Spatial pooling (SP) and cross-channel pooling (CCP) operators have been applied to aggregate spatial features and pixel-wise features from feature maps in deep neural networks (DNNs), respectively. Their main goal is to reduce computation and memory overhead without visibly weakening the performance of DNNs. However, SP often faces the problem of losing the subtle feature representations, while CCP has a high possibility of ignoring salient feature representations, which may lead to both miscalibration of confidence issues and suboptimal medical classification results. To address these problems, we propose a novel dual-view framework, the first to systematically investigate the relative roles of SP and CCP by analyzing the difference between spatial features and pixel-wise features. Based on this framework, we propose a new pooling method, termed dual-view pyramid pooling (DVPP), to aggregate multi-scale dual-view features. DVPP aims to boost both medical image classification and confidence calibration performance by fully leveraging the merits of SP and CCP operators from a dual-axis perspective. Additionally, we discuss how to fulfill DVPP with five parameter-free implementations. Extensive experiments on six 2D/3D medical image classification tasks show that our DVPP surpasses state-of-the-art pooling methods in terms of medical image classification results and confidence calibration across different DNNs.
The success of large-scale pre-trained models has established fine-tuning as a standard method for achieving significant improvements in downstream tasks. However, fine-tuning the entire parameter set of a pre-trained model is costly. Parameter-efficient transfer learning (PETL) has recently emerged as a cost-effective alternative for adapting pre-trained models to downstream tasks. Despite its advantages, the increasing model size and input resolution present challenges for PETL, as the training memory consumption is not reduced as effectively as the parameter usage. In this paper, we introduce Fine-grained Prompt Tuning plus (FPT+), a PETL method designed for high-resolution medical image classification, which significantly reduces the training memory consumption compared to other PETL methods. FPT+ performs transfer learning by training a lightweight side network and accessing pre-trained knowledge from a large pre-trained model (LPM) through fine-grained prompts and fusion modules. Specifically, we freeze the LPM of interest and construct a learnable lightweight side network. The frozen LPM processes high-resolution images to extract fine-grained features, while the side network employs corresponding down-sampled low-resolution images to minimize the memory usage. To enable the side network to leverage pre-trained knowledge, we propose fine-grained prompts and fusion modules, which collaborate to summarize information through the LPM's intermediate activations. We evaluate FPT+ on eight medical image datasets of varying sizes, modalities, and complexities. Experimental results demonstrate that FPT+ outperforms other PETL methods, using only 1.03% of the learnable parameters and 3.18% of the memory required for fine-tuning an entire ViT-B model. Our code is available https://github.com/YijinHuang/FPT.
Counterfactual explanations (CEs) aim to enhance the interpretability of machine learning models by illustrating how alterations in input features would affect the resulting predictions. Common CE approaches require an additional model and are typically constrained to binary counterfactuals. In contrast, we propose a novel method that operates directly on the latent space of a generative model, specifically a Diffusion Autoencoder (DAE). This approach offers inherent interpretability by enabling the generation of CEs and the continuous visualization of the model's internal representation across decision boundaries. Our method leverages the DAE's ability to encode images into a semantically rich latent space in an unsupervised manner, eliminating the need for labeled data or separate feature extraction models. We show that these latent representations are helpful for medical condition classification and the ordinal regression of severity pathologies, such as vertebral compression fractures (VCF) and diabetic retinopathy (DR). Beyond binary CEs, our method supports the visualization of ordinal CEs using a linear model, providing deeper insights into the model's decision-making process and enhancing interpretability. Experiments across various medical imaging datasets demonstrate the method's advantages in interpretability and versatility. The linear manifold of the DAE's latent space allows for meaningful interpolation and manipulation, making it a powerful tool for exploring medical image properties. Our code is available at https://doi.org/10.5281/zenodo.13859266.
Brain tumors are among the deadliest diseases in the world. Magnetic Resonance Imaging (MRI) is one of the most effective ways to detect brain tumors. Accurate detection of brain tumors based on MRI scans is critical, as it can potentially save many lives and facilitate better decision-making at the early stages of the disease. Within our paper, four different types of MRI-based images have been collected from the database: glioma tumor, no tumor, pituitary tumor, and meningioma tumor. Our study focuses on making predictions for brain tumor classification. Five models, including four pre-trained models (MobileNet, EfficientNet-B0, ResNet-18, and VGG16) and one new model, MobileNet-BT, have been proposed for this study.
Recent studies have underscored the capabilities of natural imaging foundation models to serve as powerful feature extractors, even in a zero-shot setting for medical imaging data. Most commonly, a shallow multi-layer perceptron (MLP) is appended to the feature extractor to facilitate end-to-end learning and downstream prediction tasks such as classification, thus representing the de facto standard. However, as graph neural networks (GNNs) have become a practicable choice for various tasks in medical research in the recent past, we direct attention to the question of how effective GNNs are compared to MLP prediction heads for the task of 3D medical image classification, proposing them as a potential alternative. In our experiments, we devise a subject-level graph for each volumetric dataset instance. Therein latent representations of all slices in the volume, encoded through a DINOv2 pretrained vision transformer (ViT), constitute the nodes and their respective node features. We use public datasets to compare the classification heads numerically and evaluate various graph construction and graph convolution methods in our experiments. Our findings show enhancements of the GNN in classification performance and substantial improvements in runtime compared to an MLP prediction head. Additional robustness evaluations further validate the promising performance of the GNN, promoting them as a suitable alternative to traditional MLP classification heads. Our code is publicly available at: https://github.com/compai-lab/2024-miccai-grail-kiechle
Deep convolutional neural networks have made significant breakthroughs in medical image classification, under the assumption that training samples from all classes are simultaneously available. However, in real-world medical scenarios, there's a common need to continuously learn about new diseases, leading to the emerging field of class incremental learning (CIL) in the medical domain. Typically, CIL suffers from catastrophic forgetting when trained on new classes. This phenomenon is mainly caused by the imbalance between old and new classes, and it becomes even more challenging with imbalanced medical datasets. In this work, we introduce two simple yet effective plug-in methods to mitigate the adverse effects of the imbalance. First, we propose a CIL-balanced classification loss to mitigate the classifier bias toward majority classes via logit adjustment. Second, we propose a distribution margin loss that not only alleviates the inter-class overlap in embedding space but also enforces the intra-class compactness. We evaluate the effectiveness of our method with extensive experiments on three benchmark datasets (CCH5000, HAM10000, and EyePACS). The results demonstrate that our approach outperforms state-of-the-art methods.
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.
With the advent of large pre-trained transformer models, fine-tuning these models for various downstream tasks is a critical problem. Paucity of training data, the existence of data silos, and stringent privacy constraints exacerbate this fine-tuning problem in the medical imaging domain, creating a strong need for algorithms that enable collaborative fine-tuning of pre-trained models. Moreover, the large size of these models necessitates the use of parameter-efficient fine-tuning (PEFT) to reduce the communication burden in federated learning. In this work, we systematically investigate various federated PEFT strategies for adapting a Vision Transformer (ViT) model (pre-trained on a large natural image dataset) for medical image classification. Apart from evaluating known PEFT techniques, we introduce new federated variants of PEFT algorithms such as visual prompt tuning (VPT), low-rank decomposition of visual prompts, stochastic block attention fine-tuning, and hybrid PEFT methods like low-rank adaptation (LoRA)+VPT. Moreover, we perform a thorough empirical analysis to identify the optimal PEFT method for the federated setting and understand the impact of data distribution on federated PEFT, especially for out-of-domain (OOD) and non-IID data. The key insight of this study is that while most federated PEFT methods work well for in-domain transfer, there is a substantial accuracy vs. efficiency trade-off when dealing with OOD and non-IID scenarios, which is commonly the case in medical imaging. Specifically, every order of magnitude reduction in fine-tuned/exchanged parameters can lead to a 4% drop in accuracy. Thus, the initial model choice is crucial for federated PEFT. It is preferable to use medical foundation models learned from in-domain medical image data (if available) rather than general vision models.
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.
Vision Transformers (ViTs) have achieved significant advancement in computer vision tasks due to their powerful modeling capacity. However, their performance notably degrades when trained with insufficient data due to lack of inherent inductive biases. Distilling knowledge and inductive biases from a Convolutional Neural Network (CNN) teacher has emerged as an effective strategy for enhancing the generalization of ViTs on limited datasets. Previous approaches to Knowledge Distillation (KD) have pursued two primary paths: some focused solely on distilling the logit distribution from CNN teacher to ViT student, neglecting the rich semantic information present in intermediate features due to the structural differences between them. Others integrated feature distillation along with logit distillation, yet this introduced alignment operations that limits the amount of knowledge transferred due to mismatched architectures and increased the computational overhead. To this end, this paper presents Hybrid Data-efficient Knowledge Distillation (HDKD) paradigm which employs a CNN teacher and a hybrid student. The choice of hybrid student serves two main aspects. First, it leverages the strengths of both convolutions and transformers while sharing the convolutional structure with the teacher model. Second, this shared structure enables the direct application of feature distillation without any information loss or additional computational overhead. Additionally, we propose an efficient light-weight convolutional block named Mobile Channel-Spatial Attention (MBCSA), which serves as the primary convolutional block in both teacher and student models. Extensive experiments on two medical public datasets showcase the superiority of HDKD over other state-of-the-art models and its computational efficiency. Source code at: https://github.com/omarsherif200/HDKD
The robustness of supervised deep learning-based medical image classification is significantly undermined by label noise. Although several methods have been proposed to enhance classification performance in the presence of noisy labels, they face some challenges: 1) a struggle with class-imbalanced datasets, leading to the frequent overlooking of minority classes as noisy samples; 2) a singular focus on maximizing performance using noisy datasets, without incorporating experts-in-the-loop for actively cleaning the noisy labels. To mitigate these challenges, we propose a two-phase approach that combines Learning with Noisy Labels (LNL) and active learning. This approach not only improves the robustness of medical image classification in the presence of noisy labels, but also iteratively improves the quality of the dataset by relabeling the important incorrect labels, under a limited annotation budget. Furthermore, we introduce a novel Variance of Gradients approach in LNL phase, which complements the loss-based sample selection by also sampling under-represented samples. Using two imbalanced noisy medical classification datasets, we demonstrate that that our proposed technique is superior to its predecessors at handling class imbalance by not misidentifying clean samples from minority classes as mostly noisy samples.
Deep learning has achieved impressive performance across various medical imaging tasks. However, its inherent bias against specific groups hinders its clinical applicability in equitable healthcare systems. A recently discovered phenomenon, Neural Collapse (NC), has shown potential in improving the generalization of state-of-the-art deep learning models. Nonetheless, its implications on bias in medical imaging remain unexplored. Our study investigates deep learning fairness through the lens of NC. We analyze the training dynamics of models as they approach NC when training using biased datasets, and examine the subsequent impact on test performance, specifically focusing on label bias. We find that biased training initially results in different NC configurations across subgroups, before converging to a final NC solution by memorizing all data samples. Through extensive experiments on three medical imaging datasets -- PAPILA, HAM10000, and CheXpert -- we find that in biased settings, NC can lead to a significant drop in F1 score across all subgroups. Our code is available at https://gitlab.com/radiology/neuro/neural-collapse-fairness
Malaria parasites pose a significant global health burden, causing widespread suffering and mortality. Detecting malaria infection accurately is crucial for effective treatment and control. However, existing automated detection techniques have shown limitations in terms of accuracy and generalizability. Many studies have focused on specific features without exploring more comprehensive approaches. In our case, we formulate a deep learning technique for malaria infected cell classification using traditional CNNs and transfer learning models notably VGG19, InceptionV3, and Xception. The models were trained using NIH datasets and tested using different performance metrics such as accuracy, precision, re- call, and F1-score. The test results showed that deep CNNs achieved the highest accuracy - 97%, followed by Xception with an accuracy of 95%. A machine learning model SVM achieved an accuracy of 83%, while an Inception-V3 achieved an accuracy of 94%. Furthermore, the system can be accessed through a web interface, where users can upload blood smear images for malaria detection
Medical image classification plays a crucial role in computer-aided clinical diagnosis. While deep learning techniques have significantly enhanced efficiency and reduced costs, the privacy-sensitive nature of medical imaging data complicates centralized storage and model training. Furthermore, low-resource healthcare organizations face challenges related to communication overhead and efficiency due to increasing data and model scales. This paper proposes a novel privacy-preserving medical image classification framework based on federated learning to address these issues, named FedMIC. The framework enables healthcare organizations to learn from both global and local knowledge, enhancing local representation of private data despite statistical heterogeneity. It provides customized models for organizations with diverse data distributions while minimizing communication overhead and improving efficiency without compromising performance. Our FedMIC enhances robustness and practical applicability under resource-constrained conditions. We demonstrate FedMIC's effectiveness using four public medical image datasets for classical medical image classification tasks.
Cross-silo federated learning (FL) enables decentralized organizations to collaboratively train models while preserving data privacy and has made significant progress in medical image classification. One common assumption is task homogeneity where each client has access to all classes during training. However, in clinical practice, given a multi-label classification task, constrained by the level of medical knowledge and the prevalence of diseases, each institution may diagnose only partial categories, resulting in task heterogeneity. How to pursue effective multi-label medical image classification under task heterogeneity is under-explored. In this paper, we first formulate such a realistic label missing setting in the multi-label FL domain and propose a two-stage method FedMLP to combat class missing from two aspects: pseudo label tagging and global knowledge learning. The former utilizes a warmed-up model to generate class prototypes and select samples with high confidence to supplement missing labels, while the latter uses a global model as a teacher for consistency regularization to prevent forgetting missing class knowledge. Experiments on two publicly-available medical datasets validate the superiority of FedMLP against the state-of-the-art both federated semi-supervised and noisy label learning approaches under task heterogeneity. Code is available at https://github.com/szbonaldo/FedMLP.
Current medical image classification efforts mainly aim for higher average performance, often neglecting the balance between different classes. This can lead to significant differences in recognition accuracy between classes and obvious recognition weaknesses. Without the support of massive data, deep learning faces challenges in fine-grained classification of fatty liver. In this paper, we propose an innovative deep learning framework that combines feature decoupling and adaptive adversarial training. Firstly, we employ two iteratively compressed decouplers to supervised decouple common features and specific features related to fatty liver in abdominal ultrasound images. Subsequently, the decoupled features are concatenated with the original image after transforming the color space and are fed into the classifier. During adversarial training, we adaptively adjust the perturbation and balance the adversarial strength by the accuracy of each class. The model will eliminate recognition weaknesses by correctly classifying adversarial samples, thus improving recognition robustness. Finally, the accuracy of our method improved by 4.16%, achieving 82.95%. As demonstrated by extensive experiments, our method is a generalized learning framework that can be directly used to eliminate the recognition weaknesses of any classifier while improving its average performance. Code is available at https://github.com/HP-ML/MICCAI2024.
The manifestation of symptoms associated with lung diseases can vary in different depths for individual patients, highlighting the significance of 3D information in CT scans for medical image classification. While Vision Transformer has shown superior performance over convolutional neural networks in image classification tasks, their effectiveness is often demonstrated on sufficiently large 2D datasets and they easily encounter overfitting issues on small medical image datasets. To address this limitation, we propose a Diffusion-based 3D Vision Transformer (Diff3Dformer), which utilizes the latent space of the Diffusion model to form the slice sequence for 3D analysis and incorporates clustering attention into ViT to aggregate repetitive information within 3D CT scans, thereby harnessing the power of the advanced transformer in 3D classification tasks on small datasets. Our method exhibits improved performance on two different scales of small datasets of 3D lung CT scans, surpassing the state of the art 3D methods and other transformer-based approaches that emerged during the COVID-19 pandemic, demonstrating its robust and superior performance across different scales of data. Experimental results underscore the superiority of our proposed method, indicating its potential for enhancing medical image classification tasks in real-world scenarios.
Test-time augmentation (TTA) is a well-known technique employed during the testing phase of computer vision tasks. It involves aggregating multiple augmented versions of input data. Combining predictions using a simple average formulation is a common and straightforward approach after performing TTA. This paper introduces a novel framework for optimizing TTA, called BayTTA (Bayesian-based TTA), which is based on Bayesian Model Averaging (BMA). First, we generate a prediction list associated with different variations of the input data created through TTA. Then, we use BMA to combine predictions weighted by the respective posterior probabilities. Such an approach allows one to take into account model uncertainty, and thus to enhance the predictive performance of the related machine learning or deep learning model. We evaluate the performance of BayTTA on various public data, including three medical image datasets comprising skin cancer, breast cancer, and chest X-ray images and two well-known gene editing datasets, CRISPOR and GUIDE-seq. Our experimental results indicate that BayTTA can be effectively integrated into state-of-the-art deep learning models used in medical image analysis as well as into some popular pre-trained CNN models such as VGG-16, MobileNetV2, DenseNet201, ResNet152V2, and InceptionRes-NetV2, leading to the enhancement in their accuracy and robustness performance. The source code of the proposed BayTTA method is freely available at: \underline {https://github.com/Z-Sherkat/BayTTA}.
The usage of medical image data for the training of large-scale machine learning approaches is particularly challenging due to its scarce availability and the costly generation of data annotations, typically requiring the engagement of medical professionals. The rapid development of generative models allows towards tackling this problem by leveraging large amounts of realistic synthetically generated data for the training process. However, randomly choosing synthetic samples, might not be an optimal strategy. In this work, we investigate the targeted generation of synthetic training data, in order to improve the accuracy and robustness of image classification. Therefore, our approach aims to guide the generative model to synthesize data with high epistemic uncertainty, since large measures of epistemic uncertainty indicate underrepresented data points in the training set. During the image generation we feed images reconstructed by an auto encoder into the classifier and compute the mutual information over the class-probability distribution as a measure for uncertainty.We alter the feature space of the autoencoder through an optimization process with the objective of maximizing the classifier uncertainty on the decoded image. By training on such data we improve the performance and robustness against test time data augmentations and adversarial attacks on several classifications tasks.
In the field of medical imaging, particularly in tasks related to early disease detection and prognosis, understanding the reasoning behind AI model predictions is imperative for assessing their reliability. Conventional explanation methods encounter challenges in identifying decisive features in medical image classifications, especially when discriminative features are subtle or not immediately evident. To address this limitation, we propose an agent model capable of generating counterfactual images that prompt different decisions when plugged into a black box model. By employing this agent model, we can uncover influential image patterns that impact the black model's final predictions. Through our methodology, we efficiently identify features that influence decisions of the deep black box. We validated our approach in the rigorous domain of medical prognosis tasks, showcasing its efficacy and potential to enhance the reliability of deep learning models in medical image classification compared to existing interpretation methods. The code will be publicly available at https://github.com/ayanglab/DiffExplainer.