NEuRT: A Transformer-Based Model for Explainable Neuronal Activity Analysis
Journal:
bioRxiv
Published Date:
Jan 14, 2026
Abstract
The study of neuronal activity is essential for understanding brain function and its alterations in neurodegenerative diseases. Advances in in vivo imaging have enabled real-time observation of neuronal dynamics, but classical statistical methods struggle to capture the complex, time-dependent interactions within neuronal networks. Machine learning offers promising solutions for analyzing high-dimensional neuronal data, yet their application in neuroscience remains limited. Here, we introduce NEuRT, a Bidirectional Encoder Representations from Transformers (BERT)-based model adapted for neuronal activity analysis. NEuRT leverages self-attention mechanisms to interpret complex neuronal interactions, providing insights into patterns that traditional methods may overlook. Pre-trained on the recently introduced large annotated dataset MICrONS for signal reconstruction, NeuRT demonstrates strong generalization, effectively reconstructing activity from both visual cortex two-photon and hippocampal miniature fluorescence microscopy. Built on the BERT architecture, the NEuRT model can be efficiently fine-tuned for a wide range of downstream tasks. We showcase its application in classifying wild-type and transgenic Alzheimers disease model mice, based on hippocampal activity, revealing group-specific features through attention map analysis. By reducing reliance on extensive labeled data, addressing a critical challenge in neuroscience, NEuRT bridges fundamental neuroscience and disease research, offering a robust framework for AI-driven and explainable neuronal activity analysis.
