Data-Efficient Learning of Anomalous Diffusion with Wavelet Representations: Enabling Direct Learning from Experimental Trajectories

TL;DR

This paper introduces a wavelet-based representation for anomalous diffusion trajectories that enables data-efficient learning directly from scarce experimental data, outperforming existing methods in both simulated and real-world scenarios.

Contribution

The authors develop a wavelet representation that allows direct, data-efficient learning from experimental trajectories, reducing reliance on large simulated datasets and improving analysis accuracy.

Findings

Outperforms feature-based and trajectory-based methods with as few as 1000 training trajectories.

Achieves lower error in diffusion exponent prediction on experimental data compared to deep learning trained on millions of simulated trajectories.

Remains superior on large training sets, demonstrating robustness and scalability.

Abstract

Machine learning (ML) has become a versatile tool for analyzing anomalous diffusion trajectories, yet most existing pipelines are trained on large collections of simulated data. In contrast, experimental trajectories, such as those from single-particle tracking (SPT), are typically scarce and may differ substantially from the idealized models used for simulation, leading to degradation or even breakdown of performance when ML methods are applied to real data. To address this mismatch, we introduce a wavelet-based representation of anomalous diffusion that enables data-efficient learning directly from experimental recordings. This representation is constructed by applying six complementary wavelet families to each trajectory and combining the resulting wavelet modulus scalograms. We first evaluate the wavelet representation on simulated trajectories from the andi-datasets benchmark, where it clearly outperforms both feature-based and trajectory-based methods with as few as 1000 training trajectories and still retains an advantage on large training sets. We then use this representation to learn directly from experimental SPT trajectories of fluorescent beads diffusing in F-actin networks, where the wavelet representation remains superior to existing alternatives for both diffusion-exponent regression and mesh-size classification. In particular, when predicting the diffusion exponents of experimental trajectories, a model trained on 1200 experimental tracks using the wavelet representation achieves significantly lower errors than state-of-the-art deep learning models trained purely on $10^6$ simulated trajectories. We associate this data efficiency with the emergence of distinct scale fingerprints disentangling underlying diffusion mechanisms in the wavelet spectra.