Search

Sparse views X-ray computed tomography has emerged as a contemporary technique to mitigate radiation dose. Because of the reduced number of projection views, traditional reconstruction methods can lead to severe artifacts. Recently, research studies utilizing deep learning methods has made promising progress in removing artifacts for Sparse-View Computed Tomography (SVCT). However, given the limitations on the generalization capability of deep learning models, current methods usually train models on fixed sampling rates, affecting the usability and flexibility of model deployment in real clinical settings. To address this issue, our study proposes a adaptive reconstruction method to achieve high-performance SVCT reconstruction at any sampling rate. Specifically, we design a novel imaging degradation operator in the proposed sampling diffusion model for SVCT (CT-SDM) to simulate the projection process in the sinogram domain. Thus, the CT-SDM can gradually add projection views to highly undersampled measurements to generalize the full-view sinograms. By choosing an appropriate starting point in diffusion inference, the proposed model can recover the full-view sinograms from any sampling rate with only one trained model. Experiments on several datasets have verified the effectiveness and robustness of our approach, demonstrating its superiority in reconstructing high-quality images from sparse-view CT scans across various sampling rates.

Sparse-View Computed Tomography (SVCT) offers low-dose and fast imaging but suffers from severe artifacts. Optimizing the sampling strategy is an essential approach to improving the imaging quality of SVCT. However, current methods typically optimize a universal sampling strategy for all types of scans, overlooking the fact that the optimal strategy may vary depending on the specific scanning task, whether it involves particular body scans (e.g., chest CT scans) or downstream clinical applications (e.g., disease diagnosis). The optimal strategy for one scanning task may not perform as well when applied to other tasks. To address this problem, we propose a deep learning framework that learns task-specific sampling strategies with a multi-task approach to train a unified reconstruction network while tailoring optimal sampling strategies for each individual task. Thus, a task-specific sampling strategy can be applied for each type of scans to improve the quality of SVCT imaging and further assist in performance of downstream clinical usage. Extensive experiments across different scanning types provide validation for the effectiveness of task-specific sampling strategies in enhancing imaging quality. Experiments involving downstream tasks verify the clinical value of learned sampling strategies, as evidenced by notable improvements in downstream task performance. Furthermore, the utilization of a multi-task framework with a shared reconstruction network facilitates deployment on current imaging devices with switchable task-specific modules, and allows for easily integrate new tasks without retraining the entire model.

Model intellectual property (IP) protection has attracted growing attention as science and technology advancements stem from human intellectual labor and computational expenses. Ensuring IP safety for trainers and owners is of utmost importance, particularly in domains where ownership verification and applicability authorization are required. A notable approach to safeguarding model IP involves proactively preventing the use of well-trained models of authorized domains from unauthorized domains. In this paper, we introduce a novel Compact Un-transferable Pyramid Isolation Domain (CUPI-Domain) which serves as a barrier against illegal transfers from authorized to unauthorized domains. Drawing inspiration from human transitive inference and learning abilities, the CUPI-Domain is designed to obstruct cross-domain transfers by emphasizing the distinctive style features of the authorized domain. This emphasis leads to failure in recognizing irrelevant private style features on unauthorized domains. To this end, we propose novel CUPI-Domain generators, which select features from both authorized and CUPI-Domain as anchors. Then, we fuse the style features and semantic features of these anchors to generate labeled and style-rich CUPI-Domain. Additionally, we design external Domain-Information Memory Banks (DIMB) for storing and updating labeled pyramid features to obtain stable domain class features and domain class-wise style features. Based on the proposed whole method, the novel style and discriminative loss functions are designed to effectively enhance the distinction in style and discriminative features between authorized and unauthorized domains, respectively. Moreover, we provide two solutions for utilizing CUPI-Domain based on whether the unauthorized domain is known: target-specified CUPI-Domain and target-free CUPI-Domain.

The rapid development of spatial transcriptomics(ST) enables the measurement of gene expression at spatial resolution, making it possible to simultaneously profile the gene expression, spatial locations of spots, and the matched histopathological images. However, the cost for collecting ST data is much higher than acquiring histopathological images, and thus several studies attempt to predict the gene expression on ST by leveraging their corresponding histopathological images. Most of the existing image-based gene prediction models treat the prediction task on each spot of ST data independently, which ignores the spatial dependency among spots. In addition, while the histology images share phenotypic characteristics with the ST data, it is still challenge to extract such common information to help align paired image and expression representations. To address the above issues, we propose a Multi-view Graph Contrastive Learning framework with HSIC-bottleneck Regularization(ST-GCHB) aiming at learning shared representation to help impute the gene expression of the queried imagingspots by considering their spatial dependency.

Source-free domain adaptation (SFDA) aims to adapt a model pre-trained on a labeled source domain to an unlabeled target domain without access to source data, preserving the source domain's privacy. While SFDA is prevalent in computer vision, it remains largely unexplored in time series analysis. Existing SFDA methods, designed for visual data, struggle to capture the inherent temporal dynamics of time series, hindering adaptation performance. This paper proposes MAsk And imPUte (MAPU), a novel and effective approach for time series SFDA. MAPU addresses the critical challenge of temporal consistency by introducing a novel temporal imputation task. This task involves randomly masking time series signals and leveraging a dedicated temporal imputer to recover the original signal within the learned embedding space, bypassing the complexities of noisy raw data. Notably, MAPU is the first method to explicitly address temporal consistency in the context of time series SFDA. Additionally, it offers seamless integration with existing SFDA methods, providing greater flexibility. We further introduce E-MAPU, which incorporates evidential uncertainty estimation to address the overconfidence issue inherent in softmax predictions. To achieve that, we leverage evidential deep learning to obtain a better-calibrated pre-trained model and adapt the target encoder to map out-of-support target samples to a new feature representation closer to the source domain's support. This fosters better alignment, ultimately enhancing adaptation performance. Extensive experiments on five real-world time series datasets demonstrate that both MAPU and E-MAPU achieve significant performance gains compared to existing methods. These results highlight the effectiveness of our proposed approaches for tackling various time series domain adaptation problems.

Deep learning has been extensively applied in medical image reconstruction, where Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) represent the predominant paradigms, each possessing distinct advantages and inherent limitations: CNNs exhibit linear complexity with local sensitivity, whereas ViTs demonstrate quadratic complexity with global sensitivity. The emerging Mamba has shown superiority in learning visual representation, which combines the advantages of linear scalability and global sensitivity. In this study, we introduce MambaMIR, an Arbitrary-Masked Mamba-based model with wavelet decomposition for joint medical image reconstruction and uncertainty estimation. A novel Arbitrary Scan Masking (ASM) mechanism "masks out" redundant information to introduce randomness for further uncertainty estimation. Compared to the commonly used Monte Carlo (MC) dropout, our proposed MC-ASM provides an uncertainty map without the need for hyperparameter tuning and mitigates the performance drop typically observed when applying dropout to low-level tasks. For further texture preservation and better perceptual quality, we employ the wavelet transformation into MambaMIR and explore its variant based on the Generative Adversarial Network, namely MambaMIR-GAN. Comprehensive experiments have been conducted for multiple representative medical image reconstruction tasks, demonstrating that the proposed MambaMIR and MambaMIR-GAN outperform other baseline and state-of-the-art methods in different reconstruction tasks, where MambaMIR achieves the best reconstruction fidelity and MambaMIR-GAN has the best perceptual quality. In addition, our MC-ASM provides uncertainty maps as an additional tool for clinicians, while mitigating the typical performance drop caused by the commonly used dropout.

The recent Mamba model has shown remarkable adaptability for visual representation learning, including in medical imaging tasks. This study introduces MambaMIR, a Mamba-based model for medical image reconstruction, as well as its Generative Adversarial Network-based variant, MambaMIR-GAN. Our proposed MambaMIR inherits several advantages, such as linear complexity, global receptive fields, and dynamic weights, from the original Mamba model. The innovated arbitrary-mask mechanism effectively adapt Mamba to our image reconstruction task, providing randomness for subsequent Monte Carlo-based uncertainty estimation. Experiments conducted on various medical image reconstruction tasks, including fast MRI and SVCT, which cover anatomical regions such as the knee, chest, and abdomen, have demonstrated that MambaMIR and MambaMIR-GAN achieve comparable or superior reconstruction results relative to state-of-the-art methods. Additionally, the estimated uncertainty maps offer further insights into the reliability of the reconstruction quality. The code is publicly available at https://github.com/ayanglab/MambaMIR.

Multiphase contrast-enhanced computed tomography (CECT) scan is clinically significant to demonstrate the anatomy at different phases. In practice, such a multiphase CECT scan inherently takes longer time and deposits much more radiation dose into a patient body than a regular CT scan, and reduction of the radiation dose typically compromise the CECT image quality and its diagnostic value. With Joint Condition and Circle-Supervision, here we propose a novel Poisson Flow Generative Model (JCCS-PFGM) to promote the progressive low-dose reconstruction for multiphase CECT. JCCS-PFGM is characterized by the following three aspects: a progressive low-dose reconstruction scheme, a circle-supervision strategy, and a joint condition mechanism. Our extensive experiments are performed on a clinical dataset consisting of 11436 images. The results show that our JCCS-PFGM achieves promising PSNR up to 46.3dB, SSIM up to 98.5%, and MAE down to 9.67 HU averagely on phases I, II and III, in quantitative evaluations, as well as gains high-quality readable visualizations in qualitative assessments. All of these findings reveal our method a great potential to be adapted for clinical CECT scans at a much-reduced radiation dose.

Failure to recognize samples from the classes unseen during training is a major limitation of artificial intelligence in the real-world implementation for recognition and classification of retinal anomalies. We established an uncertainty-inspired open-set (UIOS) model, which was trained with fundus images of 9 retinal conditions. Besides assessing the probability of each category, UIOS also calculated an uncertainty score to express its confidence. Our UIOS model with thresholding strategy achieved an F1 score of 99.55%, 97.01% and 91.91% for the internal testing set, external target categories (TC)-JSIEC dataset and TC-unseen testing set, respectively, compared to the F1 score of 92.20%, 80.69% and 64.74% by the standard AI model. Furthermore, UIOS correctly predicted high uncertainty scores, which would prompt the need for a manual check in the datasets of non-target categories retinal diseases, low-quality fundus images, and non-fundus images. UIOS provides a robust method for real-world screening of retinal anomalies.

As scientific and technological advancements result from human intellectual labor and computational costs, protecting model intellectual property (IP) has become increasingly important to encourage model creators and owners. Model IP protection involves preventing the use of well-trained models on unauthorized domains. To address this issue, we propose a novel approach called Compact Un-Transferable Isolation Domain (CUTI-domain), which acts as a barrier to block illegal transfers from authorized to unauthorized domains. Specifically, CUTI-domain blocks cross-domain transfers by highlighting the private style features of the authorized domain, leading to recognition failure on unauthorized domains with irrelevant private style features. Moreover, we provide two solutions for using CUTI-domain depending on whether the unauthorized domain is known or not: target-specified CUTI-domain and target-free CUTI-domain. Our comprehensive experimental results on four digit datasets, CIFAR10 & STL10, and VisDA-2017 dataset demonstrate that CUTI-domain can be easily implemented as a plug-and-play module with different backbones, providing an efficient solution for model IP protection.

Structural magnetic resonance imaging (sMRI) can identify subtle brain changes due to its high contrast for soft tissues and high spatial resolution. It has been widely used in diagnosing neurological brain diseases, such as Alzheimer disease (AD). However, the size of 3D high-resolution data poses a significant challenge for data analysis and processing. Since only a few areas of the brain show structural changes highly associated with AD, the patch-based methods dividing the whole image data into several small regular patches have shown promising for more efficient sMRI-based image analysis. The major challenges of the patch-based methods on sMRI include identifying the discriminative patches, combining features from the discrete discriminative patches, and designing appropriate classifiers. This work proposes a novel patch-based deep learning network (sMRI-PatchNet) with explainable patch localisation and selection for AD diagnosis using sMRI. Specifically, it consists of two primary components: 1) A fast and efficient explainable patch selection mechanism for determining the most discriminative patches based on computing the SHapley Additive exPlanations (SHAP) contribution to a transfer learning model for AD diagnosis on massive medical data; and 2) A novel patch-based network for extracting deep features and AD classfication from the selected patches with position embeddings to retain position information, capable of capturing the global and local information of inter- and intra-patches. This method has been applied for the AD classification and the prediction of the transitional state moderate cognitive impairment (MCI) conversion with real datasets.

Complementary Labels Learning (CLL) arises in many real-world tasks such as private questions classification and online learning, which aims to alleviate the annotation cost compared with standard supervised learning. Unfortunately, most previous CLL algorithms were in a stable environment rather than an open and dynamic scenarios, where data collected from unseen augmented classes in the training process might emerge in the testing phase. In this paper, we propose a novel problem setting called Complementary Labels Learning with Augmented Classes (CLLAC), which brings the challenge that classifiers trained by complementary labels should not only be able to classify the instances from observed classes accurately, but also recognize the instance from the Augmented Classes in the testing phase. Specifically, by using unlabeled data, we propose an unbiased estimator of classification risk for CLLAC, which is guaranteed to be provably consistent. Moreover, we provide generalization error bound for proposed method which shows that the optimal parametric convergence rate is achieved for estimation error. Finally, the experimental results on several benchmark datasets verify the effectiveness of the proposed method.

Unsupervised domain adaptation (UDA) has attracted considerable attention, which transfers knowledge from a label-rich source domain to a related but unlabeled target domain. Reducing inter-domain differences has always been a crucial factor to improve performance in UDA, especially for tasks where there is a large gap between source and target domains. To this end, we propose a novel style-aware feature fusion method (SAFF) to bridge the large domain gap and transfer knowledge while alleviating the loss of class-discriminative information. Inspired by the human transitive inference and learning ability, a novel style-aware self-intermediate domain (SSID) is investigated to link two seemingly unrelated concepts through a series of intermediate auxiliary synthesized concepts. Specifically, we propose a novel learning strategy of SSID, which selects samples from both source and target domains as anchors, and then randomly fuses the object and style features of these anchors to generate labeled and style-rich intermediate auxiliary features for knowledge transfer. Moreover, we design an external memory bank to store and update specified labeled features to obtain stable class features and class-wise style features. Based on the proposed memory bank, the intra- and inter-domain loss functions are designed to improve the class recognition ability and feature compatibility, respectively. Meanwhile, we simulate the rich latent feature space of SSID by infinite sampling and the convergence of the loss function by mathematical theory. Finally, we conduct comprehensive experiments on commonly used domain adaptive benchmarks to evaluate the proposed SAFF, and the experimental results show that the proposed SAFF can be easily combined with different backbone networks and obtain better performance as a plug-in-plug-out module., Comment: 13 pages, 7 figures

Positive Unlabeled (PU) learning aims to learn a binary classifier from only positive and unlabeled data, which is utilized in many real-world scenarios. However, existing PU learning algorithms cannot deal with the real-world challenge in an open and changing scenario, where examples from unobserved augmented classes may emerge in the testing phase. In this paper, we propose an unbiased risk estimator for PU learning with Augmented Classes (PUAC) by utilizing unlabeled data from the augmented classes distribution, which can be easily collected in many real-world scenarios. Besides, we derive the estimation error bound for the proposed estimator, which provides a theoretical guarantee for its convergence to the optimal solution. Experiments on multiple realistic datasets demonstrate the effectiveness of proposed approach.

Deep Neural Network (DNN) models are usually trained sequentially from one layer to another, which causes forward, backward and update locking's problems, leading to poor performance in terms of training time. The existing parallel strategies to mitigate these problems provide suboptimal runtime performance. In this work, we have proposed a novel layer-wise partitioning and merging, forward and backward pass parallel framework to provide better training performance. The novelty of the proposed work consists of 1) a layer-wise partition and merging model which can minimise communication overhead between devices without the memory cost of existing strategies during the training process; 2) a forward pass and backward pass parallelisation and optimisation to address the update locking problem and minimise the total training cost. The experimental evaluation on real use cases shows that the proposed method outperforms the state-of-the-art approaches in terms of training speed; and achieves almost linear speedup without compromising the accuracy performance of the non-parallel approach.

Adversarial training (AT) has shown excellent high performance in defending against adversarial examples. Recent studies demonstrate that examples are not equally important to the final robustness of models during AT, that is, the so-called hard examples that can be attacked easily exhibit more influence than robust examples on the final robustness. Therefore, guaranteeing the robustness of hard examples is crucial for improving the final robustness of the model. However, defining effective heuristics to search for hard examples is still difficult. In this article, inspired by the information bottleneck (IB) principle, we uncover that an example with high mutual information of the input and its associated latent representation is more likely to be attacked. Based on this observation, we propose a novel and effective adversarial training method (InfoAT). InfoAT is encouraged to find examples with high mutual information and exploit them efficiently to improve the final robustness of models. Experimental results show that InfoAT achieves the best robustness among different datasets and models in comparison with several state-of-the-art methods., Comment: Published in: IEEE Transactions on Neural Networks and Learning Systems ( Early Access )

Low-Dose Computed Tomography (LDCT) technique, which reduces the radiation harm to human bodies, is now attracting increasing interest in the medical imaging field. As the image quality is degraded by low dose radiation, LDCT exams require specialized reconstruction methods or denoising algorithms. However, most of the recent effective methods overlook the inner-structure of the original projection data (sinogram) which limits their denoising ability. The inner-structure of the sinogram represents special characteristics of the data in the sinogram domain. By maintaining this structure while denoising, the noise can be obviously restrained. Therefore, we propose an LDCT denoising network namely Sinogram Inner-Structure Transformer (SIST) to reduce the noise by utilizing the inner-structure in the sinogram domain. Specifically, we study the CT imaging mechanism and statistical characteristics of sinogram to design the sinogram inner-structure loss including the global and local inner-structure for restoring high-quality CT images. Besides, we propose a sinogram transformer module to better extract sinogram features. The transformer architecture using a self-attention mechanism can exploit interrelations between projections of different view angles, which achieves an outstanding performance in sinogram denoising. Furthermore, in order to improve the performance in the image domain, we propose the image reconstruction module to complementarily denoise both in the sinogram and image domain.

Efficient and effective attacks are crucial for reliable evaluation of defenses, and also for developing robust models. Projected Gradient Descent (PGD) attack has been demonstrated to be one of the most successful adversarial attacks. However, the effect of the standard PGD attack can be easily weakened by rescaling the logits, while the original decision of every input will not be changed. To mitigate this issue, in this paper, we propose Scale-Invariant Adversarial Attack (SI-PGD), which utilizes the angle between the features in the penultimate layer and the weights in the softmax layer to guide the generation of adversaries. The cosine angle matrix is used to learn angularly discriminative representation and will not be changed with the rescaling of logits, thus making SI-PGD attack to be stable and effective. We evaluate our attack against multiple defenses and show improved performance when compared with existing attacks. Further, we propose Scale-Invariant (SI) adversarial defense mechanism based on the cosine angle matrix, which can be embedded into the popular adversarial defenses. The experimental results show the defense method with our SI mechanism achieves state-of-the-art performance among multi-step and single-step defenses., Comment: TDSC under review

Deep neural networks are discovered to be non-robust when attacked by imperceptible adversarial examples, which is dangerous for it applied into medical diagnostic system that requires high reliability. However, the defense methods that have good effect in natural images may not be suitable for medical diagnostic tasks. The preprocessing methods (e.g., random resizing, compression) may lead to the loss of the small lesions feature in the medical image. Retraining the network on the augmented data set is also not practical for medical models that have already been deployed online. Accordingly, it is necessary to design an easy-to-deploy and effective defense framework for medical diagnostic tasks. In this paper, we propose a Robust and Retrain-Less Diagnostic Framework for Medical pretrained models against adversarial attack (i.e., MedRDF). It acts on the inference time of the pertained medical model. Specifically, for each test image, MedRDF firstly creates a large number of noisy copies of it, and obtains the output labels of these copies from the pretrained medical diagnostic model. Then, based on the labels of these copies, MedRDF outputs the final robust diagnostic result by majority voting. In addition to the diagnostic result, MedRDF produces the Robust Metric (RM) as the confidence of the result. Therefore, it is convenient and reliable to utilize MedRDF to convert pre-trained non-robust diagnostic models into robust ones. The experimental results on COVID-19 and DermaMNIST datasets verify the effectiveness of our MedRDF in improving the robustness of medical diagnostic models., Comment: TMI under review

Recently, Deep Neural Networks (DNNs) have recorded great success in handling medical and other complex classification tasks. However, as the sizes of a DNN model and the available dataset increase, the training process becomes more complex and computationally intensive, which usually takes a longer time to complete. In this work, we have proposed a generic full end-to-end hybrid parallelization approach combining both model and data parallelism for efficiently distributed and scalable training of DNN models. We have also proposed a Genetic Algorithm based heuristic resources allocation mechanism (GABRA) for optimal distribution of partitions on the available GPUs for computing performance optimization. We have applied our proposed approach to a real use case based on 3D Residual Attention Deep Neural Network (3D-ResAttNet) for efficient Alzheimer Disease (AD) diagnosis on multiple GPUs. The experimental evaluation shows that the proposed approach is efficient and scalable, which achieves almost linear speedup with little or no differences in accuracy performance when compared with the existing non-parallel DNN models.