Functional embeddings enable Aggregation of multi-area SEEG recordings over subjects and sessions

Aggregating intracranial recordings across subjects is challenging since electrode count, placement, and covered regions vary widely. Spatial normalization methods like MNI coordinates offer a shared anatomical reference, but often fail to capture true functional similarity, particularly when localization is imprecise; even at matched anatomical coordinates, the targeted brain region and underlying neural dynamics can differ substantially between individuals. We propose a scalable representation-learning framework that (i) learns a subject-agnostic functional identity for each electrode from multi-region local field potentials using a Siamese encoder with contrastive objectives, inducing an embedding geometry that is locality-sensitive to region-specific neural signatures, and (ii) tokenizes these embeddings for a transformer that models inter-regional relationships with a variable number of channels. We evaluate this framework on a 20-subject dataset spanning basal ganglia-thalamic regions collected during flexible rest/movement recording sessions with heterogeneous electrode layouts. The learned functional space supports accurate within-subject discrimination and forms clear, region-consistent clusters; it transfers zero-shot to unseen channels. The transformer, operating on functional tokens without subject-specific heads or supervision, captures cross-region dependencies and enables reconstruction of masked channels, providing a subject-agnostic backbone for downstream decoding. Together, these results indicate a path toward large-scale, cross-subject aggregation and pretrain-ing for intracranial neural data where strict task structure and uniform sensor placement are unavailable. Building models that generalize across subjects in neuroscience requires representations that remain stable despite variability in data acquisition. Intracranial neural recordings lack this stability: electrode locations, counts, sampling, and coverage differ across individuals, reflecting clinical needs rather than standardized layouts. Without a shared representational system, cross-subject aggregation is unreliable, limiting scalable modeling and clinical translation. Such recordings are uniquely valuable for studying inter-regional communication, yet their heterogeneity makes them especially challenging to align. In practice, two obstacles dominate: Anatomical variability and inconsistent electrode coverage.