Objective comparison of methods to decode anomalous diffusion.

Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers.

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

The growing interest in machine learning methods has raised the need for a careful study of their application to the experimental single-particle tracking data. In this paper, we present the differences in the classification of the fractional anomalous diffusion trajectories that arise from the selection of the features used in random forest and gradient boosting algorithms. Comparing two recently used sets of human-engineered attributes with a new one, which was tailor-made for the problem, we show the importance of a thoughtful choice of the features and parameters. We also analyse the influence of alterations of synthetic training data set on the classification results. The trained classifiers are tested on real trajectories of G proteins and their receptors on a plasma membrane.

Classification of particle trajectories in living cells: Machine learning versus statistical testing hypothesis for fractional anomalous diffusion.

Single-particle tracking (SPT) has become a popular tool to study the intracellular transport of molecules in living cells. Inferring the character of their dynamics is important, because it determines the organization and functions of the cells. For this reason, one of the first steps in the analysis of SPT data is the identification of the diffusion type of the observed particles. The most popular method to identify the class of a trajectory is based on the mean-square displacement (MSD). However, due to its known limitations, several other approaches have been already proposed. With the recent advances in algorithms and the developments of modern hardware, the classification attempts rooted in machine learning (ML) are of particular interest. In this work, we adopt two ML ensemble algorithms, i.e., random forest and gradient boosting, to the problem of trajectory classification. We present a new set of features used to transform the raw trajectories data into input vectors required by the classifiers. The resulting models are then applied to real data for G protein-coupled receptors and G proteins. The classification results are compared to recent statistical methods going beyond MSD.

Classification of diffusion modes in single-particle tracking data: Feature-based versus deep-learning approach.

Single-particle trajectories measured in microscopy experiments contain important information about dynamic processes occurring in a range of materials including living cells and tissues. However, extracting that information is not a trivial task due to the stochastic nature of the particles' movement and the sampling noise. In this paper, we adopt a deep-learning method known as a convolutional neural network (CNN) to classify modes of diffusion from given trajectories. We compare this fully automated approach working with raw data to classical machine learning techniques that require data preprocessing and extraction of human-engineered features from the trajectories to feed classifiers like random forest or gradient boosting. All methods are tested using simulated trajectories for which the underlying physical model is known. From the results it follows that CNN is usually slightly better than the feature-based methods, but at the cost of much longer processing times. Moreover, there are still some borderline cases in which the classical methods perform better than CNN.

Inhomogeneous membrane receptor diffusion explained by a fractional heteroscedastic time series model.

Single particle tracking experiments have recently uncovered that the motion of cell membrane components can undergo changes of diffusivity as a result of the heterogeneous environment, producing subdiffusion and nonergodic behavior. In this paper, we show that an autoregressive fractionally integrated moving average (ARFIMA) with noise given by generalized autoregressive conditional heteroscedasticity (GARCH) can describe inhomogeneous diffusion in the cell membrane, where the ARFIMA process models anomalous diffusion and the GARCH process explains a fluctuating diffusion parameter.

Detection of ε-ergodicity breaking in experimental data-A study of the dynamical functional sensibility.

The ergodicity breaking phenomenon has already been in the area of interest of many scientists, who tried to uncover its biological and chemical origins. Unfortunately, testing ergodicity in real-life data can be challenging, as sample paths are often too short for approximating their asymptotic behaviour. In this paper, the authors analyze the minimal lengths of empirical trajectories needed for claiming the ε-ergodicity based on two commonly used variants of an autoregressive fractionally integrated moving average model. The dependence of the dynamical functional on the parameters of the process is studied. The problem of choosing proper ε for ε-ergodicity testing is discussed with respect to especially the variation of the innovation process and the data sample length, with a presentation on two real-life examples.

Identifying ergodicity breaking for fractional anomalous diffusion: Criteria for minimal trajectory length.

In this paper, we study ergodic properties of α-stable autoregressive fractionally integrated moving average (ARFIMA) processes which form a large class of anomalous diffusions. A crucial practical question is how long trajectories one needs to observe in an experiment in order to claim that the analyzed data are ergodic or not. This will be solved by checking the asymptotic convergence to 0 of the empirical estimator F(n) for the dynamical functional D(n) defined as a Fourier transform of the n-lag increments of the ARFIMA process. Moreover, we introduce more flexible concept of the ε-ergodicity.