Change point detection has become an important part of the analysis of the single-particle tracking data, as it allows one to identify moments, in which the motion patterns of observed particles undergo significant changes. The segmentation of diffusive trajectories based on those moments may provide insight into various phenomena in soft condensed matter and biological physics. In this paper, we propose CINNAMON, a hybrid approach to classifying single-particle tracking trajectories, detecting change points within them, and estimating diffusion parameters in the segments between the change points. Our method is based on a combination of neural networks, feature-based machine learning, and statistical techniques. It has been benchmarked in the second Anomalous Diffusion Challenge. The method offers a high level of interpretability due to its analytical and feature-based components. A potential use of features from topological data analysis is also discussed.

Characterizing anomalous diffusion is crucial in order to understand the evolution of complex stochastic systems, from molecular interactions to cellular dynamics. In this work, we characterize the performances regarding such a task of Bi-Mamba, a novel state-space deep-learning architecture articulated with a bidirectional scan mechanism. Our implementation is tested on the AnDi-2 challenge datasets among others. As such, our results indicate the potential practical use of the Bi-Mamba architecture for anomalousdiffusion characterization. Deep-learning methods for advanced microscopy have thus emerged as a promising change of paradigm [13].

The rapid advancements in machine learning have made its application to anomalous diffusion analysis both essential and inevitable. This review systematically introduces the integration of machine learning techniques for enhanced analysis of anomalous diffusion, focusing on two pivotal aspects: single trajectory characterization via machine learning and representation learning of anomalous diffusion. We extensively compare various machine learning methods, including both classical machine learning and deep learning, used for the inference of diffusion parameters and trajectory segmentation. Additionally, platforms such as the Anomalous Diffusion Challenge that serve as benchmarks for evaluating these methods are highlighted. On the other hand, we outline three primary strategies for representing anomalous diffusion: the combination of predefined features, the feature vector from the penultimate layer of neural network, and the latent representation from the autoencoder, analyzing their applicability across various scenarios. This investigation paves the way for future research, offering valuable perspectives that can further enrich the study of anomalous diffusion and advance the application of artificial intelligence in statistical physics and biophysics.

While deep learning has been successfully applied to the data-driven classification of anomalous diffusion mechanisms, how the algorithm achieves the feat still remains a mystery. In this study, we use a well-known technique aimed at achieving explainable AI, namely the Gradient-weighted Class Activation Map (Grad-CAM), to investigate how deep learning (implemented by ResNets) recognizes the distinctive features of a particular anomalous diffusion model from the raw trajectory data. Our results show that Grad-CAM reveals the portions of the trajectory that hold crucial information about the underlying mechanism of anomalous diffusion, which can be utilized to enhance the robustness of the trained classifier against the measurement noise. Moreover, we observe that deep learning distills unique statistical characteristics of different diffusion mechanisms at various spatiotemporal scales, with larger-scale (smaller-scale) features identified at higher (lower) layers.

Time-fractional differential equations offer a robust framework for capturing intricate phenomena characterized by memory effects, particularly in fields like biotransport and rheology. However, solving inverse problems involving fractional derivatives presents notable challenges, including issues related to stability and uniqueness. While Physics-Informed Neural Networks (PINNs) have emerged as effective tools for solving inverse problems, most existing PINN frameworks primarily focus on integer-ordered derivatives. In this study, we extend the application of PINNs to address inverse problems involving time-fractional derivatives, specifically targeting two problems: 1) anomalous diffusion and 2) fractional viscoelastic constitutive equation. Leveraging both numerically generated datasets and experimental data, we calibrate the concentration-dependent generalized diffusion coefficient and parameters for the fractional Maxwell model. We devise a tailored residual loss function that scales with the standard deviation of observed data. We rigorously test our framework's efficacy in handling anomalous diffusion. Even after introducing 25% Gaussian noise to the concentration dataset, our framework demonstrates remarkable robustness. Notably, the relative error in predicting the generalized diffusion coefficient and the order of the fractional derivative is less than 10% for all cases, underscoring the resilience and accuracy of our approach. In another test case, we predict relaxation moduli for three pig tissue samples, consistently achieving relative errors below 10%. Furthermore, our framework exhibits promise in modeling anomalous diffusion and non-linear fractional viscoelasticity.

Anomalous diffusion processes pose a unique challenge in classification and characterization. Previously (Mangalam et al., 2023, Physical Review Research 5, 023144), we established a framework for understanding anomalous diffusion using multifractal formalism. The present study delves into the potential of multifractal spectral features for effectively distinguishing anomalous diffusion trajectories from five widely used models: fractional Brownian motion, scaled Brownian motion, continuous time random walk, annealed transient time motion, and L\'evy walk. To accomplish this, we generate extensive datasets comprising $10^6$ trajectories from these five anomalous diffusion models and extract multiple multifractal spectra from each trajectory. Our investigation entails a thorough analysis of neural network performance, encompassing features derived from varying numbers of spectra. Furthermore, we explore the integration of multifractal spectra into traditional feature datasets, enabling us to assess their impact comprehensively. To ensure a statistically meaningful comparison, we categorize features into concept groups and train neural networks using features from each designated group. Notably, several feature groups demonstrate similar levels of accuracy, with the highest performance observed in groups utilizing moving-window characteristics and $p$-variation features. Multifractal spectral features, particularly those derived from three spectra involving different timescales and cutoffs, closely follow, highlighting their robust discriminatory potential. Remarkably, a neural network exclusively trained on features from a single multifractal spectrum exhibits commendable performance, surpassing other feature groups. Our findings underscore the diverse and potent efficacy of multifractal spectral features in enhancing classification of anomalous diffusion.

Stochastic processes have found numerous applications in science, as they are broadly used to model a variety of natural phenomena. Due to their intrinsic randomness and uncertainty, they are however difficult to characterize. Here, we introduce an unsupervised machine learning approach to determine the minimal set of parameters required to effectively describe the dynamics of a stochastic process. Our method builds upon an extended $\beta$-variational autoencoder architecture. By means of simulated datasets corresponding to paradigmatic diffusion models, we showcase its effectiveness in extracting the minimal relevant parameters that accurately describe these dynamics. Furthermore, the method enables the generation of new trajectories that faithfully replicate the expected stochastic behavior. Overall, our approach enables for the autonomous discovery of unknown parameters describing stochastic processes, hence enhancing our comprehension of complex phenomena across various fields.

Anomalous diffusion, as it has come to be called, extends the concept of Brownian motion and is connected to disordered systems, non-equilibrium phenomena, flows of energy and information, and transport in living systems[3]. Anomalous diffusion is "non-universal" in the sense that physically very different systems share the same power-law form of the mean squared displacement x

The results of the Anomalous Diffusion Challenge (AnDi Challenge) have shown that machine learning methods can outperform classical statistical methodology at the characterization of anomalous diffusion in both the inference of the anomalous diffusion exponent alpha associated with each trajectory (Task 1), and the determination of the underlying diffusive regime which produced such trajectories (Task 2). Furthermore, of the five teams that finished in the top three across both tasks of the AnDi challenge, three of those teams used recurrent neural networks (RNNs). While RNNs, like the long short-term memory (LSTM) network, are effective at learning long-term dependencies in sequential data, their key disadvantage is that they must be trained sequentially. In order to facilitate training with larger data sets, by training in parallel, we propose a new transformer based neural network architecture for the characterization of anomalous diffusion. Our new architecture, the Convolutional Transformer (ConvTransformer) uses a bi-layered convolutional neural network to extract features from our diffusive trajectories that can be thought of as being words in a sentence. These features are then fed to two transformer encoding blocks that perform either regression or classification. To our knowledge, this is the first time transformers have been used for characterizing anomalous diffusion. Moreover, this may be the first time that a transformer encoding block has been used with a convolutional neural network and without the need for a transformer decoding block or positional encoding. Apart from being able to train in parallel, we show that the ConvTransformer is able to outperform the previous state of the art at determining the underlying diffusive regime in short trajectories (length 10-50 steps), which are the most important for experimental researchers.

The characterization of diffusion processes is a keystone in our understanding of a variety of physical phenomena. Many of these deviate from Brownian motion, giving rise to anomalous diffusion. Various theoretical models exists nowadays to describe such processes, but their application to experimental setups is often challenging, due to the stochastic nature of the phenomena and the difficulty to harness reliable data. The latter often consists on short and noisy trajectories, which are hard to characterize with usual statistical approaches. In recent years, we have witnessed an impressive effort to bridge theory and experiments by means of supervised machine learning techniques, with astonishing results. In this work, we explore the use of unsupervised methods in anomalous diffusion data. We show that the main diffusion characteristics can be learnt without the need of any labelling of the data. We use such method to discriminate between anomalous diffusion models and extract their physical parameters. Moreover, we explore the feasibility of finding novel types of diffusion, in this case represented by compositions of existing diffusion models. At last, we showcase the use of the method in experimental data and demonstrate its advantages for cases where supervised learning is not applicable.