The goal of medical relation extraction is to detect relations among entities, such as genes, mutations and drugs in medical texts. Dependency tree structures have been proven useful for this task. Existing approaches to such relation extraction leverage off-the-shelf dependency parsers to obtain a syntactic tree or forest for the text. However, for the medical domain, low parsing accuracy may lead to error propagation downstream the relation extraction pipeline. In this work, we propose a novel model which treats the dependency structure as a latent variable and induces it from the unstructured text in an end-to-end fashion. Our model can be understood as composing task-specific dependency forests that capture non-local interactions for better relation extraction. Extensive results on four datasets show that our model is able to significantly outperform state-of-the-art systems without relying on any direct tree supervision or pre-training.