# No More Sliding Window: Efficient 3D Medical Image Segmentation with Differentiable Top-k Patch Sampling

arXiv: https://arxiv.org/abs/2501.10814 · HTML: https://mlsanity.com/paper/2501.10814/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 46 references that are in the map.
- First posted on arXiv 18 Jan 2025.

## Builds on (most cited first, 27 of 27)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [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)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Playing Atari with Deep Reinforcement Learning](https://mlsanity.com/paper/1312.5602/) (2013)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables](https://mlsanity.com/paper/1611.00712/) (2016)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [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)
- [Stochastic Beams and Where to Find Them: The Gumbel-Top-k Trick for Sampling Sequences Without Replacement](https://mlsanity.com/paper/1903.06059/) (2019)
- [MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation](https://mlsanity.com/paper/2303.09975/) (2023)
- [A* Sampling](https://mlsanity.com/paper/1411.0030/) (2014)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)
- [VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images](https://mlsanity.com/paper/2001.09193/) (2020)
- [Anatomically-Controllable Medical Image Generation with Segmentation-Guided Diffusion Models](https://mlsanity.com/paper/2402.05210/) (2024)
- [Differentiable Patch Selection for Image Recognition](https://mlsanity.com/paper/2104.03059/) (2021)
- [Learning to Zoom: a Saliency-Based Sampling Layer for Neural Networks](https://mlsanity.com/paper/1809.03355/) (2018)
- [Efficient Medical Image Segmentation Based on Knowledge Distillation](https://mlsanity.com/paper/2108.09987/) (2021)
- [SegFormer3D: an Efficient Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.10156/) (2024)
- [Processing Megapixel Images with Deep Attention-Sampling Models](https://mlsanity.com/paper/1905.03711/) (2019)
- [A Multi-Scale CNN and Curriculum Learning Strategy for Mammogram Classification](https://mlsanity.com/paper/1707.06978/) (2017)
- [Deep Q Learning Driven CT Pancreas Segmentation with Geometry-Aware U-Net](https://mlsanity.com/paper/1904.09120/) (2019)

## Built on by (most cited first, 5 of 5)

- [SSS: Semi-Supervised SAM-2 with Efficient Prompting for Medical Imaging Segmentation](https://mlsanity.com/paper/2506.08949/) (2025)
- [Progressive Growing of Patch Size: Curriculum Learning for Accelerated and Improved Medical Image Segmentation](https://mlsanity.com/paper/2510.23241/) (2025)
- [Inpainting U-Net for seamless pedestrian-level wind prediction across urban morphologies](https://mlsanity.com/paper/2607.02560/) (2026)
- [SAM+D: Parameter-Efficient Dimensional Lifting of SAM-Family Models via Depth-Routed LoRA and Depth Shifting](https://mlsanity.com/paper/2607.29033/) (2026)
- [Solving the Needle-in-a-Haystack Problem in Mammography Vision-Language Model with Differentiable Subset Sampling](https://mlsanity.com/paper/2609.03085/) (2026)

## Abstract (arXiv)

3D models surpass 2D models in CT/MRI segmentation by effectively capturing inter-slice relationships. However, the added depth dimension substantially increases memory consumption. While patch-based training alleviates memory constraints, it significantly slows down the inference speed due to the sliding window (SW) approach. We propose No-More-Sliding-Window (NMSW), a novel end-to-end trainable framework that enhances the efficiency of generic 3D segmentation backbone during an inference step by eliminating the need for SW. NMSW employs a differentiable Top-k module to selectively sample only the most relevant patches, thereby minimizing redundant computations. When patch-level predictions are insufficient, the framework intelligently leverages coarse global predictions to refine results. Evaluated across 3 tasks using 3 segmentation backbones, NMSW achieves competitive accuracy compared to SW inference while significantly reducing computational complexity by 91% (88.0 to 8.00 TMACs). Moreover, it delivers a 9.1x faster inference on the H100 GPU (99.0 to 8.3 sec) and a 11.1x faster inference on the Xeon Gold CPU (2110 to 189 sec). NMSW is model-agnostic, further boosting efficiency when integrated with any existing efficient segmentation backbones. The code is avaialble: https://github.com/Youngseok0001/open_nmsw.