Gabriel Fernández-Fernández, Carlo Manzo, Maciej Lewenstein et al.
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 $β$-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 the autonomous discovery of unknown parameters describing stochastic processes, hence enhancing our comprehension of complex phenomena across various fields.
Jesús Pineda, Sergi Masó-Orriols, Joan Bertran et al.
Single-molecule localization microscopy generates point clouds corresponding to fluorophore localizations. Spatial cluster identification and analysis of these point clouds are crucial for extracting insights about molecular organization. However, this task becomes challenging in the presence of localization noise, high point density, or complex biological structures. Here, we introduce MIRO (Multimodal Integration through Relational Optimization), an algorithm that uses recurrent graph neural networks to transform the point clouds in order to improve clustering efficiency when applying conventional clustering techniques. We show that MIRO supports simultaneous processing of clusters of different shapes and at multiple scales, demonstrating improved performance across varied datasets. Our comprehensive evaluation demonstrates MIRO's transformative potential for single-molecule localization applications, showcasing its capability to revolutionize cluster analysis and provide accurate, reliable details of molecular architecture. In addition, MIRO's robust clustering capabilities hold promise for applications in various fields such as neuroscience, for the analysis of neural connectivity patterns, and environmental science, for studying spatial distributions of ecological data.
Gorka Muñoz-Gil, Miguel Angel Garcia-March, Carlo Manzo et al.
In order to study transport in complex environments, it is extremely important to determine the physical mechanism underlying diffusion, and precisely characterize its nature and parameters. Often, this task is strongly impacted by data consisting of trajectories with short length and limited localization precision. In this paper, we propose a machine learning method based on a random forest architecture, which is able to associate even very short trajectories to the underlying diffusion mechanism with a high accuracy. In addition, the method is able to classify the motion according to normal or anomalous diffusion, and determine its anomalous exponent with a small error. The method provides highly accurate outputs even when working with very short trajectories and in the presence of experimental noise. We further demonstrate the application of transfer learning to experimental and simulated data not included in the training/testing dataset. This allows for a full, high-accuracy characterization of experimental trajectories without the need of any prior information.