A method for performance bottleneck diagnosis and dependency discovery in distributed systems and computer networks includes receiving a real-valued end-to-end measurement matrix, a number of end-to-end measurements, a number of time points, a number of network components, a loss function, and a plurality of constraints on output matrices. The method further includes learning basic output matrices by best approximation of a transpose of the real-valued end-to-end measurement matrix, selecting a first threshold based on a real-valued mixing-weights matrix and a second threshold based on a real-valued delay matrix, converting the real-valued mixing-weights matrix and the real-valued delay matrix into respective binary matrices using the first threshold and the second threshold, and returning the real-valued mixing-weights matrix, the real-valued delay matrix, and the respective binary matrices to represent bottlenecks dependencies of the distributed system or computer network.