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

Morphological characteristics such as spiculation and lobulation play an important role in assessing pulmonary nodules on computed tomography (CT), particularly in relation to malignancy risk. This study examines whether learning radiologist-annotated morphological features together with malignancy risk from lesion-centred 3D CT volumes improves classification performance. The Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) dataset was used, comprising 3,918 reader-level nodule annotations from 742 patients after excluding indeterminate malignancy ratings. Patient-level splitting was used for training, validation, and testing, with 112 patients and 628 reader annotations in the held-out test set. A single-task 3D convolutional neural network was compared with a multi-task model predicting malignancy risk, spiculation, and lobulation. The single-task model achieved a balanced accuracy of 0.548 and receiver operating characteristic area under the curve (ROC-AUC) of 0.552, while the multi-task model achieved 0.539 and 0.558, respectively. Patient-level bootstrap analysis showed an ROC-AUC difference of 0.005 (95% confidence interval (CI): -0.087 to 0.090) and a balanced-accuracy difference of -0.009 (95% CI: -0.067 to 0.043). The auxiliary tasks were strongly imbalanced and showed limited predictive performance. Overall, including morphological features did not clearly improve malignancy-risk classification, showing the importance of class balance, label formulation, and reader-level annotation structure in multi-task pulmonary CT analysis.

The accurate classification of benign and malignant pulmonary nodules in CT scans is critical for early lung cancer screening, yet remains challenging due to the multi-scale and heterogeneous nature of pulmonary nodules. While deep learning offers potential for auxiliary diagnosis, most existing models act as "black boxes", lacking the transparency and explainability required for trustworthy clinical integration. To address this issue, we propose M3Net, a novel 3D network for pulmonary nodule classification inspired by the hierarchical diagnostic workflow of radiologists, which integrates multi-scale contextual information from fine-grained structures to global anatomical relationships. Our framework constructs a progressive multi-scale input, from fine-grained nodule structures to local semantics and global spatial relationships. M3Net employs scale-specific encoders and ensures cross-scale semantic consistency through latent space projection and mutual information maximization. Extensive experiments on the public LIDC-IDRI dataset and a self-collected clinical dataset (USTC-FHLN) demonstrate that our method achieves state-of-the-art performance, with accuracies of 86.96% and 84.24% respectively, outperforming the best baseline by 3.26% and 2.17%. The results validate that M3Net provides a more robust and clinically relevant solution for pulmonary nodule classification. The code is available at https://github.com/jylEcho/M3-Net.

In this work, we present an uncertainty-driven training framework for three-dimensional computed tomography (CT) lung nodule classification, where validation-based uncertainty estimates guide loss reweighting to enhance predictive performance and probability calibration. Two Uncertainty Quantification (UQ) methods are considered: Monte Carlo Dropout (MCD) and Evidential Deep Learning (EDL). Both provide per-class uncertainty estimates that modulate the loss and encourage focus on hard or unreliable classes. The framework is evaluated with ResNet, DenseNet, EfficientNet, Vision Transformer (ViT), and Swin Transformer backbones on two datasets: the clinical LIDC-IDRI cohort and the NoduleMNIST3D benchmark. Uncertainty-driven training achieves classification performance similar to conventional training while substantially improving calibration, with an expected calibration error (ECE) reduced by up to 65% on LIDC-IDRI. EDL attains competitive performance on shallower architectures with single-pass inference, whereas MCD is more robust on deeper networks. Analysis across architectural families reveals that uncertainty-driven training benefits convolutional backbones more consistently than transformer-based architectures: EDL in particular degrades on ViT, suggesting that the Dirichlet evidence parameterisation may interact unfavourably with attention-based architectures at lower input resolutions. A posteriori temperature scaling proves highly effective across all configurations, indicating that a simple scalar calibration can be competitive even without explicit uncertainty-aware training. Our results indicate that integrating UQ into the training loop can significantly improve probabilistic calibration and support more trustworthy deployment of three-dimensional medical imaging models.