Numerical modeling of viscoelastic properties is critical to developing the structure-property relationship of polymer nanocomposites. While it is recognized that the altered polymer region near filler particles, the interphase, significantly contributes to enhancements of composite properties, the spatial distribution of interphase properties is rarely considered due to lack of local property measurements. In recent years, the Atomic Force Microscopy (AFM) technique has begun to make local property measurements of the interphase available. In the light of the increasing availability of AFM data, in this work a new interphase representation for modeling the viscoelastic properties of polymer nanocomposites is proposed. The proposed interphase representation disentangles the interphase behavior by two separate components – single-body interphase gradient and multi-body compound effect, whose functional forms are learned via data mining. The proposed interphase representation is integrated into a Finite Element model, and the effects of each component of the interphase representations are numerically studied. In addition, the advantages of the proposed interphase representation are demonstrated by comparison to a prior simulation work in which only a uniform effective property of the interphase is considered. Moreover, the proposed interphase representation is utilized to solve the inverse problem of inferring spatial distribution of local properties using Bayesian optimization-based inference on experimental data.