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arXiv · 2607.20323

Multi-modal transformer for signal classification in nanopore blockade experiments

Sandro Kuppel·Julian Hoßbach·Samuel Tovey·Christian Holm
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Abstract

Nanopore devices have emerged as powerful tools for single-molecule sensing, with potential for rapid, portable diagnostics. They detect changes in ionic current as analytes enter nanometer-scale pores, providing a means of identifying diverse biomarkers from their characteristic signal patterns. However, these signals are highly complex, and reliably assigning them to specific molecules remains a major challenge. Here, we address this by introducing a multi-modal deep learning architecture that jointly processes multiple signal representations, including raw time-series data, wavelet-based images, and static feature vectors. Our approach surpasses existing methods by more than 10 percentage points on a 42-peptide benchmark and transfers to a 20-amino-acid dataset with near-perfect accuracy. The model integrates complementary information from these representations, with attention analysis showing that the time-series and wavelet-image inputs emphasize different features of the same event. Together, these results demonstrate the potential of machine learning to enable robust, high-accuracy molecular identification with nanopore sensors.

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Sandro Kuppel, Julian Hoßbach, Samuel Tovey, Christian Holm. 2026-07-22. Multi-modal transformer for signal classification in nanopore blockade experiments. https://arxiv.org/abs/2607.20323

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