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Breast magnetic resonance imaging (MRI) is the imaging technique with the highest sensitivity for detecting breast cancer and is routinely used for women at high risk. Despite the comprehensive multiparametric protocol of breast MRI, existing artificial intelligence-based studies predominantly rely on single sequences and have limited validation. Here we report a large mixture-of-modality-experts model (MOME) that integrates multiparametric MRI information within a unified structure, offering a noninvasive method for personalized breast cancer management. We have curated the largest multiparametric breast MRI dataset, involving 5,205 patients from three hospitals in the north, southeast, and southwest of China, for the development and extensive evaluation of our model. MOME demonstrated accurate and robust identification of breast cancer. It achieved comparable performance for malignancy recognition to that of four senior radiologists and significantly outperformed a junior radiologist, with 0.913 AUROC, 0.948 AUPRC, 0.905 F1 score, and 0.723 MCC. Our findings suggest that MOME could reduce the need for biopsies in BI-RADS 4 patients with a ratio of 7.3%, classify triple-negative breast cancer with an AUROC of 0.709, and predict pathological complete response to neoadjuvant chemotherapy with an AUROC of 0.694. The model further supports scalable and interpretable inference, adapting to missing modalities and providing decision explanations by highlighting lesions and measuring modality contributions. MOME exemplifies a discriminative, robust, scalable, and interpretable multimodal model, paving the way for noninvasive, personalized management of breast cancer patients based on multiparametric breast imaging data., Comment: 27 pages, 8 figures, 10 tables

The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Mask AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various medical vision tasks. However, due to large spatial sizes with much higher dimensions of 3D medical images, the lack of hierarchical design for MAE may hinder the performance of downstream tasks. In this paper, we propose a novel \textit{Mask in Mask (MiM)} pre-training framework for 3D medical images, which aims to advance MAE by learning discriminative representation from hierarchical visual tokens across varying scales. We introduce multiple levels of granularity for masked inputs from the volume, which are then reconstructed simultaneously ranging at both fine and coarse levels. Additionally, a cross-level alignment mechanism is applied to adjacent level volumes to enforce anatomical similarity hierarchically. Furthermore, we adopt a hybrid backbone to enhance the hierarchical representation learning efficiently during the pre-training. MiM was pre-trained on a large scale of available 3D volumetric images, \textit{i.e.,} Computed Tomography (CT) images containing various body parts. Extensive experiments on thirteen public datasets demonstrate the superiority of MiM over other SSL methods in organ/lesion/tumor segmentation and disease classification. We further scale up the MiM to large pre-training datasets with more than 10k volumes, showing that large-scale pre-training can further enhance the performance of downstream tasks. The improvement also concluded that the research community should pay more attention to the scale of the pre-training dataset towards the healthcare foundation model for 3D medical images., Comment: submitted to journal

Precision medicine tailored to individual patients has gained significant attention in recent times. Machine learning techniques are now employed to process personalized data from various sources, including images, genetics, and assessments. These techniques have demonstrated good outcomes in many clinical prediction tasks. Notably, the approach of constructing graphs by linking similar patients and then applying graph neural networks (GNNs) stands out, because related information from analogous patients are aggregated and considered for prediction. However, selecting the appropriate edge feature to define patient similarity and construct the graph is challenging, given that each patient is depicted by high-dimensional features from diverse sources. Previous studies rely on human expertise to select the edge feature, which is neither scalable nor efficient in pinpointing crucial edge features for complex diseases. In this paper, we propose a novel algorithm named \ours, which can automatically select important features to construct multiple patient similarity graphs, and train GNNs based on these graphs as weak learners in adaptive boosting. \ours{} is evaluated on two real-world medical scenarios and shows superiors performance., Comment: Extended Abstract presented at Machine Learning for Health (ML4H) symposium 2023, December 10th, 2023, New Orleans, United States, 9 pages

As deep neural networks include a high number of parameters and operations, it can be a challenge to implement these models on devices with limited computational resources. Despite the development of novel pruning methods toward resource-efficient models, it has become evident that these models are not capable of handling "imbalanced" and "limited number of data points". We proposed a novel filter pruning method by considering the input and output of filters along with the values of the filters that deal with imbalanced datasets better than others. Our pruning method considers the fact that all information about the importance of a filter may not be reflected in the value of the filter. Instead, it is reflected in the changes made to the data after the filter is applied to it. In this work, three methods are compared with the same training conditions except for the ranking values of each method, and 14 methods are compared from other papers. We demonstrated that our model performed significantly better than other methods for imbalanced medical datasets. For example, when we removed up to 58% of FLOPs for the IDRID dataset and up to 45% for the ISIC dataset, our model was able to yield an equivalent (or even superior) result to the baseline model. To evaluate FLOP and parameter reduction using our model in real-world settings, we built a smartphone app, where we demonstrated a reduction of up to 79% in memory usage and 72% in prediction time. All codes and parameters for training different models are available at https://github.com/mohofar/Beta-Rank, Comment: 13 pages, 3 figures, and 3 tables

Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. This paper provides an extensive review of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are elaborated and discussed. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging., Comment: IEEE RBME 2024

Low-dose computed tomography (LDCT) image reconstruction techniques can reduce patient radiation exposure while maintaining acceptable imaging quality. Deep learning is widely used in this problem, but the performance of testing data (a.k.a. target domain) is often degraded in clinical scenarios due to the variations that were not encountered in training data (a.k.a. source domain). Unsupervised domain adaptation (UDA) of LDCT reconstruction has been proposed to solve this problem through distribution alignment. However, existing UDA methods fail to explore the usage of uncertainty quantification, which is crucial for reliable intelligent medical systems in clinical scenarios with unexpected variations. Moreover, existing direct alignment for different patients would lead to content mismatch issues. To address these issues, we propose to leverage a probabilistic reconstruction framework to conduct a joint discrepancy minimization between source and target domains in both the latent and image spaces. In the latent space, we devise a Bayesian uncertainty alignment to reduce the epistemic gap between the two domains. This approach reduces the uncertainty level of target domain data, making it more likely to render well-reconstructed results on target domains. In the image space, we propose a sharpness-aware distribution alignment to achieve a match of second-order information, which can ensure that the reconstructed images from the target domain have similar sharpness to normal-dose CT images from the source domain. Experimental results on two simulated datasets and one clinical low-dose imaging dataset show that our proposed method outperforms other methods in quantitative and visualized performance., Comment: Accepted by IEEE Transactions on Neural Networks and Learning Systems

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework., Comment: NeurIPS 2022

Two DL models were developed using radiograph-level annotations (yes or no disease) and fine-grained lesion-level annotations (lesion bounding boxes), respectively named CheXNet and CheXDet. The models' internal classification performance and lesion localization performance were compared on a testing set (n=2,922), external classification performance was compared on NIH-Google (n=4,376) and PadChest (n=24,536) datasets, and external lesion localization performance was compared on NIH-ChestX-ray14 dataset (n=880). The models were also compared to radiologists on a subset of the internal testing set (n=496). Given sufficient training data, both models performed comparably to radiologists. CheXDet achieved significant improvement for external classification, such as in classifying fracture on NIH-Google (CheXDet area under the ROC curve [AUC]: 0.67, CheXNet AUC: 0.51; p<.001) and PadChest (CheXDet AUC: 0.78, CheXNet AUC: 0.55; p<.001). CheXDet achieved higher lesion detection performance than CheXNet for most abnormalities on all datasets, such as in detecting pneumothorax on the internal set (CheXDet jacknife alternative free-response ROC-figure of merit [JAFROC-FOM]: 0.87, CheXNet JAFROC-FOM: 0.13; p<.001) and NIH-ChestX-ray14 (CheXDet JAFROC-FOM: 0.55, CheXNet JAFROC-FOM: 0.04; p<.001). To summarize, fine-grained annotations overcame shortcut learning and enabled DL models to identify correct lesion patterns, improving the models' generalizability., Comment: Radiology: Artificial Intelligence

Spectral computed tomography (CT) has attracted much attention in radiation dose reduction, metal artifacts removal, tissue quantification and material discrimination. The x-ray energy spectrum is divided into several bins, each energy-bin-specific projection has a low signal-noise-ratio (SNR) than the current-integrating counterpart, which makes image reconstruction a unique challenge. Traditional wisdom is to use prior knowledge based iterative methods. However, this kind of methods demands a great computational cost. Inspired by deep learning, here we first develop a deep learning based reconstruction method; i.e., U-net with L_p^p-norm, Total variation, Residual learning, and Anisotropic adaption (ULTRA). Specifically, we emphasize the Various Multi-scale Feature Fusion and Multichannel Filtering Enhancement with a denser connection encoding architecture for residual learning and feature fusion. To address the image deblurring problem associated with the $L_2^2$-loss, we propose a general $L_p^p$-loss, $p>0$ Furthermore, the images from different energy bins share similar structures of the same object, the regularization characterizing correlations of different energy bins is incorporated into the $L_p^p$-loss function, which helps unify the deep learning based methods with traditional compressed sensing based methods. Finally, the anisotropically weighted total variation is employed to characterize the sparsity in the spatial-spectral domain to regularize the proposed network. In particular, we validate our ULTRA networks on three large-scale spectral CT datasets, and obtain excellent results relative to the competing algorithms. In conclusion, our quantitative and qualitative results in numerical simulation and preclinical experiments demonstrate that our proposed approach is accurate, efficient and robust for high-quality spectral CT image reconstruction.

Tomographic image reconstruction with deep learning is an emerging field, but a recent landmark study reveals that several deep reconstruction networks are unstable for computed tomography (CT) and magnetic resonance imaging (MRI). Specifically, three kinds of instabilities were reported: (1) strong image artefacts from tiny perturbations, (2) small features missing in a deeply reconstructed image, and (3) decreased imaging performance with increased input data. On the other hand, compressed sensing (CS) inspired reconstruction methods do not suffer from these instabilities because of their built-in kernel awareness. For deep reconstruction to realize its full potential and become a mainstream approach for tomographic imaging, it is thus critically important to meet this challenge by stabilizing deep reconstruction networks. Here we propose an Analytic Compressed Iterative Deep (ACID) framework to address this challenge. ACID synergizes a deep reconstruction network trained on big data, kernel awareness from CS-inspired processing, and iterative refinement to minimize the data residual relative to real measurement. Our study demonstrates that the deep reconstruction using ACID is accurate and stable, and sheds light on the converging mechanism of the ACID iteration under a Bounded Relative Error Norm (BREN) condition. In particular, the study shows that ACID-based reconstruction is resilient against adversarial attacks, superior to classic sparsity-regularized reconstruction alone, and eliminates the three kinds of instabilities. We anticipate that this integrative data-driven approach will help promote development and translation of deep tomographic image reconstruction networks into clinical applications., Comment: 78 pages, 30 figures, 149 references

Nasopharyngeal Carcinoma (NPC) is endemic cancer in the south-east Asia. With the advent of intensity-modulated radiotherapy excellent locoregional control are being achieved. Consequently, this had led to pretreatment clinical staging classification to be less prognostic of outcomes such as recurrence after treatment. Alternative pretreatment strategies for prognosis of NPC after treatment are needed to provide better risk stratification for NPC. In this study we proposed a deep convolution neural network model based on contrast-enhanced T1 (T1C) and T2 weighted (T2) MRI scan to predict 3-year disease progression of NPC patient after primary treatment. We retrospective obtained 596 non-metastatic NPC patients from four independent centres in Hong Kong and China. Our model first performs a segmentation of the primary NPC tumour to localise the tumour, and then uses the segmentation mask as prior knowledge along with the T1C and T2 scan to classify 3-year disease progression. For segmentation, we adapted and modified a VNet to encode both T1C and T2 scan and also encoding to classify T and overall stage classification. Our modified network performed better than baseline VNet with T1C and network with no T and overall classification. The classification result for 3-year disease progression achieved an AUC of 0.828 in the validation set but did not generalised well for the test set which consist of 146 patients from a different centre to the training data (AUC = 0.69). Our preliminary results show that deep learning may offer prognostication of disease progression of NPC patients after treatment. One advantage of our model is that it does not require manual segmentation of the region of interest, hence reducing clinician's burden. Further development in generalising multicentre data set are needed before clinical application of deep learning models in assessment of NPC., Comment: Medical Imaging with Deep Learning 2019 - Extended Abstract. MIDL 2019 [arXiv:1907.08612]