Automatic deformable 3D modeling is computationally expensive, especially when considering complex position, orientation and scale variations. We present a volume segmentation framework to utilize local and global regularizations in a data-driven approach. We introduce automated correspondence search to avoid manually labeling landmarks and improve scalability. We propose a novel marginal space learning technique, utilizing multi-resolution pooling to obtain local and contextual features without training numerous detectors or excessively dense patches. Unlike conventional convolutional neural network operators, graph-based operators allow spatially related features to be learned on the irregular domain of the multi-resolution space, and a graph-based convolutional neural network is proposed to learn representations for position and orientation classification. The graph-CNN classifiers are used within a marginal space learning framework to provide efficient and accurate shape pose parameter hypothesis prediction. During segmentation, a global constraint is initially non-iteratively applied, with local and geometric constraints applied iteratively for refinement. Comparison is provided against both classical deformable models and state-of-the-art techniques in the complex problem domain of segmenting aortic root structure from computerized tomography scans. The proposed method shows improvement in both pose parameter estimation and segmentation performance.