Since some VPs may deviate significantly from their target positions, those exceeding a predefined threshold z are filtered out. Next, the model predicts the merging probability between each pair of VPs and constructs a probability matrix to cluster VPs accordingly. Once the initial molecular structure W 0 is obtained, further optimization of its 3D coordinates is required to refine the molecular geometry. Similar to Particle Movement, this step, referred to as Molecule Refinement (MR), follows an iterative process in which atomic positions are continuously adjusted using a different set of model parameters. The refinement process is formulated as: