# Brain Tumor Segmentation with Deep Neural Networks

arXiv: https://arxiv.org/abs/1505.03540 · HTML: https://mlsanity.com/paper/1505.03540/

## Key facts

- Cited by 137 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 13 May 2015.

## Built on by (most cited first, 30 of 137)

- [Unified Focal loss: Generalising Dice and cross entropy-based losses to handle class imbalanced medical image segmentation](https://mlsanity.com/paper/2102.04525/) (2021)
- [Recurrent Mask Refinement for Few-Shot Medical Image Segmentation](https://mlsanity.com/paper/2108.00622/) (2021)
- [Adaptive Early-Learning Correction for Segmentation from Noisy Annotations](https://mlsanity.com/paper/2110.03740/) (2021)
- [ACN: Adversarial Co-training Network for Brain Tumor Segmentation with Missing Modalities](https://mlsanity.com/paper/2106.14591/) (2021)
- [Latent Correlation Representation Learning for Brain Tumor Segmentation with Missing MRI Modalities](https://mlsanity.com/paper/2104.06231/) (2021)
- [Loss Functions and Metrics in Deep Learning](https://mlsanity.com/paper/2307.02694/) (2023)
- [Equitable modelling of brain imaging by counterfactual augmentation with morphologically constrained 3D deep generative models](https://mlsanity.com/paper/2111.14923/) (2021)
- [Analyzing Overfitting under Class Imbalance in Neural Networks for Image Segmentation](https://mlsanity.com/paper/2102.10365/) (2021)
- [Exploring Transfer Learning in Medical Image Segmentation using Vision-Language Models](https://mlsanity.com/paper/2308.07706/) (2023)
- [Learning Self-Supervised Low-Rank Network for Single-Stage Weakly and Semi-Supervised Semantic Segmentation](https://mlsanity.com/paper/2203.10278/) (2022)
- [Few-Shot Learning with Class Imbalance](https://mlsanity.com/paper/2101.02523/) (2021)
- [Self-Regulation for Semantic Segmentation](https://mlsanity.com/paper/2108.09702/) (2021)
- [PASSION: Towards Effective Incomplete Multi-Modal Medical Image Segmentation with Imbalanced Missing Rates](https://mlsanity.com/paper/2407.14796/) (2024)
- [Free-form tumor synthesis in computed tomography images via richer generative adversarial network](https://mlsanity.com/paper/2104.09701/) (2021)
- [Weakly-Supervised Universal Lesion Segmentation with Regional Level Set Loss](https://mlsanity.com/paper/2105.01218/) (2021)
- [Uncertainty-Guided Progressive GANs for Medical Image Translation](https://mlsanity.com/paper/2106.15542/) (2021)
- [Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge](https://mlsanity.com/paper/2405.09787/) (2024)
- [A Survey on Understanding, Visualizations, and Explanation of Deep Neural Networks](https://mlsanity.com/paper/2102.01792/) (2021)
- [Enhancing Modality-Agnostic Representations via Meta-Learning for Brain Tumor Segmentation](https://mlsanity.com/paper/2302.04308/) (2023)
- [Fall of Giants: How popular text-based MLaaS fall against a simple evasion attack](https://mlsanity.com/paper/2104.05996/) (2021)
- [Centralized Feature Pyramid for Object Detection](https://mlsanity.com/paper/2210.02093/) (2022)
- [Multimodal Data Integration for Precision Oncology: Challenges and Future Directions](https://mlsanity.com/paper/2406.19611/) (2024)
- [MAD-AD: Masked Diffusion for Unsupervised Brain Anomaly Detection](https://mlsanity.com/paper/2502.16943/) (2025)
- [Building a General SimCLR Self-Supervised Foundation Model Across Neurological Diseases to Advance 3D Brain MRI Diagnoses](https://mlsanity.com/paper/2509.10620/) (2025)
- [Meningioma segmentation in T1-weighted MRI leveraging global context and attention mechanisms](https://mlsanity.com/paper/2101.07715/) (2021)
- [3D AGSE-VNet: An Automatic Brain Tumor MRI Data Segmentation Framework](https://mlsanity.com/paper/2107.12046/) (2021)
- [Brain Tumor Segmentation using Enhanced U-Net Model with Empirical Analysis](https://mlsanity.com/paper/2210.13336/) (2022)
- [Acquiring Weak Annotations for Tumor Localization in Temporal and Volumetric Data](https://mlsanity.com/paper/2310.15098/) (2023)
- [A Flexible 2.5D Medical Image Segmentation Approach with In-Slice and Cross-Slice Attention](https://mlsanity.com/paper/2405.00130/) (2024)
- [IterMask2: Iterative Unsupervised Anomaly Segmentation via Spatial and Frequency Masking for Brain Lesions in MRI](https://mlsanity.com/paper/2406.02422/) (2024)

## Abstract (arXiv)

In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we've found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test dataset reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster.