Neuronal Identity as an Organizational Basis for Analyzing Neural Population Dynamics

Individual neurons exhibit diverse molecular, morphological, and electrophysiological properties that shape their distinct roles in neural circuits. While these multimodal features are largely shared across individuals, they remain an underutilized source of information in analyzing neural population dynamics. We posit that these shared biological profiles provide a common reference for relating neural dynamics across subjects and recording sessions. Our framework leverages this structure by routing neurons into latent groups based on their biological profiles and analyzing population dynamics through group-level representations. Because these assignments are anchored in biological properties that are consistent across subjects, the learned organization supports transfer to unseen animals without retraining or neuron-wise correspondence. We evaluate our framework on whole-brain calcium imaging in larval zebrafish and large-scale electrophysiology in the mouse visual cortex. Across both species and recording modalities, the framework delivers state-of-the-art performance in both neural decoding and manifold analysis: it achieves superior decoding of behavior and stimulus labels while better preserving the temporal consistency and local geometric structure of latent trajectories on unseen data. Our experiments demonstrate that not only does providing biological features improve baseline performance, but our proposed framework achieves even stronger results by using these properties to explicitly structure the population rather than treating them as auxiliary inputs. Together, these results suggest that organizing neural populations by their multimodal biological features offers a promising framework for generalizing population dynamics across subjects and recording sessions.