Literature DB >> 30255886

Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data.

Samudrajit Thapa1, Michael A Lomholt, Jens Krog, Andrey G Cherstvy, Ralf Metzler.   

Abstract

We employ Bayesian statistics using the nested-sampling algorithm to compare and rank multiple models of ergodic diffusion (including anomalous diffusion) as well as to assess their optimal parameters for in silico-generated and real time-series. We focus on the recently-introduced model of Brownian motion with "diffusing diffusivity"-giving rise to widely-observed non-Gaussian displacement statistics-and its comparison to Brownian and fractional Brownian motion, also for the time-series with some measurement noise. We conduct this model-assessment analysis using Bayesian statistics and the nested-sampling algorithm on the level of individual particle trajectories. We evaluate relative model probabilities and compute best-parameter sets for each diffusion model, comparing the estimated parameters to the true ones. We test the performance of the nested-sampling algorithm and its predictive power both for computer-generated (idealised) trajectories as well as for real single-particle-tracking trajectories. Our approach delivers new important insight into the objective selection of the most suitable stochastic model for a given time-series. We also present first model-ranking results in application to experimental data of tracer diffusion in polymer-based hydrogels.

Entities:  

Year:  2018        PMID: 30255886     DOI: 10.1039/c8cp04043e

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  9 in total

1.  A Jump-Distance-Based Parameter Inference Scheme for Particulate Trajectories.

Authors:  Rebecca Menssen; Madhav Mani
Journal:  Biophys J       Date:  2019-06-12       Impact factor: 4.033

2.  Single-Particle Diffusion Characterization by Deep Learning.

Authors:  Naor Granik; Lucien E Weiss; Elias Nehme; Maayan Levin; Michael Chein; Eran Perlson; Yael Roichman; Yoav Shechtman
Journal:  Biophys J       Date:  2019-06-22       Impact factor: 4.033

3.  TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data.

Authors:  Francesco Reina; John M A Wigg; Mariia Dmitrieva; Bela Vogler; Joël Lefebvre; Jens Rittscher; Christian Eggeling
Journal:  F1000Res       Date:  2021-08-20

4.  NOBIAS: Analyzing anomalous diffusion in single-molecule tracks with nonparametric Bayesian inference.

Authors:  Ziyuan Chen; Laurent Geffroy; Julie S Biteen
Journal:  Front Bioinform       Date:  2021-09-10

Review 5.  Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments.

Authors:  Colin D Kinz-Thompson; Korak Kumar Ray; Ruben L Gonzalez
Journal:  Annu Rev Biophys       Date:  2021-02-03       Impact factor: 12.981

6.  Impact of Feature Choice on Machine Learning Classification of Fractional Anomalous Diffusion.

Authors:  Hanna Loch-Olszewska; Janusz Szwabiński
Journal:  Entropy (Basel)       Date:  2020-12-19       Impact factor: 2.524

7.  mRBioM: An Algorithm for the Identification of Potential mRNA Biomarkers From Complete Transcriptomic Profiles of Gastric Adenocarcinoma.

Authors:  Changlong Dong; Nini Rao; Wenju Du; Fenglin Gao; Xiaoqin Lv; Guangbin Wang; Junpeng Zhang
Journal:  Front Genet       Date:  2021-07-27       Impact factor: 4.599

8.  Detection of Anomalous Diffusion with Deep Residual Networks.

Authors:  Miłosz Gajowczyk; Janusz Szwabiński
Journal:  Entropy (Basel)       Date:  2021-05-22       Impact factor: 2.524

9.  Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion.

Authors:  Henrik D Pinholt; Søren S-R Bohr; Josephine F Iversen; Wouter Boomsma; Nikos S Hatzakis
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-03       Impact factor: 11.205

  9 in total

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