of Singapore, Singapore
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Saradha Venkatchalapathy
2Mechanobiology Institute, National University of Singapore, Singapore
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Ali C. Soylemezoglu
1Department of Electrical Engineering & Computer Science, and Institute for Data, Systems and Society, Massachusetts Institute of Technology, Cambridge, USA
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G.V. Shivashankar
2Mechanobiology Institute, National University of Singapore, Singapore
3FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
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Caroline Uhler
1Department of Electrical Engineering & Computer Science, and Institute for Data, Systems and Society, Massachusetts Institute of Technology, Cambridge, USA
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Abstract

Although we can increasingly image and measure biological processes at single-cell resolution, most assays can only take snapshots from a population of cells in time. Here we describe ImageAEOT, which combines an AutoEncoder, to map single-cell Images from different cell populations to a common latent space, with the framework of Optimal Transport to infer cellular trajectories. As a proof-of-concept, we apply ImageAEOT to nuclear and chromatin images during the activation of fibroblasts by tumor cells in engineered 3D tissues. We further validate ImageAEOT on chromatin images of various breast cancer cell lines and human tissue samples, thereby linking alterations in chromatin condensation patterns to different stages of tumor progression. Importantly, ImageAEOT can infer the trajectory of a particular cell from one snapshot in time and identify the changing features to provide early biomarkers for developmental and disease progression.

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Posted October 29, 2018.
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Autoencoder and Optimal Transport to Infer Single-Cell Trajectories of Biological Processes
Karren Dai Yang, Karthik Damodaran, Saradha Venkatchalapathy, Ali C. Soylemezoglu, G.V. Shivashankar, Caroline Uhler
bioRxiv 455469; doi: https://doi.org/10.1101/455469
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Autoencoder and Optimal Transport to Infer Single-Cell Trajectories of Biological Processes
Karren Dai Yang, Karthik Damodaran, Saradha Venkatchalapathy, Ali C. Soylemezoglu, G.V. Shivashankar, Caroline Uhler
bioRxiv 455469; doi: https://doi.org/10.1101/455469

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