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Original Research

Frontiers in Radiology ·

Volume 6 - 2026 | https://doi.org/10.3389/fradi.2026.1915426

Slice-level vs. volumetric radiomics for molecular subtyping of breast cancer: impact of patient-level data partitioning on model performance

  • Laila El Jiani1*corresponding author
  • Zouheir Banou1
  • Fatima Zahra Alaoui1
  • Hasnae Sakhi1
  • El Habib Benlahmar2
  • Sanaa El Filali1
  1. 1Laboratory of Artificial Intelligence and Systems, Faculty of Science Ben M’sick, Hassan II University, Casablanca, Morocco
  2. 2Laboratory of Information Processing and Modeling, Faculty of Science Ben M’sick, Hassan II University, Casablanca, Morocco
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Abstract

Molecular subtyping of breast cancer, particularly the discrimination between Luminal A and Basal-like tumours, is critical for guiding treatment decisions and establishing prognosis. Radiomics offers a promising complementary, non-invasive imaging biomarker to support biopsy-based subtyping; however, two methodological gaps limit the validity of existing studies: the absence of controlled 2D-vs.-3D feature comparisons, and the systematic underreporting of patient-level data leakage in multi-slice pipelines. To address both limitations, this study benchmarks slice-level (2D) and volumetric (3D) radiomic pipelines for the classification of Luminal A vs. Basal-like tumours on the TCGA-BRCA cohort, evaluating seven classifiers combined with two feature selection strategies under a Stratified Group k -Fold (k = 5) cross-validation scheme that enforces strict patient-level isolation. The 3D pipeline achieved a mean AUC of 0.682 vs. 0.631 for the 2D pipeline. In the 3D configuration, the Support Vector Machine with SelectKBest-MI feature selection attained the highest performance (AUC = 0.768 ± 0.066), while the 2D configuration was led by Logistic Regression (AUC = 0.769 ± 0.109), albeit with substantially higher fold-to-fold variability. Six out of seven classifiers yielded higher AUC scores under the 3D configuration, although a paired significance test on fold-level AUC values did not reach statistical significance (p = 0.313). These results establish a reproducible, leakage-free baseline for non-invasive breast cancer subtype classification through radiomics, with 3D radiomics offering improved robustness rather than superior peak performance. Results are derived from a single cohort (TCGA-BRCA) and external validation is required before clinical generalizability can be claimed.

Keywords

1 Introduction

Breast cancer is the most frequently diagnosed malignancy in women worldwide, accounting for approximately 2.3 million new cases and 685,000 deaths in 2020 [1]. Its clinical management is driven by molecular subtype classification, Luminal A, Luminal B, HER2-enriched, and Basal-like, established through gene expression profiling and associated with fundamentally different prognoses, therapeutic responses, and recurrence risks [2]. Luminal A tumours, characterised by high oestrogen receptor (ER) expression and low proliferative activity, carry the most favourable prognosis and respond well to endocrine therapy alone. Basal-like tumours, conversely, are ER−, PR−, and HER2−, exhibit high genomic instability and rapid proliferation, and are associated with the worst prognosis and highest recurrence rates [3]. In this study, the term Basal-like refers to the PAM50 transcriptomic subtype label as annotated in TCGA-BRCA, which correlates strongly with, but is not clinically synonymous with, triple-negative breast cancer (TNBC) defined by IHC receptor status; the two terms are not used interchangeably here.

The current gold standard for subtype determination relies on immunohistochemistry (IHC) applied to core needle biopsy specimens, combined with fluorescence in situ hybridisation (FISH) for HER2 assessment [4]. While highly reliable under optimal conditions, this paradigm carries well-documented limitations: biopsy is invasive, subject to spatial sampling bias [only ∼78% concordance between biopsy and surgical specimen receptor status [5]], carries procedural risk (2%–15% haematoma incidence [6]), and cannot characterise whole-tumour spatial heterogeneity, a critical limitation for Basal-like tumours, which exhibit high subclonal diversity [7, 8]. Radiomics, the high-throughput extraction of quantitative features from medical images, offers a non-invasive alternative that encodes tumour morphology, texture, and heterogeneity from routine imaging without additional patient contact [9, 10].

Despite growing interest in radiomics-based subtype classification, three methodological gaps persist in the literature. First, multi-slice 2D radiomics pipelines are frequently affected by patient-level leakage, assigning slices from the same patient to both training and test sets, inflating AUC by 0.08–0.15 [11] and producing results non-reproducible in prospective deployment [12]. Second, direct controlled comparisons of 2D slice-level and 3D volumetric configurations under identical classifiers and validation conditions remain rare, making it difficult to assess when the added cost of full volumetric segmentation is justified by performance gains [13]. Third, reported performance metrics often lack honest uncertainty quantification across folds, obscuring the true variability of results in small, imbalanced cohorts [14].

The purpose of this paper is to address the three mentioned gaps with three contributions. First, it provides an automated patient stratified cross- validation process free of leakage using programmatically verified patient isolation; Second, it guarantees that every classifier and both feature selection methods were tested for 7 classifiers in 2D and 3D (on TCGA-BRCA, n = 88, Luminal A vs Basal-like); Finally, it provides an exact reporting of the mean performance metrics and the variability in fold-to-fold performance. The results show that the 3D configuration achieves a higher mean AUC (0.682 vs. 0.631 for 2D) with better fold-to-fold stability (best std 0.066 vs. 0.109), while both configurations reach comparable peak performance (AUC = 0.769 for 2D and AUC = 0.768 for 3D) through different reliability profiles.

2.1 Radiomics for breast cancer molecular subtype classification

Radiogenomics is a concept that links imaging phenotypes with molecular characteristics. In breast cancer, Mazurowski et al. have described radiogenomic relationships in the form of DCE-MRI features correlated with gene expression profiles of breast invasive ductal carcinoma patients within the TCGA-BRCA cohort [15]. Their data has also shown that MRI enhancement dynamics were correlated with the Luminal B breast cancer subtype, providing initial evidence that imaging phenotypes reflect molecular states associated with cancer. Similarly, Grimm et al. also found kinetic (dynamic) features from MRI correlated with the intrinsic subtypes of breast cancer, achieving an AUC of 0.62–0.70 for separating Luminal from Non-Luminal subtypes [16]. Saha et al. [17] also transitioned from unsupervised classification of imaging features to supervised classification of Luminal A and Triple-Negative breast cancer using a radiomic signature based on 529 imaging features derived from DCE-MRI. Using Random Forest classification, they achieved an AUC of 0.71 for separating the two subtypes. The authors showed that the most discriminative features for Basal-like identification were entropy, energy, and GLCM-based descriptors. Subsequently, Li et al. demonstrated similar discrimination using multiparametric MRI (T2+DCE), achieving an AUC of 0.74 for predicting four subtypes of breast cancer while noting that T2-weighted texture features had better scanner stability than DCE kinetic features.

Studies that exceed AUC = 0.85 consistently rely on multiparametric MRI sequences (DCE, DWI, T2) unavailable in CT-only settings, or incorporate deep learning features trained on large datasets (n>500) [18, 19]. Leithner et al. achieved AUC = 0.86 for Triple-Negative vs. other subtypes using multiparametric MRI with a multi-layer perceptron, while DCE subregion analysis has reported AUC values up to 0.92 for Luminal vs. HER2 discrimination by modelling intratumoural kinetic heterogeneity [20]. For single-sequence MRI radiomics—the configuration most directly comparable to our work is Saha et al. [17] reported AUC = 0.71 on TCGA-BRCA using DCE-MRI and Random Forest, establishing the most relevant baseline for our study.

2.2 2D vs. 3D radiomics: evidence and trade-offs

According to the Image Biomarker Standardization Initiative [21], the extraction of three-dimensional characteristics of objects is recognized as the standard method for achieving reproducible radiomics, since two-dimensional characteristics depend on the selection of slices and the angle at which they are obtained. Three-dimensional features represent the complete spatial heterogeneity of a tumour through all three axes and include texture and morphology variations; which are not present on any two-dimensional slice. In [22], authors conducted an investigation with lung cancer patients and found that volumetric features of the shape of a tumour provide prognostic value independent of measurements from single slices. The transition from two-dimensional to three-dimensional radiomics has been associated with an increase in area under the receiver operating characteristic curve between 0.05 and 0.10 in brain tumour grade studies due to the added global information about the morphology of the tumour as a whole [23].

Despite these theoretical advantages, 2D slice-level extraction has practical merits that justify its continued use in clinical settings. Full volumetric segmentation is time-consuming and operator-dependent, whereas radiologists routin annotate representative slices in diagnostic workflows [24, 25]. From a machine learning perspective, 2D multi-slice extraction provides a larger effective training set per patient, a non-trivial advantage when the cohort is small [26]. In the multi-slice setting, each patient contributes multiple observations, increasing the diversity of training examples within each fold, at the cost of introducing within-patient dependencies that must be addressed through appropriate patient-level validation.

Direct controlled comparisons of 2D and 3D pipelines on the same dataset under identical classifiers, feature selection methods, and validation strategies remain rare in the breast cancer subtype literature [17–20, 25–27]. The absence of such systematic comparisons makes it difficult to assess when the added segmentation cost of 3D extraction is justified by performance gains—a clinically relevant question that this study directly addresses.

2.3 Data leakage in radiomics validation

Data leakage is a pervasive problem in radiomics, with particularly severe consequences in multi-slice 2D studies [12]. When standard k-fold cross-validation is applied without patient-level grouping, slices from the same patient appear in both training and test sets, allowing the model to recognise patients it has effectively already seen [26, 28]. Demircioğlu et al. [11] demonstrated that incorrect feature selection placement before cross-validation inflates AUC by up to 0.15 in AUC-ROC, 0.29 in AUC-F1, and 0.17 in accuracy, across ten publicly available radiomics datasets. Approximately 10%–15% of published radiomics studies using only cross-validation misapply feature selection, exacerbating the reproducibility problem in the field.

A second, often overlooked form of leakage occurs when feature selection is performed on the entire dataset before cross-validation, allowing test-set label information to influence feature ranking [12, 28]. Both forms of leakage produce AUC estimates that do not reflect genuine generalisation to unseen patients, the clinically relevant target [14, 29]. Stratified Group K-Fold cross-validation, which simultaneously enforces patient-level grouping and class stratification, is increasingly recognised as the reference standard for multi-slice radiomics validation. This study implements StratifiedGroupKFold with programmatic patient isolation verification and strictly enforces feature selection within each training fold.

Table 1 summarises the positioning of this study relative to key related works across six criteria. To our knowledge, no prior study combines leakage-free patient-stratified validation with a systematic 2D vs. 3D comparison for breast cancer molecular subtype classification under identical experimental conditions.

Table 1. Positioning of this study relative to key related works.

StudyModalityTasknMethodAUC2D/3DLeak-free
Li et al. [27]DCE-MRIER/PR/HER2/TN91LDA + LOO-CV0.893DPartial
Leithner et al. [19]mpMRI (DCE+DWI)LumA vs TN91MLP-ANN0.862DN.R.
Romeo et al. [18]PET/MRITNBC vs others86SVM + LASSO0.8873DN.R.
Huang et al. [20]DCE-MRI4-class377Logistic Reg.0.7863DN.R.
Lee et al. [26]MRI (3T)Subtypes + Ki67291Random Forest0.803DN.R.
Saha et al. [17]DCE-MRILumA vs TNBC922Random Forest0.713DPartial
This study (2D)MRILumA vs Basal887 classifiers0.7692DYes
This study (3D)MRILumA vs Basal887 classifiers0.7683DYes

N.R., Not reported; mpMRI, multiparametric MRI; LOO-CV, Leave-one-out cross-validation; LDA, Linear Discriminant Analysis.

Bold rows indicate the results of the present study (2D and 3D configurations).

3 Methodology

Figure 1 provides an overview of the complete study workflow, from patient selection to statistical comparison. The pipeline proceeds through eight stages: patient cohort selection, tumor segmentation, radiomics feature extraction, parallel 2D and 3D feature selection, classification, per-fold evaluation, patient-stratified cross-validation, and final statistical comparison between configurations. Each stage is detailed in the corresponding subsection below.

Overview of the study workflow, from patient selection through statistical comparison, illustrating the parallel 2D (slice-level) and 3D (volumetric) radiomics pipelines applied to the same segmented tumor volumes.
Figure 1. Overview of the study workflow, from patient selection through statistical comparison, illustrating the parallel 2D (slice-level) and 3D (volumetric) radiomics pipelines applied to the same segmented tumor volumes.

3.1 Dataset and patient cohort

We use the TCGA-BRCA cohort accessed via the GDC Data Portal [30], restricted to Luminal A (n=72) and Basal-like (n=16) patients with available imaging and PAM50 molecular subtype annotations (n=88 total). The class imbalance ratio is 4.5:1, addressed through class-weight balancing during classifier training. The 2D configuration yields 2,424 slice-level observations (mean 27.5 slices per patient) with 102 radiomics features after removing diagnostic columns; the 3D configuration yields 88 volumetric observations with 107 features. Table 2 summarises the dataset statistics per configuration. Missing values are imputed per-feature using the training-fold median to prevent information leakage from the test set.

Table 2. Dataset statistics per radiomics configuration.

Characteristic2D Configuration3D Configuration
Patients (n)8888
Luminal A/Basal-like72 / 1672 / 16
Class ratio4.5:14.5:1
Total observations2,424 slices88 volumes
Radiomics features102107
Cross-validationStratifiedGroupKFold (k=5)StratifiedGroupKFold (k=5)
Patient isolation verifiedYes (programmatic)Yes (structural)

3.2 Imaging data and tumor segmentation

Imaging data consist of T1-weighted, fat-saturated, dynamic contrast-enhanced (DCE) MRI, using the first post-contrast acquisition phase, obtained from the TCGA-BRCA collection on TCIA. As TCGA-BRCA aggregates data from multiple institutions, acquisition plane and scanner protocol vary by contributing site; this heterogeneity is acknowledged as a limitation (Section 5). Tumor regions of interest were manually segmented in 3D Slicer and exported as binary labelmaps in NRRD format (image–mask pairs). While automated and semi-automated segmentation approaches, including foundation models such as the Segment Anything Model, are increasingly explored for breast imaging [31], manual segmentation was adopted here to ensure high-fidelity tumor boundary delineation given the exploratory scope of this study.

Radiomic features were extracted from these NRRD volumes using PyRadiomics (v3.0.1) [32]. For the 3D configuration, features were computed directly on the full volumetric mask (force2D=False), with original voxel spacing preserved (no resampling) and a fixed bin width of 25 for gray-level discretization. For the 2D configuration, the same NRRD volumes were processed slice-by-slice (force2D=True): each axial slice containing tumor ROI was treated as an independent 2D observation, yielding the 2,424 slice-level samples described in Table 2.

3.3 Radiomics feature extraction

Radiomics features are extracted from MRI imaging data in both 2D and 3D configurations. The 2D configuration extracts features per axial slice, covering shape2D descriptors, first-order intensity statistics, and texture matrices (GLCM, GLRLM, GLSZM, NGTDM). The 3D configuration extracts features from the full tumour volume, additionally capturing volumetric shape descriptors including volume, surface area, sphericity, and elongation. All diagnostic columns generated during extraction (prefixed diagnostics_) are removed prior to analysis, as they encode pipeline metadata rather than tumour phenotypic information.

3.4 Feature selection

Two feature selection strategies are evaluated and applied strictly within each cross-validation fold on the training partition only:

Feature selection is performed exclusively within the training partition of each fold to prevent test-set label information from influencing feature ranking, a critical safeguard against the second form of leakage described in Section 2.3. Synthetic oversampling techniques such as SMOTE or ADASYN were not applied in this study. With only 16 Basal-like patients and 102–107 radiomics features, interpolation-based oversampling operates in a high-dimensional space with very few real neighbours per class, risking the generation of synthetic feature vectors that do not correspond to plausible tumour phenotypes—a known concern in small-n radiomics. Class-weight adjustment (class_weight=balanced, scale_pos_weight) was preferred as it penalizes misclassification of the minority class without fabricating feature vectors. A comparative evaluation of oversampling strategies is left for future work at larger cohort sizes.

  • SelectKBest with Mutual Information (SelectKBest-MI, k=15): ranks features by their mutual information with the target label, capturing non-linear feature–label dependencies. The top 15 features per fold are selected.
  • Variance Threshold (threshold = 0.01): removes quasi-constant features with near-zero variance, eliminating uninformative features that contribute noise without discriminative power.

3.5 Classification models

Seven supervised classifiers are evaluated to assess the robustness of the pipeline across different learning paradigms. Table 3 summarises the classifiers and their key hyperparameters. All classifiers that support class-weight adjustment are configured with class_weight=balanced; for XGBoost, scale_pos_weight is computed dynamically per training fold as the ratio of negative to positive samples.

Table 3. Classifiers and key hyperparameters.

ClassifierKey HyperparametersImbalance Handling
Logistic Regressionsolver = saga, max_iter = 2000class_weight = balanced
Random Forestn_estimators = 100, random_state = 42class_weight = balanced
Decision Treerandom_state = 42class_weight = balanced
SVMkernel = rbf, probability = Trueclass_weight = balanced
Naive BayesGaussianNB (default)N/A
KNNn_neighbours = 5N/A
XGBoostn_estimators = 100, eval_metric=loglossscale_pos_weight per fold

3.6 Validation strategy and leakage prevention

Stratified Group K-Fold cross-validation (k=5) assigns all slices from a given patient exclusively to either the training or the test partition, preventing patient-level leakage. The grouping variable is the patient identifier (patient_id). Stratification ensures that the Luminal A/Basal-like class ratio is preserved across folds. Patient isolation is verified programmatically at each fold: |train_groups ∩ test_groups| = 0 any violation triggers immediate pipeline interruption. For the 3D configuration, each patient contributes exactly one volume, making patient-level leakage structurally impossible; StratifiedGroupKFold is nonetheless applied for consistency. For the 2D configuration, slice-level predicted probabilities are aggregated to the patient level by averaging (mean-pooling) prior to AUC computation, ensuring a clinically equivalent, patient-level comparison with the 3D configuration. Performance is reported as mean ± std AUC, accuracy, and weighted F1 across five folds, using AUC as the primary metric. Inverted AUC values (< 0.5) are corrected by label flipping, consistent with standard practice.

4 Results

4.1 Full classification results

Tables 4, 5 report all 14 classifier–feature-selection combinations for the 2D and 3D configurations respectively, sorted by descending AUC. The best combination per configuration is highlighted in bold.

Table 4. 2D slice-level results, sorted by AUC.

ClassifierFeature selectionAUC±StdAccF1
Log. RegressionSelectKBest (MI)0.7690.1090.5700.564
Naive BayesVariance Threshold0.7410.1480.4810.465
Log. RegressionVariance Threshold0.6990.1500.5640.552
Naive BayesSelectKBest (MI)0.6480.1810.6190.535
SVMVariance Threshold0.6340.0990.5980.587
XGBoostSelectKBest (MI)0.6320.0780.6610.619
XGBoostVariance Threshold0.6280.0850.6480.609
Random ForestVariance Threshold0.6280.0580.6030.548
SVMSelectKBest (MI)0.6150.0740.6280.615
KNNVariance Threshold0.5900.1010.6190.580
Random ForestSelectKBest (MI)0.5860.0600.6430.575
Decision TreeSelectKBest (MI)0.5710.0620.6950.662
Decision TreeVariance Threshold0.5630.0500.6570.635
KNNSelectKBest (MI)0.5360.0260.6400.611
Mean0.631–0.6160.583

Best result in bold.

Table 5. 3D volumetric results, sorted by AUC.

ClassifierFeature selectionAUC±StdAccF1
SVMSelectKBest (MI)0.7680.0660.7830.753
Log. RegressionVariance threshold0.7480.1270.7140.705
Naive BayesVariance threshold0.7270.1570.4950.443
Random forestSelectKBest (MI)0.6980.1010.7020.613
XGBoostSelectKBest (MI)0.6970.0880.6700.636
Naive BayesSelectKBest (MI)0.6910.1730.6680.611
SVMVariance threshold0.6890.0490.6930.674
Decision treeSelectKBest (MI)0.6840.1240.7670.743
Log. regressionSelectKBest (MI)0.6800.1000.7140.696
Random forestVariance threshold0.6470.0580.6960.610
XGBoostVariance threshold0.6470.1420.6520.612
KNNVariance threshold0.6300.1220.7370.681
Decision TreeVariance Threshold0.6280.1130.7180.689
KNNSelectKBest (MI)0.6160.1300.6960.629
Mean0.682–0.6930.650

Best result in bold.

4.2 Overall 2D vs. 3D summary

Table 6 presents the key performance statistics for both configurations. The 3D configuration achieves a higher mean AUC across all 14 combinations (0.682 vs. 0.631), with an improvement of +0.051. Both configurations reach comparable peak AUC values (0.769 for 2D and 0.768 for 3D), but the 3D peak (SVM + SelectKBest-MI) carries a standard deviation of 0.066, compared to 0.109 for the 2D peak (Logistic Regression + SelectKBest-MI)—a 39% reduction in fold-to-fold variability. For their respective best-AUC configurations, the 3D pipeline also achieves markedly higher accuracy (0.783 vs. 0.570) and F1 (0.753 vs. 0.564) than 2D, indicating that, for 3D, the AUC-optimal model is also the accuracy/F1-optimal model across all 14 combinations (Table 5); this is not the case for 2D, where Decision Tree + SelectKBest-MI achieves higher accuracy (0.695) and F1 (0.662) than the best-AUC Logistic Regression model, reflecting a trade-off between AUC and thresholded classification metrics for the 2D pipeline.

Table 6. Overall 2D vs. 3D performance summary.

Metric2D3D
Mean AUC (all 14 combinations)0.6310.682
Best AUC0.7690.768
Best AUC std0.1090.066
Best classifierLog. RegressionSVM
Best feature selectionSelectKBest-MISelectKBest-MI
Accuracy of best-AUC configuration0.5700.783
F1 of best-AUC configuration0.5640.753
Mean accuracy (all combinations)0.6160.693
Gain in mean AUC (3D vs. 2D)–+0.051
Classifiers improving in 3D–6/7

Bold values indicate the better-performing configuration for each metric.

4.3 Per-classifier comparison under selectkbest-MI

Table 7 details the AUC of each classifier under SelectKBest-MI for both configurations. Six of seven classifiers improve in 3D; SVM records the largest gain (from 0.615 to 0.768, +0.153). The only exception is Logistic Regression (−0.089), which benefits disproportionately from the larger effective 2D training sample (2,424 slices vs. 88 volumes).

Table 7. Per-classifier AUC under SelectKBest-MI—2D vs. 3D.

Classifier2D AUC2D Std3D AUC3D StdGainTrend
SVM0.6150.0740.7680.066+0.153↑↑
Random forest0.5860.0600.6980.101+0.112↑↑
Decision tree0.5710.0620.6840.124+0.113↑↑
KNN0.5360.0260.6160.130+0.080↑
XGBoost0.6320.0780.6970.088+0.065↑
Naive Bayes0.6480.1810.6910.173+0.044→
Log. Regression0.7690.1090.6800.100−0.089↓

↑↑, improvement > +0.10; ↑, between +0.05 and +0.10; →, marginal; ↓, decrease.

Bold values indicate the overall best-performing configuration for each modality (peak AUC: SVM in 3D, Logistic Regression in 2D).

Across folds, SelectKBest-MI consistently ranked GLCM-based texture features (correlation, contrast, entropy) and first-order intensity statistics among the top selected features in both configurations, with volumetric shape descriptors (sphericity, surface area ratio) appearing exclusively in the 3D configuration. A full SHAP-based interpretability analysis is left for future work.

Figures 2, 3 show the per-fold ROC curves for the best 2D and 3D configurations respectively. The tighter grouping of folds in the 3D plot is visually apparent, confirming the superior stability of SVM on volumetric features compared to Logistic Regression on slice-level features. Figure 4 illustrates the per-classifier mean AUC comparison between the 2D and 3D configurations under SelectKBest-MI feature selection.

Per-fold ROC curves, 2D configuration. Logistic Regression + SelectKBest-MI. Mean AUC per fold shown; overall mean AUC = 0.769 ± 0.109 (Table 4).
Figure 2. Per-fold ROC curves, 2D configuration. Logistic Regression + SelectKBest-MI. Mean AUC per fold shown; overall mean AUC = 0.769 ± 0.109 (Table 4).
Per-fold ROC curves, 3D configuration. SVM + SelectKBest-MI. Mean AUC = 0.768 ± 0.066 (Table 5). The tighter fold grouping confirms the superior stability of the 3D configuration.
Figure 3. Per-fold ROC curves, 3D configuration. SVM + SelectKBest-MI. Mean AUC = 0.768 ± 0.066 (Table 5). The tighter fold grouping confirms the superior stability of the 3D configuration.
Mean AUC per classifier for 2D and 3D configurations under SelectKBest-MI feature selection. The 3D configuration (red) outperforms 2D (blue) for six of seven classifiers. Logistic Regression is the sole exception, benefiting from the larger effective training sample in the multi-slice 2D setting. The dashed green line indicates AUC = 0.70.
Figure 4. Mean AUC per classifier for 2D and 3D configurations under SelectKBest-MI feature selection. The 3D configuration (red) outperforms 2D (blue) for six of seven classifiers. Logistic Regression is the sole exception, benefiting from the larger effective training sample in the multi-slice 2D setting. The dashed green line indicates AUC = 0.70.

4.4 Statistical significance and clinical metrics

To assess whether the observed 3D advantage reflects a statistically meaningful difference rather than sampling variability, we performed a paired Wilcoxon signed-rank test on the five fold-level AUC values for the best 2D (Logistic Regression + SelectKBest-MI) and best 3D (SVM + SelectKBest-MI) configurations, using a common patient-level fold assignment shared across both configurations. Bootstrap 95% confidence intervals for each configuration’s AUC (1,000 resamples, patient-level resampling) were [0.410, 0.716] for the 2D configuration and [0.449, 0.701] for the 3D configuration; the substantial overlap between these intervals already suggests no strong separation between configurations. The paired Wilcoxon signed-rank test did not reach statistical significance (statistic = 3.0, p = 0.313), and a 1,000-resample bootstrap 95% confidence interval on the AUC difference (3D−2D) was 0.006 [−0.178, 0.194], which includes zero. These results indicate that, while the 3D configuration shows a favorable trend, the AUC difference between configurations is not statistically significant at n=5 folds—consistent with our framing of the 3D advantage as improved robustness (lower fold-to-fold variance) rather than a confirmed superiority in discriminative power.

Table 8 reports confusion matrices, sensitivity, specificity, and balanced accuracy for both best configurations, at both the default 0.5 probability threshold and the Youden’s J-optimal threshold. At the default threshold, the 3D (SVM) model showed reduced sensitivity (0.188) relative to 2D (0.688), reflecting a calibration shift associated with class-weight balancing under the SVM’s RBF kernel. At the Youden-optimal threshold (0.075 for 3D, 0.447 for 2D), balanced accuracy improved to 0.639 (3D) and 0.594 (2D), with 3D sensitivity reaching 1.000. This confirms that the discriminative capacity reflected in the 3D AUC is preserved but requires threshold calibration for optimal clinical deployment, a common consideration in imbalanced classification with class-weight adjustment.

Table 8. Clinical metrics for best 2D and 3D configurations (patient-level, pooled across folds).

ConfigurationThresholdSensitivitySpecificityBalanced Acc.
2D (LR + SelectKBest-MI)0.5 (default)0.6880.4030.545
2D (LR + SelectKBest-MI)0.447 (Youden)0.9380.2500.594
3D (SVM + SelectKBest-MI)0.5 (default)0.1880.7780.483
3D (SVM + SelectKBest-MI)0.075 (Youden)1.0000.2780.639

5 Discussion

5.1 Non-invasive advantage and performance contextualisation

The most important context for interpreting our AUC values is the nature of the input data: hand-crafted MRI radiomics features alone, without clinical covariates, genomic data, or specialised MRI sequences. This is not a limitation but a deliberate design choice that defines the clinical value proposition: a non-invasive, zero-cost characterisation of the tumour from imaging already acquired as part of routine care. Biopsy-based subtyping, while accurate, captures a small spatial sample of the tumour (typically <1% of total mass), is subject to spatial sampling bias [5], carries procedural risk [6], and cannot characterise whole-tumour heterogeneity. Radiomics—particularly in the 3D configuration—provides a global phenotypic description that reflects the spatial distribution of morphological and textural heterogeneity across the entire lesion, an information dimension inaccessible to needle biopsy [28].

Studies reporting AUC > 0.85 consistently use multiparametric MRI (DCE+DWI+T2) or genomic features [19] unavailable in MRI-only settings. Within the MRI radiomics literature, our AUC of 0.769 exceeds both Franzese et al. (0.65) and Saha et al. [0.71 [17]]—under stricter leakage-free validation. Rather than replacing tissue-based molecular subtyping, radiomics is positioned here as a complementary, non-invasive decision-support tool: the clinically relevant question is not whether it matches biopsy accuracy, but whether it provides sufficient discriminative capacity to support patient triage, treatment planning confirmation, and longitudinal monitoring alongside standard IHC/FISH assessment.

5.1.1 3D vs. 2D: robustness over peak performance

The 3D configuration outperforms 2D in mean AUC (0.682 vs. 0.631) and stability (best std 0.066 vs. 0.109), with six of seven classifiers improving in 3D. SVM gains most (+0.153), benefiting from the RBF kernel operating on complete volumetric descriptions that capture global tumour heterogeneity. Logistic Regression is the sole exception (−0.089), explained by the larger effective 2D training sample (2,424 slices vs. 88 volumes) favouring linear models. It is also possible that 2D slice-level features encode locally linear discriminative patterns that are partially averaged out during volumetric aggregation, reducing the linear separability that Logistic Regression relies upon. Disentangling these two effects would require ablation experiments beyond the scope of this study. Crucially, the key advantage of 3D is robustness, not peak performance—the best 2D result reaches AUC = 0.769, slightly above the best 3D result (AUC = 0.768), but the 3D peak comes with a standard deviation of 0.066 vs. 0.109 for 2D, a 39% reduction that directly impacts clinical reliability. When full volumetric segmentation is available, SVM+3D is the recommended configuration; when only slice-level annotation is available, Logistic Regression+2D provides competitive peak performance at lower segmentation cost.

5.2 Feature selection

SelectKBest-MI consistently identifies the best-performing combinations in both configurations, confirming that non-linear feature–label dependency ranking captures more discriminative information than variance-based filtering. However, Variance Threshold occasionally outperforms SelectKBest-MI for specific classifiers in 3D (notably Logistic Regression: 0.748 vs. 0.680), suggesting that retaining all features above a minimal informativeness threshold preserves complementary information that benefits linear models.

5.3 Leakage prevention

StratifiedGroupKFold with programmatic patient isolation yields honest performance estimates at the cost of higher fold variability—an unavoidable trade-off with n=88. Studies ignoring patient-level grouping in 2D pipelines report AUC inflated by 0.08–0.15 [11], producing results non-reproducible in prospective deployment. Transparent reporting of ±std alongside mean AUC is a methodological contribution in itself [29].

Four limitations should be acknowledged. (i) Cohort size: with n=88 and only 16 Basal-like patients, individual test folds contain between two and five Basal-like cases (mean ≈ 3.2 per fold), rendering fold-level AUC estimates statistically unstable. Bootstrap confidence intervals (1,000 resamples) on the mean AUC yield wide intervals, confirming that results should be interpreted as exploratory rather than definitive. (ii) No external validation: all results are produced on a single cohort (TCGA-BRCA); generalisation to independent institutions or imaging protocols remains to be demonstrated. (iii) Imaging heterogeneity: TCGA-BRCA aggregates multi-site data without explicit scanner harmonisation, introducing uncontrolled variability in radiomics features sensitive to reconstruction parameters, a challenge consistent with broader reported difficulties in breast MRI segmentation across acquisition protocols [33]. (iv) Binary task: the Luminal A vs. Basal-like binary classification does not cover the full complexity of four-class PAM50 subtype prediction.

Four directions are identified for extending this study: (i) external validation on the DUKE Breast Cancer MRI dataset (n=922); (ii) extension to four-class subtype classification using a one-vs-rest strategy; (iii) SHAP-based interpretability analysis to identify which features carry the most discriminative information for Basal-like prediction; and (iv) multi-modal fusion incorporating clinical covariates (tumour grade, staging, age) to approach the 0.85 AUC threshold of multiparametric MRI studies [19] while retaining the non-invasive advantage.

6 Conclusion

This study established a leakage-free, patient-stratified radiomics framework for Luminal A vs. Basal-like breast cancer classification, systematically comparing 2D slice-level and 3D volumetric configurations under identical experimental conditions across seven classifiers and two feature selection strategies on TCGA-BRCA (n=88). The 3D configuration is more robust (mean AUC 0.682, best AUC 0.768 ± 0.066 with SVM + SelectKBest-MI), while 2D offers competitive peak performance (0.769 ± 0.109, Logistic Regression + SelectKBest-MI) at lower segmentation cost. Achieved from MRI radiomics alone—without genomic or clinical data, and without any invasive procedure—these results demonstrate that non-invasive imaging provides clinically meaningful molecular subtype discrimination as a complementary, decision-support biomarker alongside tissue-based subtyping, exceeding comparable radiomics-only MRI baselines in the literature. The strict leakage-free validation framework produces honest and reproducible performance estimates that reflect genuine generalisation to unseen patients. As all results derive from a single cohort (TCGA-BRCA) without external validation, these findings should be regarded as exploratory. The pipeline is modality-agnostic and dataset-independent, providing a reproducible foundation for future multi-modal and multi-cohort extensions toward clinical deployment.

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Footnotes

Edited by: Viktor Vegh, The University of Queensland, Australia

Reviewed by: Hafiz Muhammad Tayyab Khushi, Superior University, Pakistan

Aykut Teymur, Antalya City Hospital, Türkiye

Statements

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Funding

The author(s) declared that financial support was not received for this work and/or its publication.

Data availability

Imaging data are publicly available from The Cancer Imaging Archive (TCIA), TCGA-BRCA collection: https://www.cancerimagingarchive.net/collection/tcga-brca/. Molecular subtype (PAM50) annotations were obtained from the TCGA-BRCA clinical data available via the GDC Data Portal: https://portal.gdc.cancer.gov/projects/TCGA-BRCA.

Ethics approval

Ethical approval was not required for the study involving humans in accordance with the local legislation and institutional requirements. Written informed consent to participate in this study was not required from the participants or the participants’ legal guardians/next of kin in accordance with the national legislation and the institutional requirements. This study used only publicly available, de-identified data from the TCGA-BRCA collection; no new human subject recruitment or primary data collection was performed by the authors.

Author contributions

LJ: Conceptualization, Investigation, Methodology, Software, Formal analysis, Writing – original draft, Writing – review & editing. ZB: Data curation, Software, Writing – original draft. FA: Data curation, Methodology, Writing – original draft. HS: Data curation, Software, Writing – review & editing. EB: Supervision, Writing – review & editing. SF: Supervision, Writing – review & editing.

Acknowledgements

The authors thank Mouna Sabiri, Ghizlane Lembarki, and Mohamed Labied (Central Radiology Department, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University) for performing the manual tumor segmentation used as the basis for radiomic feature extraction in this study. The authors also thank Ihsane Haloum and Abdellah Badou (Laboratory of Immunogenetics and Human Pathologies, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University) for project management and supervisory support at the segmentation stage.

References

  1. 1. International Agency for Research on Cancer (IARC). Global cancer observatory: cancer today. Geneva: World Health Organization (2024). Available online at: (Accessed June 2026).
  2. 2. Bertucci F, Finetti P, Goncalves A, Birnbaum D. The therapeutic response of ER+/HER2 − breast cancers differs according to the molecular Basal or Luminal subtype. npj Breast Cancer. (2020) 6: 8. doi:10.1038/s41523-020-0151-5
  3. 3. Dai X, Xiang L, Li T, Bai Z. Cancer hallmarks, biomarkers and breast cancer molecular subtypes. J Cancer. (2016) 7 (10): 1281 – 94. doi:10.7150/jca.13141
  4. 4. Furrer D, Sanschagrin F, Jacob S, Diorio C. Advantages and disadvantages of technologies for HER2 testing in breast cancer specimens. Am J Clin Pathol. (2015) 144 (5): 686 – 703. doi:10.1309/AJCPT41TCBUEVDQC
  5. 5. Brennan ME, Turner RM, Ciatto S, Marinovich ML, French JR, Macaskill P, et al. Ductal carcinoma in situ at core-needle biopsy: meta-analysis of underestimation and predictors of invasive breast cancer. Radiology. (2011) 260 (1): 119 – 28. doi:10.1148/radiol.11102368
  6. 6. Bick U, Trimboli RM, Athanasiou A, Balleyguier C, Baltzer PAT, Bernathova M, et al. Image-guided breast biopsy and localisation: recommendations for information to women and referring physicians by the European society of breast imaging. Insights Imaging. (2020) 11: 12. doi:10.1186/s13244-019-0803-x
  7. 7. Mavrommati I, Johnson F, Echeverria GV, Natrajan R, et al. Subclonal heterogeneity and evolution in breast cancer. npj Breast Cancer. (2021) 7: 155. doi:10.1038/s41523-021-00363-0
  8. 8. Gerlinger M, Rowan AJ, Horswell S, Math M, Larkin J, Endesfelder D, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. (2012) 366: 883 – 92. doi:10.1056/NEJMoa1113205
  9. 9. Scapicchio C, Gabelloni M, Barucci A, Cioni D, Saba L, Neri E, A deep look into radiomics. Radiol Med. (2021) 126: 1296 – 311. doi:10.1007/s11547-021-01389-x
  10. 10. Valdora F, Houssami N, Rossi F, Calabrese M, Tagliafico AS. Rapid review: radiomics and breast cancer. Breast Cancer Res Treat. (2018) 169: 217 – 29. doi:10.1007/s10549-018-4675-4
  11. 11. Demircioğlu A. Measuring the bias of incorrect application of feature selection when using cross-validation in radiomics. Insights Imaging. (2021) 12: 172. doi:10.1186/s13244-021-01115-1
  12. 12. Stamoulou E, Spanakis C, Manikis GC, Karanasiou GS, Grigoriadis G, Foukakis T, et al. Harmonization strategies in multicenter MRI-based radiomics. J Imaging. (2022) 8 (11): 303. doi:10.3390/jimaging8110303
  13. 13. Yue W, Zhang H, Zhou J, Li G, Tang Z, Sun Z, et al. Deep learning-based automatic segmentation for size and volumetric measurement of breast cancer on magnetic resonance imaging. Front Oncol. (2022) 12: 984626. doi:10.3389/fonc.2022.984626
  14. 14. Wang J, Jing B, Fei B. Uncertainty quantification in deep learning based breast cancer diagnosis using dynamic contrast enhanced MRI (DCE-MRI) and treatment response assessment maps (TRAMs). In Proceedings of the IEEE international conference on data mining workshops (ICDMW), Washington, DC, USA (2025), 3112–6. doi:10.1109/ICDMW69685.2025.00412
  15. 15. Mazurowski MA, Zhang J, Grimm LJ, Yoon SC, Silber JI. Radiogenomic analysis of breast cancer: luminal B molecular subtype is associated with enhancement dynamics at MR imaging. Radiology. (2014) 273 (2): 365 – 72. doi:10.1148/radiol.14132641
  16. 16. Grimm LJ, Zhang J, Mazurowski MA. Computational approach to radiogenomics of breast cancer: luminal A and luminal B molecular subtypes are associated with imaging features on routine breast MRI extracted using computer vision algorithms. J Magn Reson Imaging. (2015) 42 (4): 902 – 7. doi:10.1002/jmri.24879
  17. 17. Saha A, Harowicz MR, Grimm LJ, Kim CE, Ghate SV, Walsh R. A machine learning approach to radiogenomics of breast cancer: a study of 922 subjects and 529 DCE-MRI features. Br J Cancer. (2018) 119 (4): 508 – 16. doi:10.1038/s41416-018-0185-8
  18. 18. Romeo V, Kapetas P, Clauser P, Baltzer PAT, Rasul S, Gibbs P, et al. A simultaneous multiparametric 18 F-FDG PET/MRI radiomics model for the diagnosis of triple negative breast cancer. Cancers. (2022) 14 (16): 3944. doi:10.3390/cancers14163944
  19. 19. Leithner D, Mayerhoefer ME, Martinez DF, Jochelson MS, Morris EA, Thakur SB. Non-invasive assessment of breast cancer molecular subtypes with multiparametric MRI radiomics. J Clin Med. (2020) 9 (6): 1853. doi:10.3390/jcm9061853
  20. 20. Huang G, Du S, Gao S, Guo L, Zhao R, Bian X, et al. Molecular subtypes of breast cancer identified by dynamically enhanced MRI radiomics: the delayed phase cannot be ignored. Insights Imaging. (2024) 15: 127. doi:10.1186/s13244-024-01713-9
  21. 21. Zwanenburg A, Valliéres M, Abdalah MA, Aerts HJWL, Andrearczyk V, Apte A. The image biomarker standardization initiative: standardized quantitative radiomics for high-throughput image-based phenotyping. Radiology. (2020) 295 (2): 328 – 38. doi:10.1148/radiol.2020191145
  22. 22. Aerts HJWL, Velazquez ER, Leijenaar RTH, Parmar C, Grossmann P, Carvalho S. Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat Commun. (2014) 5: 4006. doi:10.1038/ncomms5006
  23. 23. Arefan D, Chai R, Sun M, Zuley ML, Wu S. Machine learning prediction of axillary lymph node metastasis in breast cancer: 2D versus 3D radiomic features. Med Phys. (2020) 47 (12): 6334 – 42. doi:10.1002/mp.14538
  24. 24. Ghosh T, Sheikhi F, Guo J, Singh Y, Younis K, Kuanar S, et al. Foundation models for volumetric medical imaging: opportunities, challenges, and future directions. Electronics. (2026) 15 (6): 1245. doi:10.3390/electronics15061245
  25. 25. Zhu S, Wang S, Guo S, Wu R, Zhang J, Kong M, et al. Contrast-enhanced mammography radiomics analysis for preoperative prediction of breast cancer molecular subtypes. Acad Radiol. (2024) 31: 2228 – 38. doi:10.1016/j.acra.2023.12.005
  26. 26. Lee JY, Lee K, Seo BK, Cho KR, Woo OH, Song SE, et al. Radiomic machine learning for predicting prognostic biomarkers and molecular subtypes of breast cancer using tumor heterogeneity and angiogenesis properties on MRI. Eur Radiol. (2022) 32: 650 – 60. doi:10.1007/s00330-021-08146-8
  27. 27. Li H, Zhu Y, Burnside ES, Huang E, Drukker K, Hoadley KA. Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set. npj Breast Cancer. (2016) 2: 16012. doi:10.1038/npjbcancer.2016.12
  28. 28. Henry T, Sun R, Lerousseau M, Estienne T, Robert C, Besse B, et al. Investigation of radiomics based intra-patient inter-tumor heterogeneity and the impact of tumor subsampling strategies. Sci Rep. (2022) 12 (1): 17244. doi:10.1038/s41598-022-20931-z
  29. 29. Tchokponhoue GAD, Idri A. On the value of uncertainty quantification in deep learning based breast cancer molecular subtype classification. Appl Soft Comput. (2026) 186 (Part D): 114249. doi:10.1016/j.asoc.2025.114249
  30. 30. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. (2012) 490: 61 – 70. doi:10.1038/nature11412
  31. 31. El Jiani L, Haloum I, El Filali S, Benlahmar EH. Segment anything model for breast imaging segmentation: state-of-the-art. Commun Comput Inf Sci. (2026) 2645: 42 – 52. doi:10.1007/978-3-032-14964-0_4
  32. 32. van Griethuysen JJM, Fedorov A, Parmar C, Hosny A, Aucoin N, Narayan V, et al. Computational radiomics system to decode the radiographic phenotype. Cancer Res. (2017) 77 (21): e104 – 7. doi:10.1158/0008-5472.CAN-17-0339
  33. 33. El Jiani L, Alaoui FZ, Banou Z, Moustafi K. Blood vessel segmentation in breast MRI: comprehensive review of techniques and challenges. Math Model Comput. (2025) 12 (4): 1121 – 34. doi:10.23939/mmc2025.04.1121

Citation

Jiani, L. E., et al. (2026). Slice-level vs. volumetric radiomics for molecular subtyping of breast cancer: impact of patient-level data partitioning on model performance. Frontiers in Radiology, Volume 6. https://doi.org/
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6 - 2026

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© 2026 El Jiani, Banou, Alaoui, Sakhi, Benlahmar and El Filali.

License: https://creativecommons.org/licenses/by/4.0/

*Correspondence: Laila El Jiani

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