Abstract: This disclosure relates generally to system and method for molecular property prediction. The method utilizes a set-pooling aggregation operator to derive a graph-level representation of a complete input molecular graphs to assist in inductive learning tasks. The method includes iteratively down-sampling the molecular graph into a coarsened molecular graph, and determining adjacency matrix and feature matrix of the coarsened molecular graph. The method then includes computing an average of the hidden state node attributes of the coarsened graph obtained after preforming the iterations to obtain a graph level representation vector of the molecular graph. Using a linear layer from the graph level representation vector the molecular properties are determined.