Super-resolution reconstruction (SRR) of isotropic fetal brain MR images is critical for prenatal examinations but is hindered by fetal motion and misalignment of thick-slice scans. To address these challenges comprehensively, we introduce an innovative deep learning model, namely 3D-WISE, a 3D Weighted Interpolation for Super-resolution Estimation of fetal brain MRI. The model generates high-quality isotropic fetal brain MR images by learning the interpolation weights to correct misalignments between slices and volumes. These misalignments are estimated by extracting deep features from multiple motion-corrupted stacks. Specifically, 3D-WISE incorporates two key components: (1) a weight learning module for multi-view interpolation and (2) a feature extraction module guided by multi-type attention mechanisms. The weight learning module first maps motion-corrupted thick-slice stacks into latent feature spaces. The resulting features are then fed to an implicit decoding block to estimate interpolation weights of the surrounding points for a given coordinate. We further enhance our approach by incorporating convolutional block attention and atlas-induced cross-attention mechanisms. Extensive experiments on two benchmark datasets show that our 3D-WISE achieves remarkably improved performance compared to the widely adopted registration-reconstruction framework. We also extend the experiments on anatomical structure reconstruction and achieve promising results, highlighting the significant potential of our 3D-WISE for fetal brain MR images SRR in clinical settings.

Mild cognitive impairment (MCI) is the prodromal stage of dementia involving complex interactions between the brain and peripheral organs. Emerging evidence indicates that heart dysfunction and gut microbiota dysbiosis can contribute to MCI pathogenesis. Yet, these discoveries of cross-organ interactions have not been applied to assist MCI diagnosis. In this work, we propose a novel diagnostic framework that exploits the interactions of brain, heart, and gut using whole-body PET images to guide MCI diagnosis for scenarios when only brain MRI, PET, or PET&MRI are available. Specifically, we collected a multi-cohort, multi-modal dataset comprising 1,545 whole-body PET images, 6,010 brain MR images, and 2,446 brain PET images from eight data centers. Organ-specific image encoders are first pretrained for the brain, heart, and gut individually. Then, to effectively align and integrate brain, heart, and gut features, we introduce positional prompts to act as anatomical-level attention to highlight disease-relevant spatial regions, and further develop hierarchical Transformers to model brain-heart, brain-gut, and brain-heart-gut interactions. Finally, to achieve MCI diagnosis using only brain images, we transfer the above brain-heart-gut model to a brain-only model via an introduced multi-level knowledge distillation scheme, including sample-level contrastive distillation, group-level distribution alignment, and response-level supervision. Extensive experiments on multi-center data demonstrate the superiority of our method over the state-of-the-art methods by resorting to effective integration of heart and gut interactions for MCI diagnosis.

Longitudinal magnetic resonance imaging (MRI) is essential for studying the early development of the brain, as it allows to observe and analyze how the brain changes over time. Unfortunately, existing cohort research suffers from lacking sufficient MRI data for studying the development of fetal brains. Apart from research data, a viable alternative is the use of large-scale clinical fetal brain MRI data, which is currently the primary source for longitudinal studies. Although clinical data has several benefits, it is impeded by the inherent drawback of incomplete data. In the context of clinical practice, nearly all subjects undergo only one MRI scan throughout their entire pregnancy, resulting in a lack of longitudinal data for any fetus. To address this issue and obtain longitudinal clinical fetal brain MRI data, we propose to generate MR images for two adjacent gestational weeks (GWs) within one subject, thereby bridging the information gap between three consecutive GWs. This fetal MRI prediction task suffers from two significant challenges, including 1) heterogeneous generation and 2) the lack of paired training data at adjacent GWs. To tackle these two challenges, we propose a new approach, called the Development-driven Diffusion Model (DDM). Specifically, our approach first involves training a conditional diffusion model using population development information spanning all GWs. This allows the model to generate images at various GWs. Next, during the inference stage, we incorporate individual development information of a specific subject using a specially designed perception feature guidance module. The DDM enables the generated 3D MR images to encompass both the general characteristics representative of the targeted GWs, as well as the distinct feature specific to each individual. To assess the efficacy of our approach, extensive experiments were carried out on a large-scale clinical dataset obtained from three different medical centers. The experimental results unequivocally establish the effectiveness of DDM for generating longitudinal MR images of fetal brains.

Automated breast tumor segmentation on the basis of dynamic contrast-enhancement magnetic resonance imaging (DCE-MRI) has shown great promise in clinical practice, particularly for identifying the presence of breast disease. However, accurate segmentation of breast tumor is a challenging task, often necessitating the development of complex networks. To strike an optimal trade-off between computational costs and segmentation performance, we propose a hybrid network via the combination of convolution neural network (CNN) and transformer layers. Specifically, the hybrid network consists of a encoder-decoder architecture by stacking convolution and deconvolution layers. Effective 3D transformer layers are then implemented after the encoder subnetworks, to capture global dependencies between the bottleneck features. To improve the efficiency of hybrid network, two parallel encoder subnetworks are designed for the decoder and the transformer layers, respectively. To further enhance the discriminative capability of hybrid network, a prototype learning guided prediction module is proposed, where the category-specified prototypical features are calculated through online clustering. All learned prototypical features are finally combined with the features from decoder for tumor mask prediction. The experimental results on private and public DCE-MRI datasets demonstrate that the proposed hybrid network achieves superior performance than the state-of-the-art (SOTA) methods, while maintaining balance between segmentation accuracy and computation cost. Moreover, we demonstrate that automatically generated tumor masks can be effectively applied to identify HER2-positive subtype from HER2-negative subtype with the similar accuracy to the analysis based on manual tumor segmentation. The source code is available at https://github.com/ZhouL-lab/PLHN.

Medical image analysis poses significant challenges due to limited availability of clinical data, which is crucial for training accurate models. This limitation is further compounded by the specialized and labor-intensive nature of the data annotation process. For example, despite the popularity of computed tomography angiography (CTA) in diagnosing atherosclerosis with an abundance of annotated datasets, magnetic resonance (MR) images stand out with better visualization for soft plaque and vessel wall characterization. However, the higher cost and limited accessibility of MR, as well as time-consuming nature of manual labeling, contribute to fewer annotated datasets. To address these issues, we formulate a multi-modal transfer learning network, named MT-Net, designed to learn from unpaired CTA and sparsely-annotated MR data. Additionally, we harness the Segment Anything Model (SAM) to synthesize additional MR annotations, enriching the training process. Specifically, our method first segments vessel lumen regions followed by precise characterization of carotid artery vessel walls, thereby ensuring both segmentation accuracy and clinical relevance. Validation of our method involved rigorous experimentation on publicly available datasets from COSMOS and CARE-II challenge, demonstrating its superior performance compared to existing state-of-the-art techniques.

Early and accurate severity assessment of Coronavirus disease 2019 (COVID-19) based on computed tomography (CT) images offers a great help to the estimation of intensive care unit event and the clinical decision of treatment planning. To augment the labeled data and improve the generalization ability of the classification model, it is necessary to aggregate data from multiple sites. This task faces several challenges including class imbalance between mild and severe infections, domain distribution discrepancy between sites, and presence of heterogeneous features. In this paper, we propose a novel domain adaptation (DA) method with two components to address these problems. The first component is a stochastic class-balanced boosting sampling strategy that overcomes the imbalanced learning problem and improves the classification performance on poorly-predicted classes. The second component is a representation learning that guarantees three properties: 1) domain-transferability by prototype triplet loss, 2) discriminant by conditional maximum mean discrepancy loss, and 3) completeness by multi-view reconstruction loss. Particularly, we propose a domain translator and align the heterogeneous data to the estimated class prototypes (i.e., class centers) in a hyper-sphere manifold. Experiments on cross-site severity assessment of COVID-19 from CT images show that the proposed method can effectively tackle the imbalanced learning problem and outperform recent DA approaches.

Chest computed tomography (CT) becomes an effective tool to assist the diagnosis of coronavirus disease-19 (COVID-19). Due to the outbreak of COVID-19 worldwide, using the computed-aided diagnosis technique for COVID-19 classification based on CT images could largely alleviate the burden of clinicians. In this paper, we propose an Adaptive Feature Selection guided Deep Forest (AFS-DF) for COVID-19 classification based on chest CT images. Specifically, we first extract location-specific features from CT images. Then, in order to capture the high-level representation of these features with the relatively small-scale data, we leverage a deep forest model to learn high-level representation of the features. Moreover, we propose a feature selection method based on the trained deep forest model to reduce the redundancy of features, where the feature selection could be adaptively incorporated with the COVID-19 classification model. We evaluated our proposed AFS-DF on COVID-19 dataset with 1495 patients of COVID-19 and 1027 patients of community acquired pneumonia (CAP). The accuracy (ACC), sensitivity (SEN), specificity (SPE), AUC, precision and F1-score achieved by our method are 91.79%, 93.05%, 89.95%, 96.35%, 93.10% and 93.07%, respectively. Experimental results on the COVID-19 dataset suggest that the proposed AFS-DF achieves superior performance in COVID-19 vs. CAP classification, compared with 4 widely used machine learning methods.

The coronavirus disease (COVID-19) is rapidly spreading all over the world, and has infected more than 1,436,000 people in more than 200 countries and territories as of April 9, 2020. Detecting COVID-19 at early stage is essential to deliver proper healthcare to the patients and also to protect the uninfected population. To this end, we develop a dual-sampling attention network to automatically diagnose COVID-19 from the community acquired pneumonia (CAP) in chest computed tomography (CT). In particular, we propose a novel online attention module with a 3D convolutional network (CNN) to focus on the infection regions in lungs when making decisions of diagnoses. Note that there exists imbalanced distribution of the sizes of the infection regions between COVID-19 and CAP, partially due to fast progress of COVID-19 after symptom onset. Therefore, we develop a dual-sampling strategy to mitigate the imbalanced learning. Our method is evaluated (to our best knowledge) upon the largest multi-center CT data for COVID-19 from 8 hospitals. In the training-validation stage, we collect 2186 CT scans from 1588 patients for a 5-fold cross-validation. In the testing stage, we employ another independent large-scale testing dataset including 2796 CT scans from 2057 patients. Results show that our algorithm can identify the COVID-19 images with the area under the receiver operating characteristic curve (AUC) value of 0.944, accuracy of 87.5%, sensitivity of 86.9%, specificity of 90.1%, and F1-score of 82.0%. With this performance, the proposed algorithm could potentially aid radiologists with COVID-19 diagnosis from CAP, especially in the early stage of the COVID-19 outbreak.

Big data annotation plays an important role in Artificial Intelligence model training. The proliferation of data annotation tasks has brought the issue of security of the big data delivery. This work identifies the security framework associated with encryption and compression procedures that support data delivery safety. In this paper, we propose an agile framework that caters to various types of data under RESTful web services. All the procedures are automatically operated by the server without human intervention. This work assists the company delivers the tagged data products to users with a high-security level avoiding the risk of information disclosure.