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We report on an automated runtime anomaly detection method at the application layer of multi-node computer systems. Although several network management systems are available in the market, none of them have sufficient capabilities to detect faults in multi-tier Web-based systems with redundancy. We model a Web-based system as a weighted graph, where each node represents a "service" and each edge represents a dependency between services. Since the edge weights vary greatly over time, the problem we address is that of anomaly detection from a time sequence of graphs.In our method, we first extract a feature vector from the adjacency matrix that represents the activities of all of the services. The heart of our method is to use the principal eigenvector of the eigenclusters of the graph. Then we derive a probability distribution for an anomaly measure defined for a time-series of directional data derived from the graph sequence. Given a critical probability, the threshold value is adaptively updated using a novel online algorithm.We demonstrate that a fault in a Web application can be automatically detected and the faulty services are identified without using detailed knowledge of the behavior of the system.