Computer systems and methods for constructing a model of the noise afflicting a quantum computer comprising a plurality of qubits are provided. A graph G that describes a conditional independence structure of the noise is obtained. The graph G includes a node for each qubit in the plurality of qubits. The noise afflicting the quantum computer is logically reduced to Pauli noise. The graph G is broken into a plurality of sets. Each respective set Cj in the plurality of sets (i) corresponds a respective qubit j in the plurality of qubits and (ii) comprises a representation of the respective qubit j and the parent qubits ∂