Explaining how neuronal activity gives rise to cognition arguably remains the most significant challenge in cognitive neuroscience. In the first part of this talk, I introduce neuro-cognitive multilevel causal modeling (NC-MCM), a mathematical framework that bridges the explanatory gap between neuronal activity and cognition by construing cognitive states as causally consistent abstractions of neuronal states. NC-MCM enables us to consistently reason about the neuronal- and cognitive causes of behavior while maintaining a physicalist (in contrast to a
dualist) position. In the second part of this talk, I introduce an algorithm for learning cognitive level causal models from neuronal activation patterns and demonstrate its ability to learn cognitive states of the nematode C.~elegans from calcium imaging data.