Background: Accurate MRI-based identification of extramural vascular invasion (EVI) and mesorectal fascia invasion (MFI) is pivotal for risk-stratified management of rectal cancer, yet visual assessment is subjective and vulnerable to inter-institutional variability. Purpose: To develop and externally evaluate a multicenter, foundation-model-driven framework that automatically classifies EVI and MFI on axial and sagittal T2-weighted MRI. Methods: This retrospective study used 331 pre-treatment rectal cancer MRI examinations from three European hospitals. After TotalSegmentator-guided rectal patch extraction, a self-supervised frequency-domain harmonization pipeline was trained to minimize scanner-related contrast shifts. Four classifiers were compared: ResNet50, SeResNet, the universal biomedical pretrained transformer (UMedPT) with a lightweight MLP head, and a logistic-regression variant using frozen UMedPT features (UMedPT_LR). Results: UMedPT_LR achieved the best EVI detection when axial and sagittal features were fused (AUC = 0.82; sensitivity = 0.75; F1 score = 0.73), surpassing the Chaimeleon Grand-Challenge winner (AUC = 0.74). The highest MFI performance was attained by UMedPT on axial harmonized images (AUC = 0.77), surpassing the Chaimeleon Grand-Challenge winner (AUC = 0.75). Frequency-domain harmonization improved MFI classification but variably affected EVI performance. Conventional CNNs (ResNet50, SeResNet) underperformed, especially in F1 score and balanced accuracy. Conclusion: These findings demonstrate that combining foundation model features, harmonization, and multi-view fusion significantly enhances diagnostic performance in rectal MRI.
A three-dimensional convolutional neural network was developed to classify T1-weighted brain MRI scans as healthy or Alzheimer. The network comprises 3D convolution, pooling, batch normalization, dense ReLU layers, and a sigmoid output. Using stochastic noise injection and five-fold cross-validation, the model achieved test set accuracy of 0.912 and area under the ROC curve of 0.961, an improvement of approximately 0.027 over resizing alone. Sensitivity and specificity both exceeded 0.90. These results align with prior work reporting up to 0.10 gain via synthetic augmentation. The findings demonstrate the effectiveness of simple augmentation for 3D MRI classification and motivate future exploration of advanced augmentation methods and architectures such as 3D U-Net and vision transformers.
Knee Osteoarthritis (KOA) is a degenerative musculoskeletal joint disorder that significantly impacts middle-aged and elderly individuals. Although X-rays and MRIs are clinically used to identify such disorders, combining these imaging modalities is challenging due to the distinct nature of the data, as MRI volume provides detailed views of cartilage and soft tissues, while X-rays offer a global perspective of bone anatomy and positioning in single scan. In this context, the proposed work aims to address two key challenges: (1) how to automatically select the most informative slices from large and dis-organized MRI volume in a clinically relevant way and (2) how to effectively capture the discriminative multimodal interactions between X-ray and MRI modalities. In order to solve these issues, the Context-Guided Slice Selection and Prioritization (CG-SSP) module and Xray-MRI Cross-Attention (XMRCA) module are proposed. The CG-SSP module focuses on rejecting non-efficient slices and prioritizing the efficient slices in a multi-stage approach, first by segmenting the Femoral Cartilage (FC) then extracting the sequential patches of FC located in each MRI slice followed by assigning the attention weight to each of these slices based on learned structural complexity, while the XMRCA module focuses on learning the global interactions between X-ray and MRI feature space in a computationally efficient manner. Overall, the proposed model achieved an accuracy improvement of 2.66% over the state-of-the-art in unimodal and multimodal baselines on the OAI dataset. The proposed model identifies key diagnostic slices from MRI and can provide valuable insights into interactions between X-ray and MRI data for radiological KOA diagnosis in an end-to-end manner. Code will be made available at: https://github.com/adaydar/MedCAM-OsteoCls
The integration of Artificial Intelligence (AI) in medical diagnostics is often hindered by model opacity, where high-accuracy systems function as "black boxes" without transparent reasoning. This limitation is critical in clinical settings, where trust and reliability are paramount. To address this, we have developed an explainable AI methodology tailored for medical imaging. By employing a Convolutional Neural Network (CNN) that analyzes MRI scans across both image and frequency domains, we introduce a novel approach that incorporates Uniform Manifold Approximation and Projection UMAP] for the visualization of latent input embeddings. This approach not only enhances early training efficiency but also deepens our understanding of how additional features impact the model predictions, thereby increasing interpretability and supporting more accurate and intuitive diagnostic inferences
Schizophrenia is a serious psychiatric disorder. Its pathogenesis is not completely clear, making it difficult to treat patients precisely. Because of the complicated non-Euclidean network structure of the human brain, learning critical information from brain networks remains difficult. To effectively capture the topological information of brain neural networks, a novel multimodal graph attention network based on sparse interaction mechanism (Multi-SIGATnet) was proposed for SZ classification was proposed for SZ classification. Firstly, structural and functional information were fused into multimodal data to obtain more comprehensive and abundant features for patients with SZ. Subsequently, a sparse interaction mechanism was proposed to effectively extract salient features and enhance the feature representation capability. By enhancing the strong connections and weakening the weak connections between feature information based on an asymmetric convolutional network, high-order interactive features were captured. Moreover, sparse learning strategies were designed to filter out redundant connections to improve model performance. Finally, local and global features were updated in accordance with the topological features and connection weight constraints of the higher-order brain network, the features being projected to the classification target space for disorder classification. The effectiveness of the model is verified on the Center for Biomedical Research Excellence (COBRE) and University of California Los Angeles (UCLA) datasets, achieving 81.9\% and 75.8\% average accuracy, respectively, 4.6\% and 5.5\% higher than the graph attention network (GAT) method. Experiments showed that the Multi-SIGATnet method exhibited good performance in identifying SZ.
Exploring the application of deep learning technologies in the field of medical diagnostics, Magnetic Resonance Imaging (MRI) provides a unique perspective for observing and diagnosing complex neurodegenerative diseases such as Alzheimer Disease (AD). With advancements in deep learning, particularly in Convolutional Neural Networks (CNNs) and the Xception network architecture, we are now able to analyze and classify vast amounts of MRI data with unprecedented accuracy. The progress of this technology not only enhances our understanding of brain structural changes but also opens up new avenues for monitoring disease progression through non-invasive means and potentially allows for precise diagnosis in the early stages of the disease. This study aims to classify MRI images using deep learning models to identify different stages of Alzheimer Disease through a series of innovative data processing and model construction steps. Our experimental results show that the deep learning framework based on the Xception model achieved a 99.6% accuracy rate in the multi-class MRI image classification task, demonstrating its potential application value in assistive diagnosis. Future research will focus on expanding the dataset, improving model interpretability, and clinical validation to further promote the application of deep learning technology in the medical field, with the hope of bringing earlier diagnosis and more personalized treatment plans to Alzheimer Disease patients.
More than 10.7% of people aged 65 and older are affected by Alzheimer's disease. Early diagnosis and treatment are crucial as most Alzheimer's patients are unaware of having it until the effects become detrimental. AI has been known to use magnetic resonance imaging (MRI) to diagnose Alzheimer's. However, models which produce low rates of false diagnoses are critical to prevent unnecessary treatments. Thus, we trained supervised Random Forest models with segmented brain volumes and Convolutional Neural Network (CNN) outputs to classify different Alzheimer's stages. We then applied out-of-distribution (OOD) detection to the CNN model, enabling it to report OOD if misclassification is likely, thereby reducing false diagnoses. With an accuracy of 98% for detection and 95% for classification, our model based on CNN results outperformed our segmented volume model, which had detection and classification accuracies of 93% and 87%, respectively. Applying OOD detection to the CNN model enabled it to flag brain tumor images as OOD with 96% accuracy and minimal overall accuracy reduction. By using OOD detection to enhance the reliability of MRI classification using CNNs, we lowered the rate of false positives and eliminated a significant disadvantage of using Machine Learning models for healthcare tasks. Source code available upon request.
Convolutional Neural Networks (CNNs) are frequently and successfully used in medical prediction tasks. They are often used in combination with transfer learning, leading to improved performance when training data for the task are scarce. The resulting models are highly complex and typically do not provide any insight into their predictive mechanisms, motivating the field of 'explainable' artificial intelligence (XAI). However, previous studies have rarely quantitatively evaluated the 'explanation performance' of XAI methods against ground-truth data, and transfer learning and its influence on objective measures of explanation performance has not been investigated. Here, we propose a benchmark dataset that allows for quantifying explanation performance in a realistic magnetic resonance imaging (MRI) classification task. We employ this benchmark to understand the influence of transfer learning on the quality of explanations. Experimental results show that popular XAI methods applied to the same underlying model differ vastly in performance, even when considering only correctly classified examples. We further observe that explanation performance strongly depends on the task used for pre-training and the number of CNN layers pre-trained. These results hold after correcting for a substantial correlation between explanation and classification performance.
To address the problem of medical image recognition, computer vision techniques like convolutional neural networks (CNN) are frequently used. Recently, 3D CNN-based models dominate the field of magnetic resonance image (MRI) analytics. Due to the high similarity between MRI data and videos, we conduct extensive empirical studies on video recognition techniques for MRI classification to answer the questions: (1) can we directly use video recognition models for MRI classification, (2) which model is more appropriate for MRI, (3) are the common tricks like data augmentation in video recognition still useful for MRI classification? Our work suggests that advanced video techniques benefit MRI classification. In this paper, four datasets of Alzheimer's and Parkinson's disease recognition are utilized in experiments, together with three alternative video recognition models and data augmentation techniques that are frequently applied to video tasks. In terms of efficiency, the results reveal that the video framework performs better than 3D-CNN models by 5% - 11% with 50% - 66% less trainable parameters. This report pushes forward the potential fusion of 3D medical imaging and video understanding research.
Brain tumor classification is crucial for clinical analysis and an effective treatment plan to cure patients. Deep learning models help radiologists to accurately and efficiently analyze tumors without manual intervention. However, brain tumor analysis is challenging because of its complex structure, texture, size, location, and appearance. Therefore, a novel deep residual and regional-based Res-BRNet Convolutional Neural Network (CNN) is developed for effective brain tumor (Magnetic Resonance Imaging) MRI classification. The developed Res-BRNet employed Regional and boundary-based operations in a systematic order within the modified spatial and residual blocks. Moreover, the spatial block extract homogeneity and boundary-defined features at the abstract level. Furthermore, the residual blocks employed at the target level significantly learn local and global texture variations of different classes of brain tumors. The efficiency of the developed Res-BRNet is evaluated on a standard dataset; collected from Kaggle and Figshare containing various tumor categories, including meningioma, glioma, pituitary, and healthy images. Experiments prove that the developed Res-BRNet outperforms the standard CNN models and attained excellent performances (accuracy: 98.22%, sensitivity: 0.9811, F-score: 0.9841, and precision: 0.9822) on challenging datasets. Additionally, the performance of the proposed Res-BRNet indicates a strong potential for medical image-based disease analyses.
Alzheimer's disease (AD) is one of the most common public health issues the world is facing today. This disease has a high prevalence primarily in the elderly accompanying memory loss and cognitive decline. AD detection is a challenging task which many authors have developed numerous computerized automatic diagnosis systems utilizing neuroimaging and other clinical data. MRI scans provide high-intensity visible features, making these scans the most widely used brain imaging technique. In recent years deep learning has achieved leading success in medical image analysis. But a relatively little investigation has been done to apply deep learning techniques for the brain MRI classification. This paper explores the construction of several deep learning architectures evaluated on brain MRI images and segmented images. The idea behind segmented images investigates the influence of image segmentation step on deep learning classification. The image processing presented a pipeline consisting of pre-processing to enhance the MRI scans and post-processing consisting of a segmentation method for segmenting the brain tissues. The results show that the processed images achieved a better accuracy in the binary classification of AD vs. CN (Cognitively Normal) across four different architectures. ResNet architecture resulted in the highest prediction accuracy amongst the other architectures (90.83% for the original brain images and 93.50% for the processed images).
Traditional supervised learning with deep neural networks requires a tremendous amount of labelled data to converge to a good solution. For 3D medical images, it is often impractical to build a large homogeneous annotated dataset for a specific pathology. Self-supervised methods offer a new way to learn a representation of the images in an unsupervised manner with a neural network. In particular, contrastive learning has shown great promises by (almost) matching the performance of fully-supervised CNN on vision tasks. Nonetheless, this method does not take advantage of available meta-data, such as participant's age, viewed as prior knowledge. Here, we propose to leverage continuous proxy metadata, in the contrastive learning framework, by introducing a new loss called y-Aware InfoNCE loss. Specifically, we improve the positive sampling during pre-training by adding more positive examples with similar proxy meta-data with the anchor, assuming they share similar discriminative semantic features.With our method, a 3D CNN model pre-trained on $10^4$ multi-site healthy brain MRI scans can extract relevant features for three classification tasks: schizophrenia, bipolar diagnosis and Alzheimer's detection. When fine-tuned, it also outperforms 3D CNN trained from scratch on these tasks, as well as state-of-the-art self-supervised methods. Our code is made publicly available here.
BACKGROUND:Automated volumetry software (AVS) has recently become widely available to neuroradiologists. MRI volumetry with AVS may support the diagnosis of dementias by identifying regional atrophy. Moreover, automatic classifiers using machine learning techniques have recently emerged as promising approaches to assist diagnosis. However, the performance of both AVS and automatic classifiers has been evaluated mostly in the artificial setting of research datasets.OBJECTIVE:Our aim was to evaluate the performance of two AVS and an automatic classifier in the clinical routine condition of a memory clinic.METHODS:We studied 239 patients with cognitive troubles from a single memory center cohort. Using clinical routine T1-weighted MRI, we evaluated the classification performance of: 1) univariate volumetry using two AVS (volBrain and Neuroreader$^{TM}$); 2) Support Vector Machine (SVM) automatic classifier, using either the AVS volumes (SVM-AVS), or whole gray matter (SVM-WGM); 3) reading by two neuroradiologists. The performance measure was the balanced diagnostic accuracy. The reference standard was consensus diagnosis by three neurologists using clinical, biological (cerebrospinal fluid) and imaging data and following international criteria.RESULTS:Univariate AVS volumetry provided only moderate accuracies (46% to 71% with hippocampal volume). The accuracy improved when using SVM-AVS classifier (52% to 85%), becoming close to that of SVM-WGM (52 to 90%). Visual classification by neuroradiologists ranged between SVM-AVS and SVM-WGM.CONCLUSION:In the routine practice of a memory clinic, the use of volumetric measures provided by AVS yields only moderate accuracy. Automatic classifiers can improve accuracy and could be a useful tool to assist diagnosis.
Deep learning models for MRI classification face two recurring problems: they are typically limited by low sample size, and are abstracted by their own complexity (the "black box problem"). In this paper, we train a convolutional neural network (CNN) with the largest multi-source, functional MRI (fMRI) connectomic dataset ever compiled, consisting of 43,858 datapoints. We apply this model to a cross-sectional comparison of autism (ASD) vs typically developing (TD) controls that has proved difficult to characterise with inferential statistics. To contextualise these findings, we additionally perform classifications of gender and task vs rest. Employing class-balancing to build a training set, we trained 3$\times$300 modified CNNs in an ensemble model to classify fMRI connectivity matrices with overall AUROCs of 0.6774, 0.7680, and 0.9222 for ASD vs TD, gender, and task vs rest, respectively. Additionally, we aim to address the black box problem in this context using two visualization methods. First, class activation maps show which functional connections of the brain our models focus on when performing classification. Second, by analyzing maximal activations of the hidden layers, we were also able to explore how the model organizes a large and mixed-centre dataset, finding that it dedicates specific areas of its hidden layers to processing different covariates of data (depending on the independent variable analyzed), and other areas to mix data from different sources. Our study finds that deep learning models that distinguish ASD from TD controls focus broadly on temporal and cerebellar connections, with a particularly high focus on the right caudate nucleus and paracentral sulcus.
Deep learning convolutional neural networks have proved to be a powerful tool for MRI analysis. In current work, we explore the potential of the deformable convolutional deep neural network layers for MRI data classification. We propose new 3D deformable convolutions(d-convolutions), implement them in VoxResNet architecture and apply for structural MRI data classification. We show that 3D d-convolutions outperform standard ones and are effective for unprocessed 3D MR images being robust to particular geometrical properties of the data. Firstly proposed dVoxResNet architecture exhibits high potential for the use in MRI data classification.
Deep learning methods for classifying medical images have demonstrated impressive accuracy in a wide range of tasks but often these models are hard to interpret, limiting their applicability in clinical practice. In this work we introduce a convolutional neural network model for identifying disease in temporal sequences of cardiac MR segmentations which is interpretable in terms of clinically familiar measurements. The model is based around a variational autoencoder, reducing the input into a low-dimensional latent space in which classification occurs. We then use the recently developed `concept activation vector' technique to associate concepts which are diagnostically meaningful (eg. clinical biomarkers such as `low left-ventricular ejection fraction') to certain vectors in the latent space. These concepts are then qualitatively inspected by observing the change in the image domain resulting from interpolations in the latent space in the direction of these vectors. As a result, when the model classifies images it is also capable of providing naturally interpretable concepts relevant to that classification and demonstrating the meaning of those concepts in the image domain. Our approach is demonstrated on the UK Biobank cardiac MRI dataset where we detect the presence of coronary artery disease.
In recent years, many papers have reported state-of-the-art performance on Alzheimer's Disease classification with MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset using convolutional neural networks. However, we discover that when we split that data into training and testing sets at the subject level, we are not able to obtain similar performance, bringing the validity of many of the previous studies into question. Furthermore, we point out that previous works use different subsets of the ADNI data, making comparison across similar works tricky. In this study, we present the results of three splitting methods, discuss the motivations behind their validity, and report our results using all of the available subjects.
In the recent years there have been a number of studies that applied deep learning algorithms to neuroimaging data. Pipelines used in those studies mostly require multiple processing steps for feature extraction, although modern advancements in deep learning for image classification can provide a powerful framework for automatic feature generation and more straightforward analysis. In this paper, we show how similar performance can be achieved skipping these feature extraction steps with the residual and plain 3D convolutional neural network architectures. We demonstrate the performance of the proposed approach for classification of Alzheimer's disease versus mild cognitive impairment and normal controls on the Alzheimer's Disease National Initiative (ADNI) dataset of 3D structural MRI brain scans.