Anomaly detection in multivariate time series is an important data mining task with applications to ecosystem modeling, network traffic monitoring, medical diagnosis, and other domains. This paper presents a robust algorithm for detecting anomalies in noisy multivariate time series data by employing a kernel matrix alignment method to capture the dependence relationships among variables in the time series. Anomalies are found by performing a random walk traversal on the graph induced by the aligned kernel matrix. We show that the algorithm is flexible enough to handle different types of time series anomalies including subsequence-based and local anomalies. Our framework can also be used to characterize the anomalies found in a target time series in terms of the anomalies present in other time series. We have performed extensive experiments to empirically demonstrate the effectiveness of our algorithm. A case study is also presented to illustrate the ability of the algorithm to detec...