Systems and methods are disclosed for performing error diagnosis of software errors in a program by from one or more error traces, building a repair program containing one or more modified program semantics corresponding to fixes to observed errors; encoding the repair program with constraints, biases and priortization into a constraint weighted problem; and solving the constraint weighted problem to generate one or more repair solutions, wherein the encoding includes at least one of: a) constraining one or more repairs choices guided by automatically inferring one or more partial specifications of intended program behaviors and program structure; b) biasing one or more repair choices guided by typical programming mistakes; and c) prioritizing the repair solutions based on error locations and possible changes in program semantics.