1. A computer-implemented method for run-to-run control, the method comprising: identifying contexts associated with a fabrication process, the fabrication process having one or more threads, and each thread involving one or more contexts; defining a set of input-output equations describing the fabrication process, wherein each input-output equation corresponds to a thread and includes a thread offset expressed as a summation of individual context offsets, wherein each individual context offset is estimated based on a moving horizontal state estimation; and creating a state-space model that describes an evolution of the fabrication process using the set of input-output equations, the state-space model allowing to estimate individual context offsets, wherein the thread offset is unbiased even if the individual context offsets are biased when the corresponding thread corresponds to a combination of the one or more contexts.