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In recent years, there has been increasing interest in using the methods of educational data mining (EDM) and learning analytics (LA) to study and measure learner cognition. In this chapter, we discuss how these types of methods can be used to measure complex cognition and meta‐cognition in types of environments where inference can be challenging: exploratory and inquiry learning environments, complex games, and project‐based learning. We give examples from a range of projects for the types of constructs that can be inferred using EDM/LA methods and how these measures compare to what can be obtained from more traditional methods. We conclude with a discussion of future discussion and potentials for these kinds of methods.