Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for disaggregating latent causes for computer system optimization. In one aspect, a method includes accessing a data stream for data values resulting from operations performed by a computer system; providing the data values as input to a data disaggregation machine learning model that generates descriptors of latent causes of the data values; providing the data values and the descriptors of the latent causes of the data values as inputs to a control system model that generates embedded representations of commands to modify the operations performed by the computer system; determining commands to modify the operations performed by the computer system based on the embedded representations of commands to modify the operations performed by the computer system; and providing the commands to the computer system.