# MProtoNet: A Case-Based Interpretable Model for Brain Tumor Classification with 3D Multi-parametric Magnetic Resonance Imaging

arXiv: https://arxiv.org/abs/2304.06258 · HTML: https://mlsanity.com/paper/2304.06258/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 34 references that are in the map.
- First posted on arXiv 13 Apr 2023.

## Builds on (most cited first, 22 of 22)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization](https://mlsanity.com/paper/1610.02391/) (2016)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Learning Deep Features for Discriminative Localization](https://mlsanity.com/paper/1512.04150/) (2015)
- [Shortcut Learning in Deep Neural Networks](https://mlsanity.com/paper/2004.07780/) (2020)
- [Sanity Checks for Saliency Maps](https://mlsanity.com/paper/1810.03292/) (2018)
- [Concept Bottleneck Models](https://mlsanity.com/paper/2007.04612/) (2020)
- [This Looks Like That: Deep Learning for Interpretable Image Recognition](https://mlsanity.com/paper/1806.10574/) (2018)
- [From Anecdotal Evidence to Quantitative Evaluation Methods: A Systematic Review on Evaluating Explainable AI](https://mlsanity.com/paper/2201.08164/) (2022)
- [A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises](https://mlsanity.com/paper/2008.09104/) (2020)
- [Tell Me Where to Look: Guided Attention Inference Network](https://mlsanity.com/paper/1802.10171/) (2018)
- [Deformable ProtoPNet: An Interpretable Image Classifier Using Deformable Prototypes](https://mlsanity.com/paper/2111.15000/) (2021)
- [Attention Branch Network: Learning of Attention Mechanism for Visual Explanation](https://mlsanity.com/paper/1812.10025/) (2018)
- [Interpretable Image Classification with Differentiable Prototypes Assignment](https://mlsanity.com/paper/2112.02902/) (2021)
- [ProtoPShare: Prototype Sharing for Interpretable Image Classification and Similarity Discovery](https://mlsanity.com/paper/2011.14340/) (2020)
- [Weakly Supervised Instance Segmentation using Class Peak Response](https://mlsanity.com/paper/1804.00880/) (2018)
- [XProtoNet: Diagnosis in Chest Radiography with Global and Local Explanations](https://mlsanity.com/paper/2103.10663/) (2021)
- [IAIA-BL: A Case-based Interpretable Deep Learning Model for Classification of Mass Lesions in Digital Mammography](https://mlsanity.com/paper/2103.12308/) (2021)
- [Guidelines and Evaluation of Clinical Explainable AI in Medical Image Analysis](https://mlsanity.com/paper/2202.10553/) (2022)
- [Learning Hierarchical Attention for Weakly-supervised Chest X-Ray Abnormality Localization and Diagnosis](https://mlsanity.com/paper/2112.12349/) (2021)
- [Evaluating Explainable AI on a Multi-Modal Medical Imaging Task: Can Existing Algorithms Fulfill Clinical Requirements?](https://mlsanity.com/paper/2203.06487/) (2022)
- [ProNet: Learning to Propose Object-specific Boxes for Cascaded Neural Networks](https://mlsanity.com/paper/1511.03776/) (2015)

## Built on by (most cited first, 11 of 11)

- [Self-eXplainable AI for Medical Image Analysis: A Survey and New Outlooks](https://mlsanity.com/paper/2410.02331/) (2024)
- [Rashomon Sets for Prototypical-Part Networks: Editing Interpretable Models in Real-Time](https://mlsanity.com/paper/2503.01087/) (2025)
- [Label-free Concept Based Multiple Instance Learning for Gigapixel Histopathology](https://mlsanity.com/paper/2501.02922/) (2025)
- [ProtoECGNet: Case-Based Interpretable Deep Learning for Multi-Label ECG Classification with Contrastive Learning](https://mlsanity.com/paper/2504.08713/) (2025)
- [PIPNet3D: Interpretable Detection of Alzheimer in MRI Scans](https://mlsanity.com/paper/2403.18328/) (2024)
- [ProtoAL: Interpretable Deep Active Learning with prototypes for medical imaging](https://mlsanity.com/paper/2404.04736/) (2024)
- [Enhancing Interpretability of Vertebrae Fracture Grading using Human-interpretable Prototypes](https://mlsanity.com/paper/2404.02830/) (2024)
- [ProteinPNet: Prototypical Part Networks for Concept Learning in Spatial Proteomics](https://mlsanity.com/paper/2512.02983/) (2025)
- [ProtoTTA: Prototype-Guided Test-Time Adaptation](https://mlsanity.com/paper/2604.15494/) (2026)
- [GRAPE: Graph-Augmented Prototype Explanations for Interactive Medical Image Diagnosis](https://mlsanity.com/paper/2606.30901/) (2026)
- [ProtoPointNet: Prototype-Based Interpretable Classification of 3D Dental Point Clouds with Verifiable Spatial Activations](https://mlsanity.com/paper/2607.12335/) (2026)

## Abstract (arXiv)

Recent applications of deep convolutional neural networks in medical imaging raise concerns about their interpretability. While most explainable deep learning applications use post hoc methods (such as GradCAM) to generate feature attribution maps, there is a new type of case-based reasoning models, namely ProtoPNet and its variants, which identify prototypes during training and compare input image patches with those prototypes. We propose the first medical prototype network (MProtoNet) to extend ProtoPNet to brain tumor classification with 3D multi-parametric magnetic resonance imaging (mpMRI) data. To address different requirements between 2D natural images and 3D mpMRIs especially in terms of localizing attention regions, a new attention module with soft masking and online-CAM loss is introduced. Soft masking helps sharpen attention maps, while online-CAM loss directly utilizes image-level labels when training the attention module. MProtoNet achieves statistically significant improvements in interpretability metrics of both correctness and localization coherence (with a best activation precision of 0.713±0.058) without human-annotated labels during training, when compared with GradCAM and several ProtoPNet variants. The source code is available at https://github.com/aywi/mprotonet.