In many domains we face the problem of determining the underlying causal
structure from time-course observations of a system. Whether we have neural
spike trains in neuroscience, gene expression levels in systems biology, or
stock price movements in finance, we want to determine why these systems behave
the way they do. For this purpose we must assess which of the myriad possible
causes are significant while aiming to do so with a feasible computational
complexity. At the same time, there has been much work in philosophy on what it
means for something to be a cause, but comparatively little attention has been
paid to how we can identify these causes. Algorithmic approaches from computer
science have provided the first steps in this direction, but fail to capture
the complex, probabilistic and temporal nature of the relationships we seek.
This dissertation presents a novel approach to the inference of general (type-level) and singular (token-level) causes. The approach combines philosophical notions of causality with algorithmic approaches built on model checking and statistical techniques for false discovery rate control. By using a probabilistic computation tree logic to describe both cause and effect, we allow for complex relationships and explicit description of the time between cause and effect as well as the probability of this relationship being observed (e.g. "a and b until c, causing d in 10-20 time units"). Using these causal formulas and their associated probabilities, we develop a novel measure for the significance of a cause for its effect, thus allowing discovery of those that are statistically interesting, determined using the concepts of multiple hypothesis testing and false discovery control. We develop algorithms for testing these properties in time-series observations and for relating the inferred general relationships to token-level events (described as sequences of observations). Finally, we illustrate these ideas with example data from both neuroscience and finance, comparing the results to those found with other inference methods. The results demonstrate that our approach achieves superior control of false discovery rates, due to its ability to appropriately represent and infer temporal information.