BiXformer: A Bidirectional Cross Attention Transformer for Disentangling Inter-Regional Neural Dynamics

Advances in high-throughput neural recording technologies enable simultaneous measurement of activity across multiple brain regions in behaving animals, producing datasets of unprecedented scale and richness. Interpreting these data remains challenging due to the bidirectional and temporally offset nature of inter-regional communication, where feedforward and feedback signals are superimposed within neural populations. We introduce BiXformer, a bidirectional cross-attention transformer that disentangles these interactions by decomposing inter-regional communication into temporally leading and lagging streams using directionally masked attention. By enforcing temporal constraints within attention heads, BiXformer recovers low-dimensional, directed latent dynamics and estimates communication delays without relying on linearity or stationarity assumptions. Validated on synthetic data with known ground-truth delays, BiXformer accurately recovers both the latent structure and inter-regional timing, outperforming existing methods in both accuracy and speed. Applied to simultaneous neural-behavioral recordings and multi-region neural recordings during a movement task, BiXformer reveals interpretable, temporally structured components consistent with the coexistence of sensory feedback and motor-related signals. These results establish BiXformer as a flexible framework for uncovering dynamic, directed communication in complex neural circuits.