# Submanifold Sparse Convolutional Networks for Automated 3D Segmentation of Kidneys and Kidney Tumours in Computed Tomography

arXiv: https://arxiv.org/abs/2511.04334 · HTML: https://mlsanity.com/paper/2511.04334/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 38 references that are in the map.
- First posted on arXiv 6 Nov 2025.

## Builds on (most cited first, 16 of 16)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [4D Spatio-Temporal ConvNets: Minkowski Convolutional Neural Networks](https://mlsanity.com/paper/1904.08755/) (2019)
- [3D Semantic Segmentation with Submanifold Sparse Convolutional Networks](https://mlsanity.com/paper/1711.10275/) (2017)
- [ConvNeXt V2: Co-designing and Scaling ConvNets with Masked Autoencoders](https://mlsanity.com/paper/2301.00808/) (2023)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Submanifold Sparse Convolutional Networks](https://mlsanity.com/paper/1706.01307/) (2017)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT](https://mlsanity.com/paper/2307.01984/) (2023)
- [Automated 3D Segmentation of Kidneys and Tumors in MICCAI KiTS 2023 Challenge](https://mlsanity.com/paper/2310.04110/) (2023)
- [Scalable Deep Convolutional Neural Networks for Sparse, Locally Dense Liquid Argon Time Projection Chamber Data](https://mlsanity.com/paper/1903.05663/) (2019)
- [Exploring 3D U-Net Training Configurations and Post-Processing Strategies for the MICCAI 2023 Kidney and Tumor Segmentation Challenge](https://mlsanity.com/paper/2312.05528/) (2023)

## Built on by (most cited first, 1 of 1)

- [SEMIR: Semantic Minor-Induced Representation Learning on Graphs for Visual Segmentation](https://mlsanity.com/paper/2605.12389/) (2026)

## Abstract (arXiv)

Accurate delineation of kidney tumours in Computed Tomography (CT) is essential for downstream quantitative analysis and precision oncology, but manual segmentation is a specialised task, time-consuming and difficult to scale. Automated 3D segmentation remains challenging because CT scans are large volumetric images, making high-resolution dense convolutional networks computationally expensive and often dependent on downsampling or patch-based inference. We propose a two-stage 3D segmentation methodology based on voxel sparsification and submanifold sparse convolutional networks (SSCNs). Stage 1 uses a low-resolution sparse network to identify a region of interest (ROI); Stage 2 applies a high-resolution sparse network for refined segmentation within the cropped ROI. This enables native high-resolution 3D processing while reducing memory use and inference time. We evaluate the method on the KiTS23 renal cancer CT dataset using 5-fold cross-validation. Our method achieved Dice similarity coefficients of 95.8% for kidneys + masses, 85.7% for tumours + cysts, and 80.3% for tumours alone, competitive with top KiTS23 approaches. In direct comparisons on the same cross-validation folds, the proposed sparse method achieves tumour + cyst and tumour-only Dice scores comparable to, and slightly higher than, a patch-based nnU-Net baseline, while consistently requiring less VRAM and shorter inference time across the tested hardware. Across the tested GPUs, our sparse model is markedly faster than both nnU-Net and the zero-shot zoom-out/zoom-in foundation model SegVol, which localises kidneys well but underperforms on small heterogeneous lesions. Compared to an equivalent dense implementation of the same architecture, the proposed sparse approach achieves up to a 60% reduction in inference time and up to a 75% reduction in VRAM usage across both CPU and the GPU configurations tested.