The Segment Anything Model (SAM) has demonstrated strong and versatile segmentation capabilities, along with intuitive prompt-based interactions. However, customizing SAM for medical image segmentation requires massive amounts of pixel-level annotations and precise point- or box-based prompt designs. To address these challenges, we introduce PGP-SAM, a novel prototype-based few-shot tuning approach that uses limited samples to replace tedious manual prompts. Our key idea is to leverage inter- and intra-class prototypes to capture class-specific knowledge and relationships. We propose two main components: (1) a plug-and-play contextual modulation module that integrates multi-scale information, and (2) a class-guided cross-attention mechanism that fuses prototypes and features for automatic prompt generation. Experiments on a public multi-organ dataset and a private ventricle dataset demonstrate that PGP-SAM achieves superior mean Dice scores compared with existing prompt-free SAM variants, while using only 10\% of the 2D slices.
Accurate medical image segmentation is often hindered by noisy labels in training data, due to the challenges of annotating medical images. Prior research works addressing noisy labels tend to make class-dependent assumptions, overlooking the pixel-dependent nature of most noisy labels. Furthermore, existing methods typically apply fixed thresholds to filter out noisy labels, risking the removal of minority classes and consequently degrading segmentation performance. To bridge these gaps, our proposed framework, Collaborative Learning with Curriculum Selection (CLCS), addresses pixel-dependent noisy labels with class imbalance. CLCS advances the existing works by i) treating noisy labels as pixel-dependent and addressing them through a collaborative learning framework, and ii) employing a curriculum dynamic thresholding approach adapting to model learning progress to select clean data samples to mitigate the class imbalance issue, and iii) applying a noise balance loss to noisy data samples to improve data utilization instead of discarding them outright. Specifically, our CLCS contains two modules: Curriculum Noisy Label Sample Selection (CNS) and Noise Balance Loss (NBL). In the CNS module, we designed a two-branch network with discrepancy loss for collaborative learning so that different feature representations of the same instance could be extracted from distinct views and used to vote the class probabilities of pixels. Besides, a curriculum dynamic threshold is adopted to select clean-label samples through probability voting. In the NBL module, instead of directly dropping the suspiciously noisy labels, we further adopt a robust loss to leverage such instances to boost the performance.
3D medical image segmentation has progressed considerably due to Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs), yet these methods struggle to balance long-range dependency acquisition with computational efficiency. To address this challenge, we propose UNETVL (U-Net Vision-LSTM), a novel architecture that leverages recent advancements in temporal information processing. UNETVL incorporates Vision-LSTM (ViL) for improved scalability and memory functions, alongside an efficient Chebyshev Kolmogorov-Arnold Networks (KAN) to handle complex and long-range dependency patterns more effectively. We validated our method on the ACDC and AMOS2022 (post challenge Task 2) benchmark datasets, showing a significant improvement in mean Dice score compared to recent state-of-the-art approaches, especially over its predecessor, UNETR, with increases of 7.3% on ACDC and 15.6% on AMOS, respectively. Extensive ablation studies were conducted to demonstrate the impact of each component in UNETVL, providing a comprehensive understanding of its architecture. Our code is available at https://github.com/tgrex6/UNETVL, facilitating further research and applications in this domain.
Domain shifts in medical image segmentation, particularly when data comes from different centers, pose significant challenges. Intra-center variability, such as differences in scanner models or imaging protocols, can cause domain shifts as large as, or even larger than, those between centers. To address this, we propose the "one image as one domain" (OIOD) hypothesis, which treats each image as a unique domain, enabling flexible and robust domain generalization. Based on this hypothesis, we develop a unified disentanglement-based domain generalization (UniDDG) framework, which simultaneously handles both multi-source and single-source domain generalization without requiring explicit domain labels. This approach simplifies training with a fixed architecture, independent of the number of source domains, reducing complexity and enhancing scalability. We decouple each input image into content representation and style code, then exchange and combine these within the batch for segmentation, reconstruction, and further disentanglement. By maintaining distinct style codes for each image, our model ensures thorough decoupling of content representations and style codes, improving domain invariance of the content representations. Additionally, we enhance generalization with expansion mask attention (EMA) for boundary preservation and style augmentation (SA) to simulate diverse image styles, improving robustness to domain shifts. Extensive experiments show that our method achieves Dice scores of 84.43% and 88.91% for multi-source to single-center and single-center generalization in optic disc and optic cup segmentation, respectively, and 86.96% and 88.56% for prostate segmentation, outperforming current state-of-the-art domain generalization methods, offering superior performance and adaptability across clinical settings.
In Sub-Saharan Africa (SSA), the utilization of lower-quality Magnetic Resonance Imaging (MRI) technology raises questions about the applicability of machine learning methods for clinical tasks. This study aims to provide a robust deep learning-based brain tumor segmentation (BraTS) method tailored for the SSA population using a threefold approach. Firstly, the impact of domain shift from the SSA training data on model efficacy was examined, revealing no significant effect. Secondly, a comparative analysis of 3D and 2D full-resolution models using the nnU-Net framework indicates similar performance of both the models trained for 300 epochs achieving a five-fold cross-validation score of 0.93. Lastly, addressing the performance gap observed in SSA validation as opposed to the relatively larger BraTS glioma (GLI) validation set, two strategies are proposed: fine-tuning SSA cases using the GLI+SSA best-pretrained 2D fullres model at 300 epochs, and introducing a novel neural style transfer-based data augmentation technique for the SSA cases. This investigation underscores the potential of enhancing brain tumor prediction within SSA's unique healthcare landscape.
Diffusion models have been widely used in the generative domain due to their convincing performance in modeling complex data distributions. Moreover, they have shown competitive results on discriminative tasks, such as image segmentation. While diffusion models have also been explored for automatic music transcription, their performance has yet to reach a competitive level. In this paper, we focus on discrete diffusion model's refinement capabilities and present a novel architecture for piano transcription. Our model utilizes Neighborhood Attention layers as the denoising module, gradually predicting the target high-resolution piano roll, conditioned on the finetuned features of a pretrained acoustic model. To further enhance refinement, we devise a novel strategy which applies distinct transition states during training and inference stage of discrete diffusion models. Experiments on the MAESTRO dataset show that our approach outperforms previous diffusion-based piano transcription models and the baseline model in terms of F1 score. Our code is available in https://github.com/hanshounsu/d3rm.
Recent progress in controllable image generation and editing is largely driven by diffusion-based methods. Although diffusion models perform exceptionally well in specific tasks with tailored designs, establishing a unified model is still challenging. In contrast, autoregressive models inherently feature a unified tokenized representation, which simplifies the creation of a single foundational model for various tasks. In this work, we propose EditAR, a single unified autoregressive framework for a variety of conditional image generation tasks, e.g., image editing, depth-to-image, edge-to-image, segmentation-to-image. The model takes both images and instructions as inputs, and predicts the edited images tokens in a vanilla next-token paradigm. To enhance the text-to-image alignment, we further propose to distill the knowledge from foundation models into the autoregressive modeling process. We evaluate its effectiveness across diverse tasks on established benchmarks, showing competitive performance to various state-of-the-art task-specific methods. Project page: https://jitengmu.github.io/EditAR/
This study explores the potential of graph neural networks (GNNs) to enhance semantic segmentation across diverse image modalities. We evaluate the effectiveness of a novel GNN-based U-Net architecture on three distinct datasets: PascalVOC, a standard benchmark for natural image segmentation, WoodScape, a challenging dataset of fisheye images commonly used in autonomous driving, introducing significant geometric distortions; and ISIC2016, a dataset of dermoscopic images for skin lesion segmentation. We compare our proposed UNet-GNN model against established convolutional neural networks (CNNs) based segmentation models, including U-Net and U-Net++, as well as the transformer-based SwinUNet. Unlike these methods, which primarily rely on local convolutional operations or global self-attention, GNNs explicitly model relationships between image regions by constructing and operating on a graph representation of the image features. This approach allows the model to capture long-range dependencies and complex spatial relationships, which we hypothesize will be particularly beneficial for handling geometric distortions present in fisheye imagery and capturing intricate boundaries in medical images. Our analysis demonstrates the versatility of GNNs in addressing diverse segmentation challenges and highlights their potential to improve segmentation accuracy in various applications, including autonomous driving and medical image analysis.
Hybrid CNN-Transformer models are designed to combine the advantages of Convolutional Neural Networks (CNNs) and Transformers to efficiently model both local information and long-range dependencies. However, most research tends to focus on integrating the spatial features of CNNs and Transformers, while overlooking the critical importance of channel features. This is particularly significant for model performance in low-quality medical image segmentation. Effective channel feature extraction can significantly enhance the model's ability to capture contextual information and improve its representation capabilities. To address this issue, we propose a hybrid CNN-Transformer model, CFFormer, and introduce two modules: the Cross Feature Channel Attention (CFCA) module and the X-Spatial Feature Fusion (XFF) module. The model incorporates dual encoders, with the CNN encoder focusing on capturing local features and the Transformer encoder modeling global features. The CFCA module filters and facilitates interactions between the channel features from the two encoders, while the XFF module effectively reduces the significant semantic information differences in spatial features, enabling a smooth and cohesive spatial feature fusion. We evaluate our model across eight datasets covering five modalities to test its generalization capability. Experimental results demonstrate that our model outperforms current state-of-the-art (SOTA) methods, with particularly superior performance on datasets characterized by blurry boundaries and low contrast.
Satisfactory progress has been achieved recently in universal segmentation of CT images. Following the success of vision-language methods, there is a growing trend towards utilizing text prompts and contrastive learning to develop universal segmentation models. However, there exists a significant imbalance in information density between 3D images and text prompts. Moreover, the standard fully connected layer segmentation approach faces significant challenges in handling multiple classes and exhibits poor generalizability. To address these challenges, we propose the VOxel Interacting with LAnguage method (VOILA) for universal CT image segmentation. Initially, we align voxels and language into a shared representation space and classify voxels on the basis of cosine similarity. Subsequently, we develop the Voxel-Language Interaction framework to mitigate the impact of class imbalance caused by foreground-background discrepancies and variations in target volumes. Furthermore, a Complexity-Aware Sampling method is proposed to focus on region hard to segment, achieved by generating pseudo-heatmaps from a trainable Gaussian mixture distribution. Our results indicate the proposed VOILA is capable to achieve improved performance with reduced parameters and computational cost during training. Furthermore, it demonstrates significant generalizability across diverse datasets without additional fine-tuning.
Retinal vascular morphology is crucial for diagnosing diseases such as diabetes, glaucoma, and hypertension, making accurate segmentation of retinal vessels essential for early intervention. Traditional segmentation methods assume that training and testing data share similar distributions, which can lead to poor performance on unseen domains due to domain shifts caused by variations in imaging devices and patient demographics. This paper presents a novel approach, DGSSA, for retinal vessel image segmentation that enhances model generalization by combining structural and style augmentation strategies. We utilize a space colonization algorithm to generate diverse vascular-like structures that closely mimic actual retinal vessels, which are then used to generate pseudo-retinal images with an improved Pix2Pix model, allowing the segmentation model to learn a broader range of structure distributions. Additionally, we utilize PixMix to implement random photometric augmentations and introduce uncertainty perturbations, thereby enriching stylistic diversity and significantly enhancing the model's adaptability to varying imaging conditions. Our framework has been rigorously evaluated on four challenging datasets-DRIVE, CHASEDB, HRF, and STARE-demonstrating state-of-the-art performance that surpasses existing methods. This validates the effectiveness of our proposed approach, highlighting its potential for clinical application in automated retinal vessel analysis.
Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.
Current medical image segmentation approaches have limitations in deeply exploring multi-scale information and effectively combining local detail textures with global contextual semantic information. This results in over-segmentation, under-segmentation, and blurred segmentation boundaries. To tackle these challenges, we explore multi-scale feature representations from different perspectives, proposing a novel, lightweight, and multi-scale architecture (LM-Net) that integrates advantages of both Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) to enhance segmentation accuracy. LM-Net employs a lightweight multi-branch module to capture multi-scale features at the same level. Furthermore, we introduce two modules to concurrently capture local detail textures and global semantics with multi-scale features at different levels: the Local Feature Transformer (LFT) and Global Feature Transformer (GFT). The LFT integrates local window self-attention to capture local detail textures, while the GFT leverages global self-attention to capture global contextual semantics. By combining these modules, our model achieves complementarity between local and global representations, alleviating the problem of blurred segmentation boundaries in medical image segmentation. To evaluate the feasibility of LM-Net, extensive experiments have been conducted on three publicly available datasets with different modalities. Our proposed model achieves state-of-the-art results, surpassing previous methods, while only requiring 4.66G FLOPs and 5.4M parameters. These state-of-the-art results on three datasets with different modalities demonstrate the effectiveness and adaptability of our proposed LM-Net for various medical image segmentation tasks.
This research paper delves into the development of an Optical Character Recognition (OCR) system for the recognition of Ashokan Brahmi characters using Convolutional Neural Networks. It utilizes a comprehensive dataset of character images to train the models, along with data augmentation techniques to optimize the training process. Furthermore, the paper incorporates image preprocessing to remove noise, as well as image segmentation to facilitate line and character segmentation. The study mainly focuses on three pre-trained CNNs, namely LeNet, VGG-16, and MobileNet and compares their accuracy. Transfer learning was employed to adapt the pre-trained models to the Ashokan Brahmi character dataset. The findings reveal that MobileNet outperforms the other two models in terms of accuracy, achieving a validation accuracy of 95.94% and validation loss of 0.129. The paper provides an in-depth analysis of the implementation process using MobileNet and discusses the implications of the findings. The use of OCR for character recognition is of significant importance in the field of epigraphy, specifically for the preservation and digitization of ancient scripts. The results of this research paper demonstrate the effectiveness of using pre-trained CNNs for the recognition of Ashokan Brahmi characters.
Transfer learning, by leveraging knowledge from pre-trained models, has significantly enhanced the performance of target tasks. However, as deep neural networks scale up, full fine-tuning introduces substantial computational and storage challenges in resource-constrained environments, limiting its widespread adoption. To address this, parameter-efficient fine-tuning (PEFT) methods have been developed to reduce computational complexity and storage requirements by minimizing the number of updated parameters. While matrix decomposition-based PEFT methods, such as LoRA, show promise, they struggle to fully capture the high-dimensional structural characteristics of model weights. In contrast, high-dimensional tensors offer a more natural representation of neural network weights, allowing for a more comprehensive capture of higher-order features and multi-dimensional interactions. In this paper, we propose tCURLoRA, a novel fine-tuning method based on tensor CUR decomposition. By concatenating pre-trained weight matrices into a three-dimensional tensor and applying tensor CUR decomposition, we update only the lower-order tensor components during fine-tuning, effectively reducing computational and storage overhead. Experimental results demonstrate that tCURLoRA outperforms existing PEFT methods in medical image segmentation tasks.
This paper introduces Tree-NET, a novel framework for medical image segmentation that leverages bottleneck feature supervision to enhance both segmentation accuracy and computational efficiency. While previous studies have employed bottleneck feature supervision, their applications have largely been limited to the training phase, offering no computational benefits during training or evaluation. To the best of our knowledge, this study is the first to propose a framework that incorporates two additional training phases for segmentation models, utilizing bottleneck features at both input and output stages. This approach significantly improves computational performance by reducing input and output dimensions with a negligible addition to parameter count, without compromising accuracy. Tree-NET features a three-layer architecture comprising Encoder-Net and Decoder-Net, which are autoencoders designed to compress input and label data, respectively, and Bridge-Net, a segmentation framework that supervises the bottleneck features. By focusing on dense, compressed representations, Tree-NET enhances operational efficiency and can be seamlessly integrated into existing segmentation models without altering their internal structures or increasing model size. We evaluate Tree-NET on two critical segmentation tasks -- skin lesion and polyp segmentation -- using various backbone models, including U-NET variants and Polyp-PVT. Experimental results demonstrate that Tree-NET reduces FLOPs by a factor of 4 to 13 and decreases memory usage, while achieving comparable or superior accuracy compared to the original architectures. These findings underscore Tree-NET's potential as a robust and efficient solution for medical image segmentation.
Denoising Diffusion Models (DDMs) are widely used for high-quality image generation and medical image segmentation but often rely on Unet-based architectures, leading to high computational overhead, especially with high-resolution images. This work proposes three NCA-based improvements for diffusion-based medical image segmentation. First, Multi-MedSegDiffNCA uses a multilevel NCA framework to refine rough noise estimates generated by lower level NCA models. Second, CBAM-MedSegDiffNCA incorporates channel and spatial attention for improved segmentation. Third, MultiCBAM-MedSegDiffNCA combines these methods with a new RGB channel loss for semantic guidance. Evaluations on Lesion segmentation show that MultiCBAM-MedSegDiffNCA matches Unet-based model performance with dice score of 87.84% while using 60-110 times fewer parameters, offering a more efficient solution for low resource medical settings.
Recently, the state-of-art models for medical image segmentation is U-Net and their variants. These networks, though succeeding in deriving notable results, ignore the practical problem hanging over the medical segmentation field: overfitting and small dataset. The over-complicated deep neural networks unnecessarily extract meaningless information, and a majority of them are not suitable for lung slice CT image segmentation task. To overcome the two limitations, we proposed a new whole-process network merging advanced UNet++ model. The network comprises three main modules: data augmentation, optimized neural network, parameter fine-tuning. By incorporating diverse methods, the training results demonstrate a significant advantage over similar works, achieving leading accuracy of 98.03% with the lowest overfitting. potential. Our network is remarkable as one of the first to target on lung slice CT images.
Cardiovascular disease (CVD) and cardiac dyssynchrony are major public health problems in the United States. Precise cardiac image segmentation is crucial for extracting quantitative measures that help categorize cardiac dyssynchrony. However, achieving high accuracy often depends on centralizing large datasets from different hospitals, which can be challenging due to privacy concerns. To solve this problem, Federated Learning (FL) is proposed to enable decentralized model training on such data without exchanging sensitive information. However, bandwidth limitations and data heterogeneity remain as significant challenges in conventional FL algorithms. In this paper, we propose a novel efficient and adaptive federate learning method for cardiac segmentation that improves model performance while reducing the bandwidth requirement. Our method leverages the low-rank adaptation (LoRA) to regularize model weight update and reduce communication overhead. We also propose a \mymethod{} aggregation technique to address data heterogeneity among clients. This technique adaptively penalizes the aggregated weights from different clients by comparing the validation accuracy in each client, allowing better generalization performance and fast local adaptation. In-client and cross-client evaluations on public cardiac MR datasets demonstrate the superiority of our method over other LoRA-based federate learning approaches.
Decoupling domain-variant information (DVI) from domain-invariant information (DII) serves as a prominent strategy for mitigating domain shifts in the practical implementation of deep learning algorithms. However, in medical settings, concerns surrounding data collection and privacy often restrict access to both training and test data, hindering the empirical decoupling of information by existing methods. To tackle this issue, we propose an Autonomous Information Filter-driven Source-free Domain Adaptation (AIF-SFDA) algorithm, which leverages a frequency-based learnable information filter to autonomously decouple DVI and DII. Information Bottleneck (IB) and Self-supervision (SS) are incorporated to optimize the learnable frequency filter. The IB governs the information flow within the filter to diminish redundant DVI, while SS preserves DII in alignment with the specific task and image modality. Thus, the autonomous information filter can overcome domain shifts relying solely on target data. A series of experiments covering various medical image modalities and segmentation tasks were conducted to demonstrate the benefits of AIF-SFDA through comparisons with leading algorithms and ablation studies. The code is available at https://github.com/JingHuaMan/AIF-SFDA.