CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data
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Publication:115102
DOI10.48550/ARXIV.2006.09003arXiv2006.09003OpenAlexW4287756599MaRDI QIDQ115102FDOQ115102
Authors: Paul Freulon, Jérémie Bigot, Boris Hejblum, Paul Freulon, Jérémie Bigot, Boris P. Hejblum 
Publication date: 16 June 2020
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: The automated analysis of flow cytometry measurements is an active research field. We introduce a new algorithm, referred to as CytOpT, using regularized optimal transport to directly estimate the different cell population proportions from a biological sample characterized with flow cytometry measurements. We rely on the regularized Wasserstein metric to compare cytometry measurements from different samples, thus accounting for possible mis-alignment of a given cell population across sample (due to technical variability from the technology of measurements). In this work, we rely on a supervised learning technique based on the Wasserstein metric that is used to estimate an optimal re-weighting of class proportions in a mixture model from a source distribution (with known segmentation into cell sub-populations) to fit a target distribution with unknown segmentation. Due to the high-dimensionality of flow cytometry data, we use stochastic algorithms to approximate the regularized Wasserstein metric to solve the optimization problem involved in the estimation of optimal weights representing the cell population proportions in the target distribution. Several flow cytometry data sets are used to illustrate the performances of CytOpT that are also compared to those of existing algorithms for automatic gating based on supervised learning.
Full work available at URL: https://arxiv.org/abs/2006.09003
Cites Work
- Optimal transport, mean partition, and uncertainty assessment in cluster analysis
- Optimal transport for applied mathematicians. Calculus of variations, PDEs, and modeling
- Wasserstein discriminant analysis
- Asymptotic distribution and convergence rates of stochastic algorithms for entropic optimal transportation between probability measures
- Sequential Dirichlet process mixtures of multivariate skew \(t\)-distributions for model-based clustering of flow cytometry data
- Convolutional Wasserstein distances: efficient optimal transportation on geometric domains
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