Limited medical imaging datasets challenge deep learning models by increasing risks of overfitting and reduced generalization, particularly in Generative Adversarial Networks (GANs), where discriminators may overfit, leading to training divergence. This constraint also impairs classification models trained on small datasets. Generative Data Augmentation (GDA) addresses this by expanding training datasets with synthetic data, although it requires training a generative model. We propose and evaluate two local lesion generation approaches to address the challenge of augmenting small medical image datasets. The first approach employs the Poisson Image Editing algorithm, a classical image processing technique, to create realistic image composites that outperform current state-of-the-art methods. The second approach introduces a novel generative method, leveraging a fine-tuned Image Inpainting GAN to synthesize realistic lesions within specified regions of real training images. A comprehensive comparison of the two proposed methods demonstrates that effective local lesion generation in a data-constrained setting allows for reaching new state-of-the-art results in capsule endoscopy lesion classification. Combination of our techniques achieves a macro F1-score of 33.07%, surpassing the previous best result by 7.84 percentage points (p.p.) on the highly imbalanced Kvasir Capsule Dataset, a benchmark for capsule endoscopy. To the best of our knowledge, this work is the first to apply a fine-tuned Image Inpainting GAN for GDA in medical imaging, demonstrating that an image-conditional GAN can be adapted effectively to limited datasets to generate high-quality examples, facilitating effective data augmentation. Additionally, we show that combining this GAN-based approach with classical image processing techniques further improves the results.
In the realm of dermatological diagnoses, where the analysis of dermatoscopic and microscopic skin lesion images is pivotal for the accurate and early detection of various medical conditions, the costs associated with creating diverse and high-quality annotated datasets have hampered the accuracy and generalizability of machine learning models. We propose an innovative unsupervised augmentation solution that harnesses Generative Adversarial Network (GAN) based models and associated techniques over their latent space to generate controlled semiautomatically-discovered semantic variations in dermatoscopic images. We created synthetic images to incorporate the semantic variations and augmented the training data with these images. With this approach, we were able to increase the performance of machine learning models and set a new benchmark amongst non-ensemble based models in skin lesion classification on the HAM10000 dataset; and used the observed analytics and generated models for detailed studies on model explainability, affirming the effectiveness of our solution.
The efficacy of deep learning-based Computer-Aided Diagnosis (CAD) methods for skin diseases relies on analyzing multiple data modalities (i.e., clinical+dermoscopic images, and patient metadata) and addressing the challenges of multi-label classification. Current approaches tend to rely on limited multi-modal techniques and treat the multi-label problem as a multiple multi-class problem, overlooking issues related to imbalanced learning and multi-label correlation. This paper introduces the innovative Skin Lesion Classifier, utilizing a Multi-modal Multi-label TransFormer-based model (SkinM2Former). For multi-modal analysis, we introduce the Tri-Modal Cross-attention Transformer (TMCT) that fuses the three image and metadata modalities at various feature levels of a transformer encoder. For multi-label classification, we introduce a multi-head attention (MHA) module to learn multi-label correlations, complemented by an optimisation that handles multi-label and imbalanced learning problems. SkinM2Former achieves a mean average accuracy of 77.27% and a mean diagnostic accuracy of 77.85% on the public Derm7pt dataset, outperforming state-of-the-art (SOTA) methods.
Skin lesions are an increasingly significant medical concern, varying widely in severity from benign to cancerous. Accurate diagnosis is essential for ensuring timely and appropriate treatment. This study examines the implementation of deep learning methods to assist in the diagnosis of skin lesions using the HAM10000 dataset, which contains seven distinct types of lesions. First, we evaluated three pre-trained models: MobileNetV2, ResNet18, and VGG11, achieving accuracies of 0.798, 0.802, and 0.805, respectively. To further enhance classification accuracy, we developed ensemble models employing max voting, average voting, and stacking, resulting in accuracies of 0.803, 0.82, and 0.83. Building on the best-performing ensemble learning model, stacking, we developed our proposed model, SkinNet, which incorporates a customized architecture and fine-tuning, achieving an accuracy of 0.867 and an AUC of 0.96. This substantial improvement over individual models demonstrates the effectiveness of ensemble learning in improving skin lesion classification.
The influence of bias in datasets on the fairness of model predictions is a topic of ongoing research in various fields. We evaluate the performance of skin lesion classification using ResNet-based CNNs, focusing on patient sex variations in training data and three different learning strategies. We present a linear programming method for generating datasets with varying patient sex and class labels, taking into account the correlations between these variables. We evaluated the model performance using three different learning strategies: a single-task model, a reinforcing multi-task model, and an adversarial learning scheme. Our observations include: 1) sex-specific training data yields better results, 2) single-task models exhibit sex bias, 3) the reinforcement approach does not remove sex bias, 4) the adversarial model eliminates sex bias in cases involving only female patients, and 5) datasets that include male patients enhance model performance for the male subgroup, even when female patients are the majority. To generalise these findings, in future research, we will examine more demographic attributes, like age, and other possibly confounding factors, such as skin colour and artefacts in the skin lesions. We make all data and models available on GitHub.
Limited training data and severe class imbalance pose significant challenges to developing clinically robust deep learning models. Federated learning (FL) addresses the former by enabling different medical clients to collaboratively train a deep model without sharing privacy-sensitive data. However, class imbalance worsens due to variation in inter-client class distribution. We propose federated learning with non-parametric regularization (FedNPR and FedNPR-Per, a personalized version of FedNPR) to regularize the feature extractor and enhance useful and discriminative signal in the feature space. Our extensive experiments show that FedNPR outperform the existing state-of-the art FL approaches in class imbalance skin lesion classification and intracranial hemorrhage identification. Additionally, the non-parametric regularization module consistently improves the performance of existing state-of-the-art FL approaches. We believe that NPR is a valuable tool in FL under clinical settings.
Existing multi-modal approaches primarily focus on enhancing multi-label skin lesion classification performance through advanced fusion modules, often neglecting the associated rise in parameters. In clinical settings, both clinical and dermoscopy images are captured for diagnosis; however, dermoscopy images exhibit more crucial visual features for multi-label skin lesion classification. Motivated by this observation, we introduce a novel asymmetric multi-modal fusion method in this paper for efficient multi-label skin lesion classification. Our fusion method incorporates two innovative schemes. Firstly, we validate the effectiveness of our asymmetric fusion structure. It employs a light and simple network for clinical images and a heavier, more complex one for dermoscopy images, resulting in significant parameter savings compared to the symmetric fusion structure using two identical networks for both modalities. Secondly, in contrast to previous approaches using mutual attention modules for interaction between image modalities, we propose an asymmetric attention module. This module solely leverages clinical image information to enhance dermoscopy image features, considering clinical images as supplementary information in our pipeline. We conduct the extensive experiments on the seven-point checklist dataset. Results demonstrate the generality of our proposed method for both networks and Transformer structures, showcasing its superiority over existing methods We will make our code publicly available.
Continual Learning (CL) is crucial for enabling networks to dynamically adapt as they learn new tasks sequentially, accommodating new data and classes without catastrophic forgetting. Diverging from conventional perspectives on CL, our paper introduces a new perspective wherein forgetting could actually benefit the sequential learning paradigm. Specifically, we present BiasPruner, a CL framework that intentionally forgets spurious correlations in the training data that could lead to shortcut learning. Utilizing a new bias score that measures the contribution of each unit in the network to learning spurious features, BiasPruner prunes those units with the highest bias scores to form a debiased subnetwork preserved for a given task. As BiasPruner learns a new task, it constructs a new debiased subnetwork, potentially incorporating units from previous subnetworks, which improves adaptation and performance on the new task. During inference, BiasPruner employs a simple task-agnostic approach to select the best debiased subnetwork for predictions. We conduct experiments on three medical datasets for skin lesion classification and chest X-Ray classification and demonstrate that BiasPruner consistently outperforms SOTA CL methods in terms of classification performance and fairness. Our code is available here.
Federated Learning (FL) enables multiple institutes to train models collaboratively without sharing private data. Current FL research focuses on communication efficiency, privacy protection, and personalization and assumes that the data of FL have already been ideally collected. In medical scenarios, however, data annotation demands both expertise and intensive labor, which is a critical problem in FL. Active learning (AL), has shown promising performance in reducing the number of data annotations in medical image analysis. We propose a federated AL (FedAL) framework in which AL is executed periodically and interactively under FL. We exploit a local model in each hospital and a global model acquired from FL to construct an ensemble. We use ensemble-entropy-based AL as an efficient data-annotation strategy in FL. Therefore, our FedAL framework can decrease the amount of annotated data and preserve patient privacy while maintaining the performance of FL. To our knowledge, this is the first FedAL framework applied to medical images. We validated our framework on real-world dermoscopic datasets. Using only 50% of samples, our framework was able to achieve state-of-the-art performance on a skin-lesion classification task. Our framework performed better than several state-of-the-art AL methods under FL and achieved comparable performance to full-data FL.
Deep learning-based diagnostic systems have demonstrated potential in skin disease diagnosis. However, their performance can easily degrade on test domains due to distribution shifts caused by input-level corruptions, such as imaging equipment variability, brightness changes, and image blur. This will reduce the reliability of model deployment in real-world scenarios. Most existing solutions focus on adapting the source model through retraining on different target domains. Although effective, this retraining process is sensitive to the amount of data and the hyperparameter configuration for optimization. In this paper, we propose a test-time image adaptation method to enhance the accuracy of the model on test data by simultaneously updating and predicting test images. We modify the target test images by projecting them back to the source domain using a diffusion model. Specifically, we design a structure guidance module that adds refinement operations through low-pass filtering during reverse sampling, regularizing the diffusion to preserve structural information. Additionally, we introduce a self-ensembling scheme automatically adjusts the reliance on adapted and unadapted inputs, enhancing adaptation robustness by rejecting inappropriate generative modeling results. To facilitate this study, we constructed the ISIC2019-C and Dermnet-C corruption robustness evaluation benchmarks. Extensive experiments on the proposed benchmarks demonstrate that our method makes the classifier more robust across various corruptions, architectures, and data regimes. Our datasets and code will be available at \url{https://github.com/minghu0830/Skin-TTA_Diffusion}.
Deep models trained on large amounts of data often incorporate implicit biases present during training time. If later such a bias is discovered during inference or deployment, it is often necessary to acquire new data and retrain the model. This behavior is especially problematic in critical areas such as autonomous driving or medical decision-making. In these scenarios, new data is often expensive and hard to come by. In this work, we present a method based on change penalization that takes a pre-trained model and adapts the weights to mitigate a previously detected bias. We achieve this by tuning a zero-initialized copy of a frozen pre-trained network. Our method needs very few, in extreme cases only a single, examples that contradict the bias to increase performance. Additionally, we propose an early stopping criterion to modify baselines and reduce overfitting. We evaluate our approach on a well-known bias in skin lesion classification and three other datasets from the domain shift literature. We find that our approach works especially well with very few images. Simple fine-tuning combined with our early stopping also leads to performance benefits for a larger number of tuning samples.
Today, skin cancer is considered as one of the most dangerous and common cancers in the world which demands special attention. Skin cancer may be developed in different types; including melanoma, actinic keratosis, basal cell carcinoma, squamous cell carcinoma, and Merkel cell carcinoma. Among them, melanoma is more unpredictable. Melanoma cancer can be diagnosed at early stages increasing the possibility of disease treatment. Automatic classification of skin lesions is a challenging task due to diverse forms and grades of the disease, demanding the requirement of novel methods implementation. Deep convolution neural networks (CNN) have shown an excellent potential for data and image classification. In this article, we inspect skin lesion classification problem using CNN techniques. Remarkably, we present that prominent classification accuracy of lesion detection can be obtained by proper designing and applying of transfer learning framework on pre-trained neural networks, without any requirement for data enlargement procedures i.e. merging VGG16 and VGG19 architectures pre-trained by a generic dataset with modified AlexNet network, and then, fine-tuned by a subject-specific dataset containing dermatology images. The convolution neural network was trained using 2541 images and, in particular, dropout was used to prevent the network from overfitting. Finally, the validity of the model was checked by applying the K-fold cross validation method. The proposed model increased classification accuracy by 3% (from 94.2% to 98.18%) in comparison with other methods.
In this study, we introduce a multi-modal approach that efficiently integrates multi-scale clinical and dermoscopy features within a single network, thereby substantially reducing model parameters. The proposed method includes three novel fusion schemes. Firstly, unlike current methods that usually employ two individual models for for clinical and dermoscopy modalities, we verified that multimodal feature can be learned by sharing the parameters of encoder while leaving the individual modal-specific classifiers. Secondly, the shared cross-attention module can replace the individual one to efficiently interact between two modalities at multiple layers. Thirdly, different from current methods that equally optimize dermoscopy and clinical branches, inspired by prior knowledge that dermoscopy images play a more significant role than clinical images, we propose a novel biased loss. This loss guides the single-shared network to prioritize dermoscopy information over clinical information, implicitly learning a better joint feature representation for the modal-specific task. Extensive experiments on a well-recognized Seven-Point Checklist (SPC) dataset and a collected dataset demonstrate the effectiveness of our method on both CNN and Transformer structures. Furthermore, our method exhibits superiority in both accuracy and model parameters compared to currently advanced methods.
In the realm of skin lesion image classification, the intricate spatial and semantic features pose significant challenges for conventional Convolutional Neural Network (CNN)-based methodologies. These challenges are compounded by the imbalanced nature of skin lesion datasets, which hampers the ability of models to learn minority class features effectively. Despite augmentation strategies, such as those using Generative Adversarial Networks (GANs), previous attempts have not fully addressed these complexities. This study introduces an innovative approach by integrating Graph Neural Networks (GNNs) with Capsule Networks to enhance classification performance. GNNs, known for their proficiency in handling graph-structured data, offer an advanced mechanism for capturing complex patterns and relationships beyond the capabilities of traditional CNNs. Capsule Networks further contribute by providing superior recognition of spatial hierarchies within images. Our research focuses on evaluating and enhancing the Tiny Pyramid Vision GNN (Tiny Pyramid ViG) architecture by incorporating it with a Capsule Network. This hybrid model was applied to the MNIST:HAM10000 dataset, a comprehensive skin lesion dataset designed for benchmarking classification models. After 75 epochs of training, our model achieved a significant accuracy improvement, reaching 89.23% and 95.52%, surpassing established benchmarks such as GoogLeNet (83.94%), InceptionV3 (86.82%), MobileNet V3 (89.87%), EfficientNet-B7 (92.07%), ResNet18 (92.22%), ResNet34 (91.90%), ViT-Base (73.70%), and IRv2-SA (93.47%) on the same dataset. This outcome underscores the potential of our approach in overcoming the inherent challenges of skin lesion classification, contributing to the advancement of image-based diagnosis in dermatology.
Accurate classification of laryngeal vascular as benign or malignant is crucial for early detection of laryngeal cancer. However, organizations with limited access to laryngeal vascular images face challenges due to the lack of large and homogeneous public datasets for effective learning. Distinguished from the most familiar works, which directly transfer the ImageNet pre-trained models to the target domain for fine-tuning, this work pioneers exploring two-step heterogeneous transfer learning (THTL) for laryngeal lesion classification with nine deep-learning models, utilizing the diabetic retinopathy color fundus images, semantically non-identical yet vascular images, as the intermediate domain. Attention visualization technique, Layer Class Activate Map (LayerCAM), reveals a novel finding that yet the intermediate and the target domain both reflect vascular structure to a certain extent, the prevalent radial vascular pattern in the intermediate domain prevents learning the features of twisted and tangled vessels that distinguish the malignant class in the target domain, summarizes a vital rule for laryngeal lesion classification using THTL. To address this, we introduce an enhanced fine-tuning strategy in THTL called Step-Wise Fine-Tuning (SWFT) and apply it to the ResNet models. SWFT progressively refines model performance by accumulating fine-tuning layers from back to front, guided by the visualization results of LayerCAM. Comparison with the original THTL approach shows significant improvements. For ResNet18, the accuracy and malignant recall increases by 26.1% and 79.8%, respectively, while for ResNet50, these indicators improve by 20.4% and 62.2%, respectively.
Automated classification of liver lesions in multi-phase CT and MR scans is of clinical significance but challenging. This study proposes a novel Siamese Dual-Resolution Transformer (SDR-Former) framework, specifically designed for liver lesion classification in 3D multi-phase CT and MR imaging with varying phase counts. The proposed SDR-Former utilizes a streamlined Siamese Neural Network (SNN) to process multi-phase imaging inputs, possessing robust feature representations while maintaining computational efficiency. The weight-sharing feature of the SNN is further enriched by a hybrid Dual-Resolution Transformer (DR-Former), comprising a 3D Convolutional Neural Network (CNN) and a tailored 3D Transformer for processing high- and low-resolution images, respectively. This hybrid sub-architecture excels in capturing detailed local features and understanding global contextual information, thereby, boosting the SNN's feature extraction capabilities. Additionally, a novel Adaptive Phase Selection Module (APSM) is introduced, promoting phase-specific intercommunication and dynamically adjusting each phase's influence on the diagnostic outcome. The proposed SDR-Former framework has been validated through comprehensive experiments on two clinical datasets: a three-phase CT dataset and an eight-phase MR dataset. The experimental results affirm the efficacy of the proposed framework. To support the scientific community, we are releasing our extensive multi-phase MR dataset for liver lesion analysis to the public. This pioneering dataset, being the first publicly available multi-phase MR dataset in this field, also underpins the MICCAI LLD-MMRI Challenge. The dataset is accessible at:https://bit.ly/3IyYlgN.
The rising global prevalence of skin conditions, some of which can escalate to life-threatening stages if not timely diagnosed and treated, presents a significant healthcare challenge. This issue is particularly acute in remote areas where limited access to healthcare often results in delayed treatment, allowing skin diseases to advance to more critical stages. One of the primary challenges in diagnosing skin diseases is their low inter-class variations, as many exhibit similar visual characteristics, making accurate classification challenging. This research introduces a novel multimodal method for classifying skin lesions, integrating smartphone-captured images with essential clinical and demographic information. This approach mimics the diagnostic process employed by medical professionals. A distinctive aspect of this method is the integration of an auxiliary task focused on super-resolution image prediction. This component plays a crucial role in refining visual details and enhancing feature extraction, leading to improved differentiation between classes and, consequently, elevating the overall effectiveness of the model. The experimental evaluations have been conducted using the PAD-UFES20 dataset, applying various deep-learning architectures. The results of these experiments not only demonstrate the effectiveness of the proposed method but also its potential applicability under-resourced healthcare environments.
Invasive Coronary Angiography (ICA) images are considered the gold standard for assessing the state of the coronary arteries. Deep learning classification methods are widely used and well-developed in different areas where medical imaging evaluation has an essential impact due to the development of computer-aided diagnosis systems that can support physicians in their clinical procedures. In this paper, a new performance analysis of deep learning methods for binary ICA classification with different lesion degrees is reported. To reach this goal, an annotated dataset of ICA images that contains the ground truth, the location of lesions and seven possible severity degrees ranging between 0% and 100% was employed. The ICA images were divided into 'lesion' or 'non-lesion' patches. We aim to study how binary classification performance is affected by the different lesion degrees considered in the positive class. Therefore, five known convolutional neural network architectures were trained with different input images where different lesion degree ranges were gradually incorporated until considering the seven lesion degrees. Besides, four types of experiments with and without data augmentation were designed, whose F-measure and Area Under Curve (AUC) were computed. Reported results achieved an F-measure and AUC of 92.7% and 98.1%, respectively. However, lesion classification is highly affected by the degree of the lesion intended to classify, with 15% less accuracy when <99% lesion patches are present.
Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.
Accurate lesion classification in Wireless Capsule Endoscopy (WCE) images is vital for early diagnosis and treatment of gastrointestinal (GI) cancers. However, this task is confronted with challenges like tiny lesions and background interference. Additionally, WCE images exhibit higher intra-class variance and inter-class similarities, adding complexity. To tackle these challenges, we propose Decoupled Supervised Contrastive Learning for WCE image classification, learning robust representations from zoomed-in WCE images generated by Saliency Augmentor. Specifically, We use uniformly down-sampled WCE images as anchors and WCE images from the same class, especially their zoomed-in images, as positives. This approach empowers the Feature Extractor to capture rich representations from various views of the same image, facilitated by Decoupled Supervised Contrastive Learning. Training a linear Classifier on these representations within 10 epochs yields an impressive 92.01% overall accuracy, surpassing the prior state-of-the-art (SOTA) by 0.72% on a blend of two publicly accessible WCE datasets. Code is available at: https://github.com/Qiukunpeng/DSCL.