Patterns of endogenous activity in the brain reflect a stochastic exploration of the neuronal state space that is constrained by the underlying assembly organization of neurons. Yet it remains to be shown that this interplay between neurons and their assembly dynamics indeed suffices to generate whole-brain data statistics. Here we recorded the activity from ~40,000 neurons simultaneously in zebrafish larvae, and show that a data-driven network model of neuron-assembly interactions can

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... y reproduce the mean activity and pairwise correlation statistics of their spontaneous activity. This model, the compositional Restricted Boltzmann Machine, unveils ~200 neural assemblies, which compose neurophysiological circuits and whose various combinations form successive brain states. From this, we mathematically derived an interregional functional connectivity matrix, which is conserved across individual animals and correlates well with structural connectivity. This novel, assembly-based generative model of brain-wide neural dynamics enables physiology-bound perturbation experiments in silico.