These finds emphasize the well-known fact that any particular variant of the graph-theoretical MCS problem does not always identify the chemically correct atom correspondences between molecular graphs. The combination of multiple variations, as implemented in the ensemble method, can achieve at least a moderate improvement, Figure . However, given the additional computational cost of computing multiple MCS solutions, Configuration 3 appears to be best pragmatic choice given its performance and reduced computational requirements. This observation that the ensemble approach improved chemical correctness, albeit slightly, however, can serve as a natural starting point for the development of an improved combinatorial atom-atom-mapping method. The warm colors in the contour plot represent regions of high confidence, indicating areas where our method demonstrates high accuracy. Conversely, the cool colors denote regions of lower confidence, reflecting areas where our method's accuracy is comparatively lower.