A method for solving an under-determined inverse problem or network inference/tomography problem in per-flow size, delay, loss and throughput inference in a computer network, through a system is presented. The method includes the following steps, which are not necessarily in order. First, establishing the computer network having a plurality of nodes wherein the per-flow size, the delay, the loss and the throughput inference are unknown. An original observation or routing matrix determines how flows are appeared on the links and construct the measurements. Next, performing a learning phase to obtain an optimal observation matrix or pseudo-optimal observation matrix. After that, performing a computer controller adaptive measurement and inference phase to estimate the set of unknowns using the measurement quantities, and a function of one of the set consisting of: the optimal observation matrix, the original observation matrix, or both.