Monitoring the status of network slices is a priority for network operators to ensure that SLAs are not violated. To overcome the limitations of direct slices' monitoring, network tomography (NT) is seen as a promising solution. NT-based solutions require constraining monitoring traffic to follow specific paths, which we can achieve by using segment-based routing (SR). This allows deploying customized probing scheme, such as cycles' probing. A major challenge with SR is, however, the limited length of the monitoring path. In this paper, we focus on the complexity of that task and propose MonGNN, a standalone solution based on Graph Neural Networks (GNNs) and genetic algorithms to find a trade-off between the quality of monitors' placement and the cost to achieve it. Simulation results show the efficiency of our approach compared to existing methods.