In one embodiment, a device receives sensor data from a plurality of nodes in a computer network. The device uses the sensor data and a graph that represents a topology of the nodes in the network as input to a graph convolutional neural network. The device provides an output of the graph convolutional neural network as input to a convolutional long short-term memory recurrent neural network. The device detects an anomaly in the computer network by comparing a reconstruction error associated with an output of the convolutional long short-term memory recurrent neural network to a defined threshold. The device initiates a mitigation action in the computer network for the detected anomaly.