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Sequence-to-sequence learning with neural networks has become the de facto standard for sequence modeling. This approach typically models the local distribution over the next element with a powerful neural network that can condition on arbitrary context. While flexible and performant, these models often require large datasets for training and can fail spectacularly on benchmarks designed to test for compositional generalization. This work explores an alternative, hierarchical approach to sequence-to-sequence learning with synchronous grammars, where each node in the target tree is transduced by a subset of nodes in the source tree. The source and target trees are treated as fully latent and marginalized out during training. We develop a neural parameterization of the grammar which enables parameter sharing over combinatorial structures without the need for manual feature engineering. We apply this latent neural grammar to various domains---a diagnostic language navigation task designed to test for compositional generalization (SCAN), style transfer, and small-scale machine translation---and find that it performs respectably compared to standard baselines.