In medical imaging, developing generalized segmentation models that can handle multiple organs and lesions is crucial. However, the scarcity of fully annotated datasets and strict privacy regulations present significant barriers to data sharing. Federated Learning (FL) allows decentralized model training, but existing FL methods often struggle with partial labeling, leading to model divergence and catastrophic forgetting. We propose ConDistFL, a novel FL framework incorporating conditional distillation to address these challenges. ConDistFL enables effective learning from partially labeled datasets, significantly improving segmentation accuracy across distributed and non-uniform datasets. In addition to its superior segmentation performance, ConDistFL maintains computational and communication efficiency, ensuring its scalability for real-world applications. Furthermore, ConDistFL demonstrates remarkable generalizability, significantly outperforming existing FL methods in out-of-federation tests, even adapting to unseen contrast phases (e.g., non-contrast CT images) in our experiments. Extensive evaluations on 3D CT and 2D chest X-ray datasets show that ConDistFL is an efficient, adaptable solution for collaborative medical image segmentation in privacy-constrained settings.
Creating fully annotated labels for medical image segmentation is prohibitively time-intensive and costly, emphasizing the necessity for innovative approaches that minimize reliance on detailed annotations. Scribble annotations offer a more cost-effective alternative, significantly reducing the expenses associated with full annotations. However, scribble annotations offer limited and imprecise information, failing to capture the detailed structural and boundary characteristics necessary for accurate organ delineation. To address these challenges, we propose HELPNet, a novel scribble-based weakly supervised segmentation framework, designed to bridge the gap between annotation efficiency and segmentation performance. HELPNet integrates three modules. The Hierarchical perturbations consistency (HPC) module enhances feature learning by employing density-controlled jigsaw perturbations across global, local, and focal views, enabling robust modeling of multi-scale structural representations. Building on this, the Entropy-guided pseudo-label (EGPL) module evaluates the confidence of segmentation predictions using entropy, generating high-quality pseudo-labels. Finally, the structural prior refinement (SPR) module incorporates connectivity and bounded priors to enhance the precision and reliability and pseudo-labels. Experimental results on three public datasets ACDC, MSCMRseg, and CHAOS show that HELPNet significantly outperforms state-of-the-art methods for scribble-based weakly supervised segmentation and achieves performance comparable to fully supervised methods. The code is available at https://github.com/IPMI-NWU/HELPNet.
The growing need for accurate and efficient 3D identification of tumors, particularly in liver segmentation, has spurred considerable research into deep learning models. While many existing architectures offer strong performance, they often face challenges such as overfitting and excessive computational costs. An adjustable and flexible architecture that strikes a balance between time efficiency and model complexity remains an unmet requirement. In this paper, we introduce proKAN, a progressive stacking methodology for Kolmogorov-Arnold Networks (KANs) designed to address these challenges. Unlike traditional architectures, proKAN dynamically adjusts its complexity by progressively adding KAN blocks during training, based on overfitting behavior. This approach allows the network to stop growing when overfitting is detected, preventing unnecessary computational overhead while maintaining high accuracy. Additionally, proKAN utilizes KAN's learnable activation functions modeled through B-splines, which provide enhanced flexibility in learning complex relationships in 3D medical data. Our proposed architecture achieves state-of-the-art performance in liver segmentation tasks, outperforming standard Multi-Layer Perceptrons (MLPs) and fixed KAN architectures. The dynamic nature of proKAN ensures efficient training times and high accuracy without the risk of overfitting. Furthermore, proKAN provides better interpretability by allowing insight into the decision-making process through its learnable coefficients. The experimental results demonstrate a significant improvement in accuracy, Dice score, and time efficiency, making proKAN a compelling solution for 3D medical image segmentation tasks.
Recently, deep learning based methods have revolutionized remote sensing image segmentation. However, these methods usually rely on a pre-defined semantic class set, thus needing additional image annotation and model training when adapting to new classes. More importantly, they are unable to segment arbitrary semantic classes. In this work, we introduce Open-Vocabulary Remote Sensing Image Semantic Segmentation (OVRSISS), which aims to segment arbitrary semantic classes in remote sensing images. To address the lack of OVRSISS datasets, we develop LandDiscover50K, a comprehensive dataset of 51,846 images covering 40 diverse semantic classes. In addition, we propose a novel framework named GSNet that integrates domain priors from special remote sensing models and versatile capabilities of general vision-language models. Technically, GSNet consists of a Dual-Stream Image Encoder (DSIE), a Query-Guided Feature Fusion (QGFF), and a Residual Information Preservation Decoder (RIPD). DSIE first captures comprehensive features from both special models and general models in dual streams. Then, with the guidance of variable vocabularies, QGFF integrates specialist and generalist features, enabling them to complement each other. Finally, RIPD is proposed to aggregate multi-source features for more accurate mask predictions. Experiments show that our method outperforms other methods by a large margin, and our proposed LandDiscover50K improves the performance of OVRSISS methods. The proposed dataset and method will be made publicly available at https://github.com/yecy749/GSNet.
Recent advances in Large Vision-Language Models (LVLMs) have sparked significant progress in general-purpose vision tasks through visual instruction tuning. While some works have demonstrated the capability of LVLMs to generate segmentation masks that align phrases with natural language descriptions in a single image, they struggle with segmentation-grounded comparisons across multiple images, particularly at finer granularities such as object parts. In this paper, we introduce the new task of part-focused semantic co-segmentation, which seeks to identify and segment common and unique objects and parts across images. To address this task, we present CALICO, the first LVLM that can segment and reason over multiple masks across images, enabling object comparison based on their constituent parts. CALICO features two proposed components, a novel Correspondence Extraction Module, which captures semantic-rich information to identify part-level correspondences between objects, and a Correspondence Adaptation Module, which embeds this information into the LVLM to facilitate multi-image understanding in a parameter-efficient manner. To support training and evaluation, we curate MixedParts, a comprehensive multi-image segmentation dataset containing $\sim$2.4M samples across $\sim$44K images with diverse object and part categories. Experimental results show CALICO, finetuned on only 0.3% of its architecture, achieves robust performance in part-focused semantic co-segmentation.
Image forgery localization, which centers on identifying tampered pixels within an image, has seen significant advancements. Traditional approaches often model this challenge as a variant of image segmentation, treating the binary segmentation of forged areas as the end product. We argue that the basic binary forgery mask is inadequate for explaining model predictions. It doesn't clarify why the model pinpoints certain areas and treats all forged pixels the same, making it hard to spot the most fake-looking parts. In this study, we mitigate the aforementioned limitations by generating salient region-focused interpretation for the forgery images. To support this, we craft a Multi-Modal Tramper Tracing (MMTT) dataset, comprising facial images manipulated using deepfake techniques and paired with manual, interpretable textual annotations. To harvest high-quality annotation, annotators are instructed to meticulously observe the manipulated images and articulate the typical characteristics of the forgery regions. Subsequently, we collect a dataset of 128,303 image-text pairs. Leveraging the MMTT dataset, we develop ForgeryTalker, an architecture designed for concurrent forgery localization and interpretation. ForgeryTalker first trains a forgery prompter network to identify the pivotal clues within the explanatory text. Subsequently, the region prompter is incorporated into multimodal large language model for finetuning to achieve the dual goals of localization and interpretation. Extensive experiments conducted on the MMTT dataset verify the superior performance of our proposed model. The dataset, code as well as pretrained checkpoints will be made publicly available to facilitate further research and ensure the reproducibility of our results.
Electrical impedance tomography (EIT) plays a crucial role in non-invasive imaging, with both medical and industrial applications. In this paper, we present three data-driven reconstruction methods for EIT imaging. These three approaches were originally submitted to the Kuopio tomography challenge 2023 (KTC2023). First, we introduce a post-processing approach, which achieved first place at KTC2023. Further, we present a fully learned and a conditional diffusion approach. All three methods are based on a similar neural network as a backbone and were trained using a synthetically generated data set, providing with an opportunity for a fair comparison of these different data-driven reconstruction methods.
Computer Vision (CV) has yet to fully achieve the zero-shot task generalization observed in Natural Language Processing (NLP), despite following many of the milestones established in NLP, such as large transformer models, extensive pre-training, and the auto-regression paradigm, among others. In this paper, we explore the idea that CV adopts discrete and terminological task definitions (\eg, ``image segmentation''), which may be a key barrier to zero-shot task generalization. Our hypothesis is that without truly understanding previously-seen tasks--due to these terminological definitions--deep models struggle to generalize to novel tasks. To verify this, we introduce Explanatory Instructions, which provide an intuitive way to define CV task objectives through detailed linguistic transformations from input images to outputs. We create a large-scale dataset comprising 12 million ``image input $\to$ explanatory instruction $\to$ output'' triplets, and train an auto-regressive-based vision-language model (AR-based VLM) that takes both images and explanatory instructions as input. By learning to follow these instructions, the AR-based VLM achieves instruction-level zero-shot capabilities for previously-seen tasks and demonstrates strong zero-shot generalization for unseen CV tasks. Code and dataset will be openly available on our GitHub repository.
Federated Learning (FL) enables multiple clients to train a collaborative model without sharing their local data. Split Learning (SL) allows a model to be trained in a split manner across different locations. Split-Federated (SplitFed) learning is a more recent approach that combines the strengths of FL and SL. SplitFed minimizes the computational burden of FL by balancing computation across clients and servers, while still preserving data privacy. This makes it an ideal learning framework across various domains, especially in healthcare, where data privacy is of utmost importance. However, SplitFed networks encounter numerous communication challenges, such as latency, bandwidth constraints, synchronization overhead, and a large amount of data that needs to be transferred during the learning process. In this paper, we propose SplitFedZip -- a novel method that employs learned compression to reduce data transfer in SplitFed learning. Through experiments on medical image segmentation, we show that learned compression can provide a significant data communication reduction in SplitFed learning, while maintaining the accuracy of the final trained model. The implementation is available at: \url{https://github.com/ChamaniS/SplitFedZip}.
Gene silencing via small interfering RNA (siRNA) represents a transformative tool in cancer therapy, offering specificity and reduced off-target effects compared to conventional treatments. A crucial step in siRNA-based therapies is endosomal escape, the release of siRNA from endosomes into the cytoplasm. Quantifying endosomal escape is challenging due to the dynamic nature of the process and limitations in imaging and analytical techniques. Traditional methods often rely on fluorescence intensity measurements or manual image processing, which are time-intensive and fail to capture continuous dynamics. This paper presents a novel computational framework that integrates automated image processing to analyze time-lapse fluorescent microscopy data of endosomal escape, hierarchical Bayesian inference, and stochastic simulations. Our method employs image segmentation techniques such as binary masks, Gaussian filters, and multichannel color quantification to extract precise spatial and temporal data from microscopy images. Using a hierarchical Bayesian approach, we estimate the parameters of a compartmental model that describes endosomal escape dynamics, accounting for variability over time. These parameters inform a Gillespie stochastic simulation algorithm, ensuring realistic simulations of siRNA release events over time. Our framework provides a scalable and reproducible method for quantifying endosomal escape. The model captures uncertainty and variability in parameter estimation, and endosomal escape dynamics. Additionally, synthetic data generation allows researchers to validate experimental findings and explore alternative conditions without extensive laboratory work. This integrated approach not only improves the accuracy of endosomal escape quantification but also provides predictive insights for optimizing siRNA delivery systems and advancing gene therapy research.
Clustering algorithms remain valuable tools for grouping and summarizing the most important aspects of data. Example areas where this is the case include image segmentation, dimension reduction, signals analysis, model order reduction, numerical analysis, and others. As a consequence, many clustering approaches have been developed to satisfy the unique needs of each particular field. In this article, we present a family of data-adaptive partitioning algorithms that unifies several well-known methods (e.g., k-means and k-subspaces). Indexed by a single parameter and employing a common minimization strategy, the algorithms are easy to use and interpret, and scale well to large, high-dimensional problems. In addition, we develop an adaptive mechanism that (a) exhibits skill at automatically uncovering data structures and problem parameters without any expert knowledge and, (b) can be used to augment other existing methods. By demonstrating the performance of our methods on examples from disparate fields including subspace clustering, model order reduction, and matrix approximation, we hope to highlight their versatility and potential for extending the boundaries of existing scientific domains. We believe our family's parametrized structure represents a synergism of algorithms that will foster new developments and directions, not least within the data science community.
With the rapid development of deep learning and computer vision technologies, medical image segmentation plays a crucial role in the early diagnosis of breast cancer. However, due to the characteristics of breast ultrasound images, such as low contrast, speckle noise, and the highly diverse morphology of tumors, existing segmentation methods exhibit significant limitations in terms of accuracy and robustness. To address these challenges, this study proposes a PINN-based and Enhanced Multi-Scale Feature Fusion Network. The network introduces a Hierarchical Aggregation Encoder in the backbone, which efficiently integrates and globally models multi-scale features through several structural innovations and a novel PCAM module. In the decoder section, a Multi-Scale Feature Refinement Decoder is employed, which, combined with a Multi-Scale Supervision Mechanism and a correction module, significantly improves segmentation accuracy and adaptability. Additionally, the loss function incorporating the PINN mechanism introduces physical constraints during the segmentation process, enhancing the model's ability to accurately delineate tumor boundaries. Comprehensive evaluations on two publicly available breast ultrasound datasets, BUSIS and BUSI, demonstrate that the proposed method outperforms previous segmentation approaches in terms of segmentation accuracy and robustness, particularly under conditions of complex noise and low contrast, effectively improving the accuracy and reliability of tumor segmentation. This method provides a more precise and robust solution for computer-aided diagnosis of breast ultrasound images.
With the rapid advancement of deep learning, the model robustness has become a significant research hotspot, \ie, adversarial attacks on deep neural networks. Existing works primarily focus on image classification tasks, aiming to alter the model's predicted labels. Due to the output complexity and deeper network architectures, research on adversarial examples for segmentation models is still limited, particularly for universal adversarial perturbations. In this paper, we propose a novel universal adversarial attack method designed for segmentation models, which includes dual feature separation and low-frequency scattering modules. The two modules guide the training of adversarial examples in the pixel and frequency space, respectively. Experiments demonstrate that our method achieves high attack success rates surpassing the state-of-the-art methods, and exhibits strong transferability across different models.
Despite the advances in learning-based image segmentation approach, the accurate segmentation of cardiac structures from magnetic resonance imaging (MRI) remains a critical challenge. While existing automatic segmentation methods have shown promise, they still require extensive manual corrections of the segmentation results by human experts, particularly in complex regions such as the basal and apical parts of the heart. Recent efforts have been made on developing interactive image segmentation methods that enable human-in-the-loop learning. However, they are semi-automatic and inefficient, due to their reliance on click-based prompts, especially for 3D cardiac MRI volumes. To address these limitations, we propose VerSe, a Versatile Segmentation framework to unify automatic and interactive segmentation through mutiple queries. Our key innovation lies in the joint learning of object and click queries as prompts for a shared segmentation backbone. VerSe supports both fully automatic segmentation, through object queries, and interactive mask refinement, by providing click queries when needed. With the proposed integrated prompting scheme, VerSe demonstrates significant improvement in performance and efficiency over existing methods, on both cardiac MRI and out-of-distribution medical imaging datasets. The code is available at https://github.com/bangwayne/Verse.
Medical image segmentation is crucial in assisting medical doctors in making diagnoses and enabling accurate automatic diagnosis. While advanced convolutional neural networks (CNNs) excel in segmenting regions of interest with pixel-level precision, they often struggle with long-range dependencies, which is crucial for enhancing model performance. Conversely, transformer architectures leverage attention mechanisms to excel in handling long-range dependencies. However, the computational complexity of transformers grows quadratically, posing resource-intensive challenges, especially with high-resolution medical images. Recent research aims to combine CNN and transformer architectures to mitigate their drawbacks and enhance performance while keeping resource demands low. Nevertheless, existing approaches have not fully leveraged the strengths of both architectures to achieve high accuracy with low computational requirements. To address this gap, we propose a novel architecture for 2D medical image segmentation (QTSeg) that leverages a feature pyramid network (FPN) as the image encoder, a multi-level feature fusion (MLFF) as the adaptive module between encoder and decoder and a multi-query mask decoder (MQM Decoder) as the mask decoder. In the first step, an FPN model extracts pyramid features from the input image. Next, MLFF is incorporated between the encoder and decoder to adapt features from different encoder stages to the decoder. Finally, an MQM Decoder is employed to improve mask generation by integrating query tokens with pyramid features at all stages of the mask decoder. Our experimental results show that QTSeg outperforms state-of-the-art methods across all metrics with lower computational demands than the baseline and the existing methods. Code is available at https://github.com/tpnam0901/QTSeg (v0.1.0)
Although semi-supervised learning has made significant advances in the field of medical image segmentation, fully annotating a volumetric sample slice by slice remains a costly and time-consuming task. Even worse, most of the existing approaches pay much attention to image-level information and ignore semantic features, resulting in the inability to perceive weak boundaries. To address these issues, we propose a novel Semantic-Guided Triplet Co-training (SGTC) framework, which achieves high-end medical image segmentation by only annotating three orthogonal slices of a few volumetric samples, significantly alleviating the burden of radiologists. Our method consist of two main components. Specifically, to enable semantic-aware, fine-granular segmentation and enhance the quality of pseudo-labels, a novel semantic-guided auxiliary learning mechanism is proposed based on the pretrained CLIP. In addition, focusing on a more challenging but clinically realistic scenario, a new triple-view disparity training strategy is proposed, which uses sparse annotations (i.e., only three labeled slices of a few volumes) to perform co-training between three sub-networks, significantly improving the robustness. Extensive experiments on three public medical datasets demonstrate that our method outperforms most state-of-the-art semi-supervised counterparts under sparse annotation settings. The source code is available at https://github.com/xmeimeimei/SGTC.
This work proposes a novel framework, Uncertainty-Guided Cross Attention Ensemble Mean Teacher (UG-CEMT), for achieving state-of-the-art performance in semi-supervised medical image segmentation. UG-CEMT leverages the strengths of co-training and knowledge distillation by combining a Cross-attention Ensemble Mean Teacher framework (CEMT) inspired by Vision Transformers (ViT) with uncertainty-guided consistency regularization and Sharpness-Aware Minimization emphasizing uncertainty. UG-CEMT improves semi-supervised performance while maintaining a consistent network architecture and task setting by fostering high disparity between sub-networks. Experiments demonstrate significant advantages over existing methods like Mean Teacher and Cross-pseudo Supervision in terms of disparity, domain generalization, and medical image segmentation performance. UG-CEMT achieves state-of-the-art results on multi-center prostate MRI and cardiac MRI datasets, where object segmentation is particularly challenging. Our results show that using only 10\% labeled data, UG-CEMT approaches the performance of fully supervised methods, demonstrating its effectiveness in exploiting unlabeled data for robust medical image segmentation. The code is publicly available at \url{https://github.com/Meghnak13/UG-CEMT}
Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.
The biological brain has inspired multiple advances in machine learning. However, most state-of-the-art models in computer vision do not operate like the human brain, simply because they are not capable of changing or improving their decisions/outputs based on a deeper analysis. The brain is recurrent, while these models are not. It is therefore relevant to explore what would be the impact of adding recurrent mechanisms to existing state-of-the-art architectures and to answer the question of whether recurrency can improve existing architectures. To this end, we build on a feed-forward segmentation model and explore multiple types of recurrency for image segmentation. We explore self-organizing, relational, and memory retrieval types of recurrency that minimize a specific energy function. In our experiments, we tested these models on artificial and medical imaging data, while analyzing the impact of high levels of noise and few-shot learning settings. Our results do not validate our initial hypothesis that recurrent models should perform better in these settings, suggesting that these recurrent architectures, by themselves, are not sufficient to surpass state-of-the-art feed-forward versions and that additional work needs to be done on the topic.
Fruit tree image segmentation is an essential problem in automating a variety of agricultural tasks such as phenotyping, harvesting, spraying, and pruning. Many research papers have proposed a diverse spectrum of solutions suitable to specific tasks and environments. The review scope of this paper is confined to the front views of fruit trees and based on 158 relevant papers collected using a newly designed crawling review method. These papers are systematically reviewed based on a taxonomy that sequentially considers the method, image, task, and fruit. This taxonomy will assist readers to intuitively grasp the big picture of these research activities. Our review reveals that the most noticeable deficiency of the previous studies was the lack of a versatile dataset and segmentation model that could be applied to a variety of tasks and environments. Six important future research tasks are suggested, with the expectation that these will pave the way to building a versatile tree segmentation module.