Ziyu Lu

Ziyu Lu, Anika Tabassum, Shruti Kulkarni et al.

This paper explores the potential of the transformer models for learning Granger causality in networks with complex nonlinear dynamics at every node, as in neurobiological and biophysical networks. Our study primarily focuses on a proof-of-concept investigation based on simulated neural dynamics, for which the ground-truth causality is known through the underlying connectivity matrix. For transformer models trained to forecast neuronal population dynamics, we show that the cross attention module effectively captures the causal relationship among neurons, with an accuracy equal or superior to that for the most popular Granger causality analysis method. While we acknowledge that real-world neurobiology data will bring further challenges, including dynamic connectivity and unobserved variability, this research offers an encouraging preliminary glimpse into the utility of the transformer model for causal representation learning in neuroscience.

Ziyu Lu, Anna J. Li, Alexander E. Ladd et al.

Neural activity forecasting is central to understanding neural systems and enabling closed-loop control. While deep learning has recently advanced the state-of-the-art in the time series forecasting literature, its application to neural activity forecasting remains limited. To bridge this gap, we systematically evaluated eight probabilistic deep learning models, including two foundation models, that have demonstrated strong performance on general forecasting benchmarks. We compared them against four classical statistical models and two baseline methods on spontaneous neural activity recorded from mouse cortex via widefield imaging. Across prediction horizons, several deep learning models consistently outperformed classical approaches, with the best model producing informative forecasts up to 1.5 seconds into the future. Our findings point toward future control applications and open new avenues for probing the intrinsic temporal structure of neural activity.