ProtoPointNet: Prototype-Based Interpretable Classification of 3D Dental Point Clouds with Verifiable Spatial Activations

Prototype-based networks provide inherently interpretable classification by linking predictions to learned exemplars, but their use in 3D point clouds and clinical surface-pair reasoning remains limited. We introduce ProtoPointNet, a prototype-based model for dental occlusion classification from registered upper--lower intraoral arch pairs. Each point is encoded by a 14-dimensional descriptor combining local surface geometry, curvature, and explicit inter-arch displacement and clearance, exposing occlusal relationships to prototype matching. A shared multi-task point-cloud backbone learns axis-specific prototype heads for sagittal-left, sagittal-right, vertical, transverse, and midline classification. To support limited clinical data, we train prototypes from scratch using auxiliary supervision and encoder-freeze hand-off. On Bits2Bites, ProtoPointNet achieves mean test macro-F1 of 0.724 and AUROC of 0.825, with strongest performance on vertical (F1 0.828) and sagittal-left classification (F1 0.807). Projected prototype activations localise to anatomically plausible regions, including posterior molars and premolars for cross-bite evidence and anterior incisors for bite-depth evidence. These results support prototype-based reasoning as a transparent, spatially grounded alternative to black-box 3D classifiers for dental surface-pair analysis.