Spectral imprint of structural embedding in effective connectivity

Neural fluctuations exhibit rich spectral profiles that reflects both local dynamics and structural (or anatomical) embedding. Yet, standard models of resting-state effective connectivity neglect structural embedding and assume uniformity in the timescales of regions' endogenous fluctuations. We introduce a chromatic dynamic causal model (DCM) in which structural valency (or degree) modulates the spectral 'color' of endogenous fluctuations. Specifically, we assume a linear mapping between regional structural valency and the spectral exponent of scale-free auto-spectra. Simulations show this mapping can emerge as a generic consequence of structural embedding under minimal coupling in a non-equilibrium regime. We show chromatic DCM reliably recovers ground-truth parameters across network sizes and noise conditions, outperforming standard spectral DCM. Applied to empirical data, chromatic DCM reveals that valency–exponent mappings vary across a cortical hierarchy, and that its parameters are conserved across a homologous network in humans, macaques, marmosets, and mice. These findings advance a generative account of structure–function coupling and expand the repertoire of biophysical mechanisms available for inference in effective connectivity modeling.