CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data
| dc.rights.license | open | en_US |
| hal.structure.identifier | Institut de Mathématiques de Bordeaux [IMB] | |
| dc.contributor.author | FREULON, Paul | |
| hal.structure.identifier | Institut de Mathématiques de Bordeaux [IMB] | |
| dc.contributor.author | BIGOT, Jeremie
IDREF: 075404877 | |
| hal.structure.identifier | Statistics In System biology and Translational Medicine [SISTM] | |
| hal.structure.identifier | Bordeaux population health [BPH] | |
| dc.contributor.author | HEJBLUM, Boris
ORCID: 0000-0003-0646-452X IDREF: 189970316 | |
| dc.date.accessioned | 2021-05-07T09:49:58Z | |
| dc.date.available | 2021-05-07T09:49:58Z | |
| dc.date.created | 2020 | |
| dc.identifier.uri | https://oskar-bordeaux.fr/handle/20.500.12278/27198 | |
| dc.description.abstractEn | 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. | |
| dc.language.iso | EN | en_US |
| dc.subject.en | Automatic gating | |
| dc.subject.en | Flow cytometry | |
| dc.subject.en | Optimal Transport | |
| dc.subject.en | Stochastic Optimization | |
| dc.title.en | CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data | |
| dc.type | Document de travail - Pré-publication | en_US |
| dc.subject.hal | Statistiques [stat]/Machine Learning [stat.ML] | en_US |
| dc.subject.hal | Sciences du Vivant [q-bio]/Biologie cellulaire | en_US |
| dc.identifier.arxiv | 2006.09003 | en_US |
| bordeaux.journal | Annals of Applied Statistics | |
| bordeaux.hal.laboratories | Bordeaux Population Health Research Center (BPH) - UMR 1219 | en_US |
| bordeaux.institution | Université de Bordeaux | en_US |
| bordeaux.institution | INSERM | en_US |
| bordeaux.team | SISTM_BPH | |
| bordeaux.import.source | hal | |
| hal.identifier | hal-03100405 | |
| hal.version | 1 | |
| hal.export | false | |
| workflow.import.source | hal | |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Annals%20of%20Applied%20Statistics&rft.au=FREULON,%20Paul&BIGOT,%20Jeremie&HEJBLUM,%20Boris&rft.genre=preprint |
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