arXiv:2507.22488v1 Announce Type: cross Abstract: In vertical federated learning (VFL), multiple enterprises address aligned sample scarcity by leveraging massive locally unaligned samples to facilitate collaborative learning. However, unaligned samples across different parties in VFL can be extremely class-imbalanced, leading to insufficient feature representation and limited model prediction space. Specifically, class-imbalanced problems consist of intra-party class imbalance and inter-party class imbalance, which can further cause local model bias and feature contribution inconsistency issues, respectively. To address the above challenges, we propose Proto-EVFL, an enhanced VFL framework via dual prototypes. We first introduce class prototypes for each party to learn relationships between classes in the latent space, allowing the active party to predict unseen classes. We further design a probabilistic dual prototype learning scheme to dynamically select unaligned samples by conditional optimal transport cost with class prior probability. Moreover, a mixed prior guided module guides this selection process by combining local and global class prior probabilities. Finally, we adopt an \textit{adaptive gated feature aggregation strategy} to mitigate feature contribution inconsistency by dynamically weighting and aggregating local features across different parties. We proved that Proto-EVFL, as the first bi-level optimization framework in VFL, has a convergence rate of 1/\sqrt T. Extensive experiments on various datasets validate the superiority of our Proto-EVFL. Even in a zero-shot scenario with one unseen class, it outperforms baselines by at least 6.97%