new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Nov 27

U-Bench: A Comprehensive Understanding of U-Net through 100-Variant Benchmarking

Over the past decade, U-Net has been the dominant architecture in medical image segmentation, leading to the development of thousands of U-shaped variants. Despite its widespread adoption, there is still no comprehensive benchmark to systematically evaluate their performance and utility, largely because of insufficient statistical validation and limited consideration of efficiency and generalization across diverse datasets. To bridge this gap, we present U-Bench, the first large-scale, statistically rigorous benchmark that evaluates 100 U-Net variants across 28 datasets and 10 imaging modalities. Our contributions are threefold: (1) Comprehensive Evaluation: U-Bench evaluates models along three key dimensions: statistical robustness, zero-shot generalization, and computational efficiency. We introduce a novel metric, U-Score, which jointly captures the performance-efficiency trade-off, offering a deployment-oriented perspective on model progress. (2) Systematic Analysis and Model Selection Guidance: We summarize key findings from the large-scale evaluation and systematically analyze the impact of dataset characteristics and architectural paradigms on model performance. Based on these insights, we propose a model advisor agent to guide researchers in selecting the most suitable models for specific datasets and tasks. (3) Public Availability: We provide all code, models, protocols, and weights, enabling the community to reproduce our results and extend the benchmark with future methods. In summary, U-Bench not only exposes gaps in previous evaluations but also establishes a foundation for fair, reproducible, and practically relevant benchmarking in the next decade of U-Net-based segmentation models. The project can be accessed at: https://fenghetan9.github.io/ubench. Code is available at: https://github.com/FengheTan9/U-Bench.

More complex encoder is not all you need

U-Net and its variants have been widely used in medical image segmentation. However, most current U-Net variants confine their improvement strategies to building more complex encoder, while leaving the decoder unchanged or adopting a simple symmetric structure. These approaches overlook the true functionality of the decoder: receiving low-resolution feature maps from the encoder and restoring feature map resolution and lost information through upsampling. As a result, the decoder, especially its upsampling component, plays a crucial role in enhancing segmentation outcomes. However, in 3D medical image segmentation, the commonly used transposed convolution can result in visual artifacts. This issue stems from the absence of direct relationship between adjacent pixels in the output feature map. Furthermore, plain encoder has already possessed sufficient feature extraction capability because downsampling operation leads to the gradual expansion of the receptive field, but the loss of information during downsampling process is unignorable. To address the gap in relevant research, we extend our focus beyond the encoder and introduce neU-Net (i.e., not complex encoder U-Net), which incorporates a novel Sub-pixel Convolution for upsampling to construct a powerful decoder. Additionally, we introduce multi-scale wavelet inputs module on the encoder side to provide additional information. Our model design achieves excellent results, surpassing other state-of-the-art methods on both the Synapse and ACDC datasets.

  • 7 authors
·
Sep 20, 2023

A Comprehensive Survey of Mamba Architectures for Medical Image Analysis: Classification, Segmentation, Restoration and Beyond

Mamba, a special case of the State Space Model, is gaining popularity as an alternative to template-based deep learning approaches in medical image analysis. While transformers are powerful architectures, they have drawbacks, including quadratic computational complexity and an inability to address long-range dependencies efficiently. This limitation affects the analysis of large and complex datasets in medical imaging, where there are many spatial and temporal relationships. In contrast, Mamba offers benefits that make it well-suited for medical image analysis. It has linear time complexity, which is a significant improvement over transformers. Mamba processes longer sequences without attention mechanisms, enabling faster inference and requiring less memory. Mamba also demonstrates strong performance in merging multimodal data, improving diagnosis accuracy and patient outcomes. The organization of this paper allows readers to appreciate the capabilities of Mamba in medical imaging step by step. We begin by defining core concepts of SSMs and models, including S4, S5, and S6, followed by an exploration of Mamba architectures such as pure Mamba, U-Net variants, and hybrid models with convolutional neural networks, transformers, and Graph Neural Networks. We also cover Mamba optimizations, techniques and adaptations, scanning, datasets, applications, experimental results, and conclude with its challenges and future directions in medical imaging. This review aims to demonstrate the transformative potential of Mamba in overcoming existing barriers within medical imaging while paving the way for innovative advancements in the field. A comprehensive list of Mamba architectures applied in the medical field, reviewed in this work, is available at Github.

  • 9 authors
·
Oct 3, 2024 4

Dino U-Net: Exploiting High-Fidelity Dense Features from Foundation Models for Medical Image Segmentation

Foundation models pre-trained on large-scale natural image datasets offer a powerful paradigm for medical image segmentation. However, effectively transferring their learned representations for precise clinical applications remains a challenge. In this work, we propose Dino U-Net, a novel encoder-decoder architecture designed to exploit the high-fidelity dense features of the DINOv3 vision foundation model. Our architecture introduces an encoder built upon a frozen DINOv3 backbone, which employs a specialized adapter to fuse the model's rich semantic features with low-level spatial details. To preserve the quality of these representations during dimensionality reduction, we design a new fidelity-aware projection module (FAPM) that effectively refines and projects the features for the decoder. We conducted extensive experiments on seven diverse public medical image segmentation datasets. Our results show that Dino U-Net achieves state-of-the-art performance, consistently outperforming previous methods across various imaging modalities. Our framework proves to be highly scalable, with segmentation accuracy consistently improving as the backbone model size increases up to the 7-billion-parameter variant. The findings demonstrate that leveraging the superior, dense-pretrained features from a general-purpose foundation model provides a highly effective and parameter-efficient approach to advance the accuracy of medical image segmentation. The code is available at https://github.com/yifangao112/DinoUNet.

  • 5 authors
·
Aug 28

UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

  • 4 authors
·
Dec 10, 2019

Squeezeformer: An Efficient Transformer for Automatic Speech Recognition

The recently proposed Conformer model has become the de facto backbone model for various downstream speech tasks based on its hybrid attention-convolution architecture that captures both local and global features. However, through a series of systematic studies, we find that the Conformer architecture's design choices are not optimal. After re-examining the design choices for both the macro and micro-architecture of Conformer, we propose Squeezeformer which consistently outperforms the state-of-the-art ASR models under the same training schemes. In particular, for the macro-architecture, Squeezeformer incorporates (i) the Temporal U-Net structure which reduces the cost of the multi-head attention modules on long sequences, and (ii) a simpler block structure of multi-head attention or convolution modules followed up by feed-forward module instead of the Macaron structure proposed in Conformer. Furthermore, for the micro-architecture, Squeezeformer (i) simplifies the activations in the convolutional block, (ii) removes redundant Layer Normalization operations, and (iii) incorporates an efficient depthwise down-sampling layer to efficiently sub-sample the input signal. Squeezeformer achieves state-of-the-art results of 7.5%, 6.5%, and 6.0% word-error-rate (WER) on LibriSpeech test-other without external language models, which are 3.1%, 1.4%, and 0.6% better than Conformer-CTC with the same number of FLOPs. Our code is open-sourced and available online.

  • 8 authors
·
Jun 2, 2022

Assessing the value of Geo-Foundational Models for Flood Inundation Mapping: Benchmarking models for Sentinel-1, Sentinel-2, and Planetscope for end-users

Geo-Foundational Models (GFMs) enable fast and reliable extraction of spatiotemporal information from satellite imagery, improving flood inundation mapping by leveraging location and time embeddings. Despite their potential, it remains unclear whether GFMs outperform traditional models like U-Net. A systematic comparison across sensors and data availability scenarios is still lacking, which is an essential step to guide end-users in model selection. To address this, we evaluate three GFMs, Prithvi 2.0, Clay V1.5, DOFA, and UViT (a Prithvi variant), against TransNorm, U-Net, and Attention U-Net using PlanetScope, Sentinel-1, and Sentinel-2. We observe competitive performance among all GFMs, with only 2-5% variation between the best and worst models across sensors. Clay outperforms others on PlanetScope (0.79 mIoU) and Sentinel-2 (0.70), while Prithvi leads on Sentinel-1 (0.57). In leave-one-region-out cross-validation across five regions, Clay shows slightly better performance across all sensors (mIoU: 0.72(0.04), 0.66(0.07), 0.51(0.08)) compared to Prithvi (0.70(0.05), 0.64(0.09), 0.49(0.13)) and DOFA (0.67(0.07), 0.64(0.04), 0.49(0.09)) for PlanetScope, Sentinel-2, and Sentinel-1, respectively. Across all 19 sites, leave-one-region-out cross-validation reveals a 4% improvement by Clay compared to U-Net. Visual inspection highlights Clay's superior ability to retain fine details. Few-shot experiments show Clay achieves 0.64 mIoU on PlanetScope with just five training images, outperforming Prithvi (0.24) and DOFA (0.35). In terms of computational time, Clay is a better choice due to its smaller model size (26M parameters), making it ~3x faster than Prithvi (650M) and 2x faster than DOFA (410M). Contrary to previous findings, our results suggest GFMs offer small to moderate improvements in flood mapping accuracy at lower computational cost and labeling effort compared to traditional U-Net.

  • 4 authors
·
Nov 3

Performance Analysis of Various EfficientNet Based U-Net++ Architecture for Automatic Building Extraction from High Resolution Satellite Images

Building extraction is an essential component of study in the science of remote sensing, and applications for building extraction heavily rely on semantic segmentation of high-resolution remote sensing imagery. Semantic information extraction gap constraints in the present deep learning based approaches, however can result in inadequate segmentation outcomes. To address this issue and extract buildings with high accuracy, various efficientNet backbone based U-Net++ has been proposed in this study. The designed network, based on U-Net, can improve the sensitivity of the model by deep supervision, voluminous redesigned skip-connections and hence reducing the influence of irrelevant feature areas in the background. Various effecientNet backbone based encoders have been employed when training the network to enhance the capacity of the model to extract more relevant feature. According on the experimental findings, the suggested model significantly outperforms previous cutting-edge approaches. Among the 5 efficientNet variation Unet++ based on efficientb4 achieved the best result by scoring mean accuracy of 92.23%, mean iou of 88.32%, and mean precision of 93.2% on publicly available Massachusetts building dataset and thus showing the promises of the model for automatic building extraction from high resolution satellite images.

  • 5 authors
·
Sep 5, 2023

Improved Robustness for Deep Learning-based Segmentation of Multi-Center Myocardial Perfusion MRI Datasets Using Data Adaptive Uncertainty-guided Space-time Analysis

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

  • 11 authors
·
Aug 8, 2024

Region-Adaptive Sampling for Diffusion Transformers

Diffusion models (DMs) have become the leading choice for generative tasks across diverse domains. However, their reliance on multiple sequential forward passes significantly limits real-time performance. Previous acceleration methods have primarily focused on reducing the number of sampling steps or reusing intermediate results, failing to leverage variations across spatial regions within the image due to the constraints of convolutional U-Net structures. By harnessing the flexibility of Diffusion Transformers (DiTs) in handling variable number of tokens, we introduce RAS, a novel, training-free sampling strategy that dynamically assigns different sampling ratios to regions within an image based on the focus of the DiT model. Our key observation is that during each sampling step, the model concentrates on semantically meaningful regions, and these areas of focus exhibit strong continuity across consecutive steps. Leveraging this insight, RAS updates only the regions currently in focus, while other regions are updated using cached noise from the previous step. The model's focus is determined based on the output from the preceding step, capitalizing on the temporal consistency we observed. We evaluate RAS on Stable Diffusion 3 and Lumina-Next-T2I, achieving speedups up to 2.36x and 2.51x, respectively, with minimal degradation in generation quality. Additionally, a user study reveals that RAS delivers comparable qualities under human evaluation while achieving a 1.6x speedup. Our approach makes a significant step towards more efficient diffusion transformers, enhancing their potential for real-time applications.

  • 7 authors
·
Feb 14 3

On the Scalability of Diffusion-based Text-to-Image Generation

Scaling up model and data size has been quite successful for the evolution of LLMs. However, the scaling law for the diffusion based text-to-image (T2I) models is not fully explored. It is also unclear how to efficiently scale the model for better performance at reduced cost. The different training settings and expensive training cost make a fair model comparison extremely difficult. In this work, we empirically study the scaling properties of diffusion based T2I models by performing extensive and rigours ablations on scaling both denoising backbones and training set, including training scaled UNet and Transformer variants ranging from 0.4B to 4B parameters on datasets upto 600M images. For model scaling, we find the location and amount of cross attention distinguishes the performance of existing UNet designs. And increasing the transformer blocks is more parameter-efficient for improving text-image alignment than increasing channel numbers. We then identify an efficient UNet variant, which is 45% smaller and 28% faster than SDXL's UNet. On the data scaling side, we show the quality and diversity of the training set matters more than simply dataset size. Increasing caption density and diversity improves text-image alignment performance and the learning efficiency. Finally, we provide scaling functions to predict the text-image alignment performance as functions of the scale of model size, compute and dataset size.

  • 10 authors
·
Apr 3, 2024

LightM-UNet: Mamba Assists in Lightweight UNet for Medical Image Segmentation

UNet and its variants have been widely used in medical image segmentation. However, these models, especially those based on Transformer architectures, pose challenges due to their large number of parameters and computational loads, making them unsuitable for mobile health applications. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as competitive alternatives to CNN and Transformer architectures. Building upon this, we employ Mamba as a lightweight substitute for CNN and Transformer within UNet, aiming at tackling challenges stemming from computational resource limitations in real medical settings. To this end, we introduce the Lightweight Mamba UNet (LightM-UNet) that integrates Mamba and UNet in a lightweight framework. Specifically, LightM-UNet leverages the Residual Vision Mamba Layer in a pure Mamba fashion to extract deep semantic features and model long-range spatial dependencies, with linear computational complexity. Extensive experiments conducted on two real-world 2D/3D datasets demonstrate that LightM-UNet surpasses existing state-of-the-art literature. Notably, when compared to the renowned nnU-Net, LightM-UNet achieves superior segmentation performance while drastically reducing parameter and computation costs by 116x and 21x, respectively. This highlights the potential of Mamba in facilitating model lightweighting. Our code implementation is publicly available at https://github.com/MrBlankness/LightM-UNet.

  • 6 authors
·
Mar 8, 2024

LoRA-based methods on Unet for transfer learning in Subarachnoid Hematoma Segmentation

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

  • 7 authors
·
Aug 3

Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images

Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited kernel size of convolution layers in FCNNs, their performance of modeling long-range information is sub-optimal, and this can lead to deficiencies in the segmentation of tumors with variable sizes. On the other hand, transformer models have demonstrated excellent capabilities in capturing such long-range information in multiple domains, including natural language processing and computer vision. Inspired by the success of vision transformers and their variants, we propose a novel segmentation model termed Swin UNEt TRansformers (Swin UNETR). Specifically, the task of 3D brain tumor semantic segmentation is reformulated as a sequence to sequence prediction problem wherein multi-modal input data is projected into a 1D sequence of embedding and used as an input to a hierarchical Swin transformer as the encoder. The swin transformer encoder extracts features at five different resolutions by utilizing shifted windows for computing self-attention and is connected to an FCNN-based decoder at each resolution via skip connections. We have participated in BraTS 2021 segmentation challenge, and our proposed model ranks among the top-performing approaches in the validation phase. Code: https://monai.io/research/swin-unetr

  • 6 authors
·
Jan 4, 2022