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Topology optimization algorithms often employ a smooth density function to implicitly represent geometries in a discretized domain. While this implicit representation offers great flexibility to parametrize the optimized geometry, it also leads to a transition region. Previous approaches, such as the Solid Isotropic Material Penalty (SIMP) method, have been proposed to modify the objective function aiming to converge toward integer density values and eliminate this non-physical transition region. However, the iterative nature of topology optimization renders this process computationally demanding, emphasizing the importance of achieving fast convergence. Accelerating convergence without significantly compromising the final solution can be challenging. In this work, we introduce a machine learning approach that leverages the message-passing Graph Neural Network (GNN) to eliminate the non-physical transition zone for the topology optimization problems. By representing the optimized structures as weighted graphs, we introduce a generalized filtering algorithm based on the topology of the spatial discretization. As such, the resultant algorithm can be applied to two- and three-dimensional space for both Cartesian (structured grid) and non-Cartesian discretizations (e.g. polygon finite element). The numerical experiments indicate that applying this filter throughout the optimization process may avoid excessive iterations and enable a more efficient optimization procedure.