# Multi-modal transformer for signal classification in nanopore blockade experiments

arXiv: https://arxiv.org/abs/2607.20323 · HTML: https://mlsanity.com/paper/2607.20323/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 37 references that are in the map.
- First posted on arXiv 22 Jul 2026.

## Builds on (most cited first, 10 of 10)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [CrossViT: Cross-Attention Multi-Scale Vision Transformer for Image Classification](https://mlsanity.com/paper/2103.14899/) (2021)
- [Quantifying Attention Flow in Transformers](https://mlsanity.com/paper/2005.00928/) (2020)
- [catch22: CAnonical Time-series CHaracteristics](https://mlsanity.com/paper/1901.10200/) (2019)
- [Pre-training of Lightweight Vision Transformers on Small Datasets with Minimally Scaled Images](https://mlsanity.com/paper/2402.03752/) (2024)
- [Deep Learning-Driven Peptide Classification in Biological Nanopores](https://mlsanity.com/paper/2509.14029/) (2025)

## Abstract (arXiv)

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.