arXiv subjects

Patrycja Kowalek

Publications and source records attributed to Patrycja Kowalek.

4 recordsLinked to original sources

arXiv2025

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.

physics.data-an↗

arXiv2023

Boosting the performance of anomalous diffusion classifiers with the proper choice of features

Understanding and identifying different types of single molecules' diffusion that occur in a broad range of systems (including living matter) is extremely important, as it can provide information on the physical and chemical characteristics of particles' surroundings. In recent years, an ever-growing number of methods have been proposed to overcome some of the limitations of the mean-squared displacements approach to tracer diffusion. In March 2020, the Anomalous Diffusion (AnDi) Challenge was launched by a community of international scientists to provide a framework for an objective comparison of the available methods for anomalous diffusion. In this paper, we introduce a feature-based machine learning method developed in response to Task 2 of the challenge, i.e. the classification of different types of diffusion. We discuss two sets of attributes that may be used for the classification of single-particle tracking data. The first one was proposed as our contribution to the AnDi Challenge. The latter is the result of our attempt to improve the performance of the classifier after the deadline of the competition. Extreme gradient boosting was used as the classification model. Although the deep-learning approach constitutes the state-of-the-art technology for data classification in many domains, we deliberately decided to pick this traditional machine learning algorithm due to its superior interpretability. After the extension of the feature set our classifier achieved the accuracy of 0.83, which is comparable with the top methods based on neural networks.

q-bio.QM↗

arXiv2020

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.

q-bio.QM↗

arXiv2019

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 undergoing 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 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 costs of much longer processing times. Moreover, there are still some borderline cases, in which the classical methods perform better than CNN.

q-bio.QM↗