From Slices to Volumes: Comparing 2D, 2.5D, and 3D Residual Networks for Pulmonary Nodule Malignancy-Risk Classification

Bahodir Nazarov, Zineb Gharib, Fatima Zazoul

Purpose: To compare 2D, 2.5D, and 3D residual networks for pulmonary nodule malignancy-risk classification and evaluate momentum-contrast pretraining, mild augmentation, and exclusion of indeterminate ratings. Methods: A retrospectively prepared LIDC-IDRI cohort contained 2,654 nodules labeled benign, indeterminate, or malignant using median radiologist ratings. Patient-disjoint splits comprised 1,876 training, 382 validation, and 396 test nodules. Representations included one axial slice, five neighboring slices, and a local CT volume. Each track evaluated a randomly initialized baseline, momentum-contrast pretraining followed by fine-tuning, and supervised training with mild augmentation. Checkpoints were selected by validation Macro-F1. The 2D experiments used three seeds; 2.5D and 3D results were single-run estimates. A separate binary experiment excluded indeterminate nodules. Results: Augmented models achieved test Macro-F1 values of $0.6134\pm0.0075$ for 2D, $0.6537$ for 2.5D, and $0.5403$ for 3D; the 2D uncertainty denotes population standard deviation across seeds. Corresponding accuracies were $0.6128$, $0.6869$, and $0.5455$. Augmentation improved Macro-F1 within every…