Sequences of event intervals occur in several application domains, while their inherent complexity hinders scalable solutions to tasks such as clustering and classification. In this paper, we propose a novel spectral embedding representation of event interval sequences that relies on bipartite graphs. More concretely, each event interval sequence is represented by a bipartite graph by following three main steps: (1) creating a hash table that can quickly convert a collection of event interval sequences into a bipartite graph representation, (2) creating and regularizing a bi-adjacency matrix corresponding to the bipartite graph, (3) defining a spectral embedding mapping on the bi-adjacency matrix. In addition, we show that substantial improvements can be achieved with regard to classification performance through pruning parameters that capture the nature of the relations formed by the event intervals. We demonstrate through extensive experimental evaluation on five real-world datasets that our approach can obtain runtime speedups of up to two orders of magnitude compared to other state-of-the-art methods and similar or better clustering and classification performance.