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We propose a framework that uses deep neural networks (DNN) to optimize inventory decisions in complex multi-echelon supply chains. We first introduce pairwise modeling of general stochastic multi-echelon inventory optimization (SMEIO). Then, we present a framework which uses DNN agents to directly determine order-up-to levels between any adjacent pair of nodes in the supply chain. Our model considers a finite horizon and accounts for the initial inventory conditions. Our method is suitable for a wide variety of supply chain networks, including general topologies that may contain both assembly and distribution nodes, and systems with nonlinear cost structures. We first numerically demonstrate the effectiveness of the method by showing that its solutions are close to the optimal solutions for single-node and serial supply chain networks, for which exact methods are available. Then, we investigate more general supply chain networks and find that the proposed method performs better in terms of both objective function values and the number of interactions with the environment compared to alternate methods.