The Bregman divergence, which is generated from a convex function, is commonly used as a pseudo-distance for comparing vectors or functions in continuous spaces. In contrast, defining an analog of the Bregman divergence for discrete spaces is nontrivial. Iyer & Bilmes (2012b) considered Bregman divergences on discrete domains using submodular functions as generating functions, the discrete analogs of convex functions. In this paper, we further generalize this framework to cases where the generating function is neither submodular nor supermodular, thus increasing the flexibility and representational capacity of the resulting divergence, which we term the difference-of-submodular Bregman divergence. Additionally, we introduce a learnable form of this divergence using permutation-invariant neural networks (NNs) and demonstrate through experiments that it effectively captures key structural properties in discrete data. As a result, the proposed method significantly improves the performance of existing methods on tasks such as clustering and set retrieval problems. This work addresses the challenge of defining meaningful divergences in discrete settings and provides a new tool for tasks requiring structure-preserving distance measures.