Deciphering anomalous heterogeneous intracellular transport with neural networks
- University of Manchester, United Kingdom
Abstract
Intracellular transport is predominantly heterogeneous in both time and space, exhibiting varying non-Brownian behavior. Characterization of this movement through averaging methods over an ensemble of trajectories or over the course of a single trajectory often fails to capture this heterogeneity. Here, we developed a deep learning feedforward neural network trained on fractional Brownian motion, providing a novel, accurate and efficient method for resolving heterogeneous behavior of intracellular transport in space and time. The neural network requires significantly fewer data points compared to established methods. This enables robust estimation of Hurst exponents for very short time series data, making possible direct, dynamic segmentation and analysis of experimental tracks of rapidly moving cellular structures such as endosomes and lysosomes. By using this analysis, fractional Brownian motion with a stochastic Hurst exponent was used to interpret, for the first time, anomalous intracellular dynamics, revealing unexpected differences in behavior between closely related endocytic organelles.
Data availability
Supporting files are on GitHub and Zenodo.
Article and author information
Author details
Funding
Wellcome Trust (215189/Z/19/Z)
- Daniel Han
EPSRC (EP/J019526/1)
- Nickolay Korabel
- Victoria J Allan
- Sergei Fedotov
- Thomas A Waigh
BBSRC (BB/H017828/1)
- Victoria J Allan
Wellcome Trust (108867/Z/15/Z)
- Anna Gavrilova
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Robert H Singer, Albert Einstein College of Medicine, United States
Publication history
- Received: September 26, 2019
- Accepted: March 22, 2020
- Accepted Manuscript published: March 24, 2020 (version 1)
- Version of Record published: April 8, 2020 (version 2)
- Version of Record updated: May 26, 2020 (version 3)
Copyright
© 2020, Han et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Deciphering anomalous heterogeneous intracellular transport with neural networks
eLife 9:e52224.
https://doi.org/10.7554/eLife.52224
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