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Learning vector representations for programs is a critical step in applying deep learning techniques for program understanding tasks. Various neural network models are proposed to learn from tree-structured program representations, e.g., abstract syntax tree (AST) and concrete syntax tree (CST). However, most neural architectures either fail to capture long-range dependencies which are ubiquitous in programs, or cannot learn effective representations for syntax tree nodes, making them incapable of performing the node-level prediction tasks, e.g., bug localization. In this paper, we propose Tree-Transformer, a novel recursive tree-structured neural network to learn the vector representations for source codes. We propose a multi-head attention mechanism to model the dependency between siblings and parent-children node pairs. Moreover, we propose a bi-directional propagation strategy to allow node information passing in two directions, bottom-up and top-down along trees. In this way, Tree-Transformer can learn the information of the node features as well as the global contextual information. The extensive experimental results show that our Tree-Transformer significantly outperforms the existing tree-based and graph-based program representation learning approaches in both the tree-level and node-level prediction tasks.