Scientists often use observational time series data to study complex natural processes, but regression analyses often assume simplistic dynamics. Recent advances in deep learning have yielded startling improvements to the performance of models of complex processes, but deep learning is generally not used for scientific analysis. Here we show that deep learning can be used to analyze complex processes, providing flexible function approximation while preserving interpretability. Our approach relaxes standard simplifying assumptions (e.g., linearity, stationarity, and homoscedasticity) that are implausible for many natural systems and may critically affect the interpretation of data. We evaluate our model on incremental human language processing, a domain with complex continuous dynamics. We demonstrate substantial improvements on behavioral and neuroimaging data, and we show that our model enables discovery of novel patterns in exploratory analyses, controls for diverse confounds in confirmatory analyses, and opens up research questions that are otherwise hard to study.