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Résumé : This dissertation examines how latent neural and behavioural dynamics can be inferred from indirect, limited measurements in two areas of systems neuroscience, where the most salient feature of the recorded signal does not coincide with the structure in which the phenomenon of interest resides. Part I concerns functional near-infrared spectroscopy (fNIRS). Chapter 2 introduces a Riemannian-geometry classification framework for fNIRS data that nearly doubles accuracy in decoding eight brain states relative to traditional, channel-wise methods. Chapter 3 applies this framework to a clinical proof-of-principle for disorders of consciousness. Part II addresses the temporal structure of saccadic eye movements during naturalistic viewing. Chapter 4 shows that saccade timing combines a locally rhythmic interval-generating process with a slowly fluctuating rate, and that rhythmicity increases with saccade rate across humans, macaques and a marmoset. Chapter 5 uses inhibitory continuous theta-burst TMS over the right frontal eye field to show that this cortical area influences saccade rhythmicity causally.