Graph neural networks are promising architecture for learning and inference with graph-structured data. Yet difficulties in modelling the ``parts'' and their ``interactions'' still persist in terms of graph classification, where graph-level representations are usually obtained by squeezing the whole graph into a single vector through graph pooling. From complex systems point of view, mixing all the parts of a system together can affect both model interpretability and predictive performance, because properties of a complex system arise largely from the interaction among its components. We analyze the intrinsic difficulty in graph classification under the unified concept of ``resolution dilemmas'' with learning theoretic recovery guarantees, and propose ``SLIM'', an inductive neural network model for Structural Landmarking and Interaction Modelling. It turns out, that by solving the resolution dilemmas, and leveraging explicit interacting relation between component parts of a graph to explain its complexity, SLIM is more interpretable, accurate, and offers new insight in graph representation learning.