1. A computer-implemented method for improving a lithographic process for imaging a portion of a design layout onto a substrate using a lithographic projection apparatus, the method comprising: determining a stochastic effect function of the lithographic process that produces as an output a value of a stochastic effect as a function of a plurality of design variables associated with the lithographic process that are inputs to the function and which cause quantifiable changes in the stochastic effect value, wherein the plurality of design variables include at least an adjustable parameter of projection optics of the lithographic process; defining a multi-variable cost function using the stochastic effect function of the lithographic process such that the multi-variable cost function includes the adjustable parameter of projection optics that causes the quantifiable changes in the stochastic effect value for a desired substrate throughput of the lithographic projection apparatus; and reconfiguring, by the computer, one or more characteristics of the lithographic process by adjusting one or more of the design variables until a certain termination condition of the cost function is satisfied, thereby achieving the desired substrate throughput.