Bayesian inference with scaled Brownian motion

We present a Bayesian inference scheme for scaled Brownian motion, and investigate its performance on synthetic data for parameter estimation and model selection in a combined inference with fractional Brownian motion. We include the possibility of measurement noise in both models. We find that for trajectories of a few hundred time points the procedure is able to resolve well the true model and parameters. Using the prior of the synthetic data generation process also for the inference, the approach is optimal based on decision theory. We include a comparison with inference using a prior different from the data generating one.

[1]  Doreen Eichel,et al.  Data Analysis A Bayesian Tutorial , 2016 .

[2]  A. Einstein Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen [AdP 17, 549 (1905)] , 2005, Annalen der Physik.

[3]  Ralf Metzler,et al.  Non-Gaussian, non-ergodic, and non-Fickian diffusion of tracers in mucin hydrogels. , 2019, Soft matter.

[4]  Schwartz,et al.  Diffusion propagator as a probe of the structure of porous media. , 1992, Physical review letters.

[5]  M. A. Lomholt,et al.  Bayesian inference with information content model check for Langevin equations. , 2017, Physical review. E.

[6]  S. Thapa,et al.  Bayesian inference of Lévy walks via hidden Markov models , 2021, Journal of Physics A: Mathematical and Theoretical.

[7]  Christian P. Robert,et al.  The Bayesian choice , 1994 .

[8]  M. Weiss,et al.  From sub- to superdiffusion: fractional Brownian motion of membraneless organelles in early C. elegans embryos , 2021 .

[9]  D. Reichman,et al.  Anomalous diffusion probes microstructure dynamics of entangled F-actin networks. , 2004, Physical review letters.

[10]  M. Saxton,et al.  Anomalous subdiffusion in fluorescence photobleaching recovery: a Monte Carlo study. , 2001, Biophysical journal.

[11]  Gernot Guigas,et al.  The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved , 2007, FEBS letters.

[12]  D. Dunson,et al.  Discontinuous Hamiltonian Monte Carlo for discrete parameters and discontinuous likelihoods , 2017, 1705.08510.

[13]  E. Montroll,et al.  Anomalous transit-time dispersion in amorphous solids , 1975 .

[14]  Frederik W. Lund,et al.  Bayesian model selection with fractional Brownian motion , 2018, Journal of Statistical Mechanics: Theory and Experiment.

[15]  Mark Johnston,et al.  Deciphering anomalous heterogeneous intracellular transport with neural networks , 2019, bioRxiv.

[16]  E. Montroll Random walks on lattices , 1969 .

[17]  R. Metzler,et al.  Inequivalence of time and ensemble averages in ergodic systems: exponential versus power-law relaxation in confinement. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  S. C. Lim,et al.  Self-similar Gaussian processes for modeling anomalous diffusion. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[19]  Konstantin Speckner,et al.  Single-Particle Tracking Reveals Anti-Persistent Subdiffusion in Cell Extracts , 2021, Entropy.

[20]  M. Weiss,et al.  Elucidating the origin of anomalous diffusion in crowded fluids. , 2009, Physical review letters.

[21]  Andrey G. Cherstvy,et al.  Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking. , 2014, Physical chemistry chemical physics : PCCP.

[22]  Ralf Metzler,et al.  Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion. , 2014, Physical chemistry chemical physics : PCCP.

[23]  John K Kruschke,et al.  Bayesian data analysis. , 2010, Wiley interdisciplinary reviews. Cognitive science.

[24]  A. Timmermann,et al.  Economic Forecasting , 2007 .

[25]  R. Metzler,et al.  Manipulation and Motion of Organelles and Single Molecules in Living Cells. , 2017, Chemical reviews.

[26]  I. Sokolov,et al.  Scaled Brownian motion as a mean-field model for continuous-time random walks. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[27]  A S Verkman,et al.  Analysis of fluorophore diffusion by continuous distributions of diffusion coefficients: application to photobleaching measurements of multicomponent and anomalous diffusion. , 1998, Biophysical journal.

[28]  K. Burnecki,et al.  Fractional Lévy stable motion can model subdiffusive dynamics. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[29]  R. Friedrich,et al.  Continuous-time random walks: simulation of continuous trajectories. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[30]  B. Mandelbrot,et al.  Fractional Brownian Motions, Fractional Noises and Applications , 1968 .

[31]  Igor M. Sokolov,et al.  Models of anomalous diffusion in crowded environments , 2012 .

[32]  E. Barkai,et al.  Ergodic properties of fractional Brownian-Langevin motion. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[33]  Elliott W. Montroll,et al.  Random Walks on Lattices. III. Calculation of First‐Passage Times with Application to Exciton Trapping on Photosynthetic Units , 1969 .

[34]  R. Metzler,et al.  Anomalous diffusion and power-law relaxation of the time averaged mean squared displacement in worm-like micellar solutions , 2013 .

[35]  Aubrey V. Weigel,et al.  Ergodic and nonergodic processes coexist in the plasma membrane as observed by single-molecule tracking , 2011, Proceedings of the National Academy of Sciences.

[36]  J. Theriot,et al.  Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm. , 2010, Physical review letters.

[37]  Solomon,et al.  Observation of anomalous diffusion and Lévy flights in a two-dimensional rotating flow. , 1993, Physical review letters.

[38]  R. Metzler,et al.  In vivo anomalous diffusion and weak ergodicity breaking of lipid granules. , 2010, Physical review letters.

[39]  J. Klafter,et al.  Fractional brownian motion versus the continuous-time random walk: a simple test for subdiffusive dynamics. , 2009, Physical review letters.

[40]  I. Nordlund Eine neue Bestimmung der Avogadroschen Konstante aus der Brownschen Bewegung kleiner, in Wasser suspendierten Quecksilberkügelchen , 1914 .

[41]  R. Hołyst,et al.  Movement of proteins in an environment crowded by surfactant micelles: anomalous versus normal diffusion. , 2006, The journal of physical chemistry. B.

[42]  K. Berland,et al.  Propagators and time-dependent diffusion coefficients for anomalous diffusion. , 2008, Biophysical journal.

[43]  M. Garcia-Parajo,et al.  A review of progress in single particle tracking: from methods to biophysical insights , 2015, Reports on progress in physics. Physical Society.

[44]  N. Seeman,et al.  Subdiffusion of a sticky particle on a surface. , 2011, Physical review letters.

[45]  J. Klafter,et al.  Detecting origins of subdiffusion: P-variation test for confined systems. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[46]  J. Skilling Nested sampling for general Bayesian computation , 2006 .

[47]  David J. C. MacKay,et al.  Information Theory, Inference, and Learning Algorithms , 2004, IEEE Transactions on Information Theory.

[48]  Microscopic theory of anomalous diffusion based on particle interactions. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[49]  Òscar Garibo i Orts,et al.  Objective comparison of methods to decode anomalous diffusion , 2021, Nature Communications.

[50]  R. Brown XXVII. A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies , 1828 .

[51]  Benoit B. Mandelbrot,et al.  Fractal Geometry of Nature , 1984 .

[52]  Andrey G. Cherstvy,et al.  Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data. , 2018, Physical chemistry chemical physics : PCCP.