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An abduction-based diagnosis technique for a class of discrete-event systems (DESs), called deep DESs (DDESs), is presented. A DDES has a tree structure, where each node is a network of communicating automata, called an active unit (AU). The interaction of components within an AU gives rise to emergent events. An emergent event occurs when specific components collectively perform a sequence of transitions matching a given regular language. Any event emerging in an AU triggers the transition of a component in its parent AU. We say that the DDES has a deep behavior, in the sense that the behavior of an AU is governed not only by the events exchanged by the components within the AU but also by the events emerging from child AUs. Deep behavior characterizes not only living beings, including humans, but also artifacts, such as robots that operate in contexts at varying abstraction levels. Surprisingly, experimental results indicate that the hierarchical complexity of the system translates into a decreased computational complexity of the diagnosis task. Hence, the diagnosis technique is shown to be (formally) correct as well as (empirically) efficient.