The Molecule Extraction stage involves two tasks. The first task is to predict the deviation between VPs and their target positions, where the error is binned into one-hot encoding, converting it into a classification task to ensure stable training. The second task is to predict which VPs should be merged. Ideally, VPs assigned to the same target atom should be merged. Thus, for VP pairs with the same target atom, the training label is set to True. However, in practice, the distribution of True and False labels in VP pairs is highly imbalanced, so Focal Loss (FL) is adopted to handle this issue. The loss function for the molecule extraction stage is defined as: