Background: Many computational methods have been developedthat leverage the results from biological experiments (such as Hi-C)to infer the 3D organization of the genome. Formally, this is referredto as the 3D genome reconstruction problem (3D-GRP). Hi-C datais now being generated at increasingly high resolutions. As thisresolution increases, it has become computationally infeasible topredict a 3D genome organization with the majority of existingmethods. None of the existing solution methods have utilized a nonproceduralprogramming approach (such as integer programming)despite the established advantages and successful applications ofsuch approaches for predicting high-resolution 3D structures ofother biomolecules. Our objective was to develop a new solution tothe 3D-GRP that utilizes non-procedural programming to realizethe same advantages.