Authors: Julia Dietlmeier, Vayangi Ganepola, Oluwabukola G. Adegboro, Mayug Maniparambil, Claudia Mazo, Noel E. O'Connor
Organizations: Insight Research Ireland Centre for Data Analytics, Dublin City University, Glasnevin 9, Dublin, Ireland · Research Ireland Centre for Research Training in Machine Learning (ML-Labs), Dublin City University, Glasnevin 9, Dublin, Ireland · School of Computing, Dublin City University, Glasnevin 9, Dublin, Ireland
Directly inspired by findings in biological vision, high-dimensional hypercolumns are feature vectors built by concatenating multi-scale activations of convolutional neural networks for a single image pixel location. Together with powerful classifiers, they can be used for image segmentation i.e. pixel classification. However, in practice, there are only very few works dedicated to the use of hypercolumns. One reason is the computational complexity of processing concatenated dense hypercolumns that grows linearly with the size N of the training set. In this work, we address this challenge by applying stratified subsampling to the VGG16 based hypercolumns. Furthermore, we investigate the performance of ensemble learning on sparse hypercolumns. Our experiments on a brain tumor dataset show that stacking and voting ensembles deliver competitive performance, but in the extreme low-shot case of N≤20, a simple Logistic Regression classifier is the most effective method. For 10% stratified subsampling rate, our best average Dice score is 0.66 for N=20. This is a statistically significant improvement of 24.53% over the standard multi-scale UNet baseline (p-value = [3.07e−11], Wilcoxon signed-rank test), which is less effective due to overfitting.
Figures & tables
Figure 1: Our hypercolumn-based processing pipeline for binary pixel classification.
Base classifiers
Number of estimators
Max iterations
Random Forest Classifier (RF)
10
n/a
Linear Support Vector Classifier (SVC)
n/a
1000
Logistic Regression Classifier (LR)
n/a
1000
Table 1: Base classifier configuration.
Subsampling rate
N
hypercolumn+LR ↑
UNet ↑
Dice gain ↑
p -value ↓
\Block 3-11%
2
0.11 ± 0.05
0.34 ± 0.16
−67.65 %
2.23e−05
10
0.53 ± 0.05
0.43 ± 0.21
23.26 %
1.59e−07
20
0.61 ± 0.03
0.56 ± 0.26
8.93 %
0.663
\Block 3-110%
2
0.45 ± 0.05
0.33 ± 0.18
36.36 %
1.52e−14
10
0.56 ± 0.06
0.39 ± 0.21
43.59 %
1.40e−20
20
0.66 ± 0.02
0.53 ± 0.25
24.53 %
3.07e−11
Table 2: Comparison between the hypercolumn+LR and the UNet models. Dice performance gains are computed based on the mean values.
Models
Accuracy ↑
Precision ↑
Recall ↑
Jaccard ↑
Dice ↑
\Block 6-1 \rotate N=2
hypercolumn+LR
0.98 ± 0.00
0.35 ± 0.12
0.08 ± 0.04
0.08 ± 0.04
0.11 ± 0.05
hypercolumn+RF
0.98 ± 0.00
0.04 ± 0.03
0.00 ± 0.00
0.00 ± 0.00
0.00 ± 0.00
hypercolumn+SVC
0.98 ± 0.00
0.02 ± 0.01
0.00 ± 0.00
0.00 ± 0.00
0.00 ± 0.00
hypercolumn+stacking
0.93 ± 0.04
0.08 ± 0.05
0.20 ± 0.12
0.05 ± 0.03
0.08 ± 0.04
hypercolumn+voting
0.98 ± 0.00
0.08 ± 0.04
0.01 ± 0.01
0.01 ± 0.01
0.01 ± 0.01
UNet
0.79 ± 0.38
0.40 ± 0.20
0.57 ± 0.23
0.25 ± 0.12
0.34 ± 0.16
Table 3: Selected quantitative results (mean and standard deviation) for the case of 1% stratified subsampling rate. Best results are in red and second best in blue.
Figure 2: Dice score coefficient performance of LR versus UNet (left) and stacking versus voting (right). All models were trained on the same amount of images for 1% stratified subsampling rate. Graphs are showing mean (lines) ± standard deviation (filled areas).
Models
Accuracy ↑
Precision ↑
Recall ↑
Jaccard ↑
Dice ↑
\Block 6-1 \rotate N=2
hypercolumn+LR
0.99 ± 0.00
0.69 ± 0.03
0.39 ± 0.06
0.34 ± 0.05
0.45 ± 0.05
hypercolumn+RF
0.98 ± 0.00
0.21 ± 0.12
0.03 ± 0.03
0.03 ± 0.05
0.05 ± 0.05
hypercolumn+SVC
0.98 ± 0.00
0.27 ± 0.13
0.06 ± 0.03
0.06 ± 0.03
0.08 ± 0.04
hypercolumn+stacking
0.94 ± 0.02
0.18 ± 0.06
0.41 ± 0.12
0.13 ± 0.05
0.20 ± 0.08
hypercolumn+voting
0.99 ± 0.00
0.36 ± 0.15
0.10 ± 0.06
0.10 ± 0.06
0.13 ± 0.07
UNet
0.79 ± 0.39
0.41 ± 0.21
0.57 ± 0.29
0.26 ± 0.14
0.33 ± 0.18
Table 4: Selected quantitative results (mean and standard deviation) for the case of 10% stratified subsampling rate. Best results are in red and second best in blue.
Figure 3: Dice score coefficient performance of LR versus UNet (left) and stacking versus voting (right). All models were trained on the same amount of images for 10% stratified subsampling rate. Graphs are showing mean (lines) ± standard deviation (filled areas).
Models
Total parameters
Inference time
Training time
Device
hypercolumn model
14,714,688
-
-
GPU
+LR
1,473
0.48
7.66
CPU
+RF
5,290
0.17
13.56
CPU
+SVC
2,536,257
63.38
1062.97
CPU
+stacking
1,486
0.61
254.95
CPU
+voting
2,886,604
80.40
1347.26
CPU
Table 5: Computational details. The total number of parameters for base and ensemble classifiers are obtained after training on N=20 images with the 10% subsampling rate. Inference time is given per image. Times are in seconds.
Figure 4: Selected qualitative results for N=10 training images. The first three rows show results for 1% subsampling rate and the last three rows show the results for 10% subsampling rate. Note that UNet is trained on N=10 images without subsampling.
Multimodal MRI provides complementary information for brain tumor segmentation, but high accuracy alone does not reveal whether a model relies on clinically appropriate imaging evidence. Radiologists use different sequences for different findings, such as T1ce for enhancing tumor and FLAIR for peritumoral edema. Yet most 3D segmentation networks fuse MRI sequences through fixed connections, regardless of patient, region, or depth. We frame multimodal segmentation as grounded multimodal reasoning and introduce (i) a model agnostic probing framework combining per region modality ablation, Dominant Sensitivity Enhancement (DSE), and gate trajectory analysis to reveal sequence reliance, and (ii) evidence that adaptive Hyper-Connections (HC) induce clinically aligned modality reliance without modality supervision. Across nnU Net, SwinUNETR, and VT-UNet on BraTS 2021, most HC configurations increase reliance on clinically appropriate sequences. This interpretable pattern recurs across all three backbones, suggesting it arises from adaptive connections rather than a single architecture. HC also improves segmentation accuracy at negligible parameter cost. On validation, the best HC configuration increases mean Dice by 0.43 to 0.81 percentage points across the three backbones. On the held-out test set, it reduces mean HD95 by 1.17 to 1.78 mm (approximately 20 to 27 percent) for nnU-Net and VT UNet, adding at most 0.53 percent parameters. Our framework offers an inspectable measure of clinical grounding and extends naturally to multimodal medical foundation models.
Convolutional neural networks (CNNs) have become increasingly difficult to deploy in resource-constrained environments due to their large memory and computational requirements. Although low-rank compression methods can reduce this burden, most existing approaches compress spatial and channel redundancy independently and therefore do not fully exploit the localised structure within convolutional feature maps. This paper proposes a hierarchical spatio-channel low-rank compression framework for CNNs that exploits redundancy across spatial regions and channel activations. Unlike conventional methods, which apply a uniform decomposition across an entire layer, the proposed approach first partitions feature maps into spatial regions, then groups channels according to their co-activation patterns within each region, and finally applies rank-adaptive SVD to each resulting spatio-channel cluster. The method is evaluated on an AlexNet-based brain tumour MRI classification model and compared with Global SVD and Tucker decomposition under 3× and 6× compression budgets. Our method outperforms both baselines, reducing FLOPs from 8.21G to 1.55G (81.1% reduction), achieving a 1.38× inference speed-up, and increasing classification accuracy from 87.76% to 89.80%. The method also improves the macro F1-score and performance on challenging classes such as meningioma. A hyper-parameter trade-off analysis demonstrates that the framework provides Pareto-optimal configurations, enabling control over the balance between compression and predictive performance. Moderate clustering with adaptive rank selection yields strong results. Bootstrap standard errors are reported for all classification metrics.
Department of Mathematics, Rhodes University, Makhanda 6140, South Africa · Department of Statistics, Rhodes University, Makhanda 6140, South Africa · National Institute for Theoretical and Computational Sciences, Stellenbosch 7600, South Africa +8
The rapid growth of image data has produced large-scale datasets, raising concerns about the time and memory costs of model training. Selecting representative training subsets, however, remains challenging: individual sample contributions are unclear, and model behavior varies across datasets and runs. We address these challenges with a framework that combines coreset selection with an ensemble aggregation over multiple runs. For coreset selection, we propose SCOre-Stratified Selection (SCOSS), which partitions the training data into intervals based on a chosen score and samples from each interval. The ensemble combines predictions from multiple runs, each performed on an independently sampled training subset. As baselines, we use moderate and random selection, each in original and class-balanced versions. We assess the framework with Simple Graph Convolution (SGC) and Support Vector Machine (SVM) classifiers under different sampling ratios. Experiments show that SCOSS is competitive with baselines, often the best choice for SGC, and enables favorable trade-offs between accuracy and efficiency. On the fine-grained dataset, SGC with SCOSS outperforms SVMs when using fewer labeled samples. The code and supplementary materials are publicly available at http://scoss.lucasvalem.com.
Pedro Rocha Dantas, Lucas Pascotti Valem
Institute of Mathematics and Computer Science (ICMC) University of S˜ao Paulo (USP) S˜ao Carlos – SP – Brazil