With the growing global threat of coronary artery disease (CAD), automated CAD diagnosis techniques based on coronary CT angiography (CCTA) have been developed. However, their clinical applicability remains limited due to the heterogeneity of stenosis and plaque attributes, as well as confounders within the causal relationships of CAD diagnosis. This work introduces the Attribute-Decoupled Intervention Network (ADI-Net), a confounder-free CAD diagnosis framework designed for fine-grained analysis at both the artery and patient levels, aligning with real-world clinical practice. ADI-Net employs an attribute-decoupled representation that effectively captures the heterogeneous features of stenosis and plaque with differential constraints, enabling precise, fine-grained classification. Additionally, the dynamic-updating causal intervention continuously refines confounder banks and applies the Do-expression within a complete causality, ensuring comprehensive, cross-level assessments. Experiments on CCTA datasets from three clinical centers demonstrate that ADI-Net outperforms state-of-the-art methods in cross-level, fine-grained CAD diagnosis, exhibiting superior robustness, domain adaptability, and data efficiency.

Coronary Artery Disease (CAD) poses a significant threat to cardiovascular patients worldwide, underscoring the critical importance of automated CAD diagnostic technologies in clinical practice. Previous technologies for lesion assessment in Coronary CT Angiography (CCTA) images have been insufficient in terms of interpretability, resulting in solutions that lack clinical reliability in both network architecture and prediction outcomes, even when diagnoses are accurate. To address the limitation of interpretability, we introduce the Trusted Lesion-Assessment Network (TLA-Net), which provides a clinically reliable solution for multi-view CAD diagnosis: (1) The causality-informed evidence collection constructs a causal graph for the diagnostic process and implements causal interventions, preventing confounders' interference and enhancing the transparency of the network architecture. (2) The clinically-aligned uncertainty integration hierarchically combines Dirichlet distributions from various views based on clinical priors, offering confidence coefficients for prediction outcomes that align with physicians' image analysis procedures. Experimental results on a dataset of 2,618 lesions demonstrate that TLA-Net, supported by its interpretable methodological design, exhibits superior performance with outstanding generalization, domain adaptability, and robustness.

The latest clinical guideline of the Coronary Artery Disease Reporting and Data System (CAD-RADS) emphasizes comprehensive CAD risk evaluation, driving the development of automated diagnosis technologies toward a unified multi-task framework. Previous task-specific architectures, relying on varied pre- and post-processing, showed redundancy and prediction inconsistencies. To address this, we first proposed synergistic multitask learning and constructed a unified CAD-RADS framework. It provides a collaborative diagnosis of the CAD-RADS level, coronary artery calcium, the segment involvement score, and abnormality modifiers based on the patient's CT Angiography (CTA) volume. On the one hand, we integrate offset features across multiple scales to learn distinct attention distributions for different tasks in the latent space, thereby meeting the representation requirements for task customization within a unified architecture. On the other hand, we employ ExpectationMaximization (EM)-driven iterative optimization to interactively learn a compact basis consensus among tasks, balancing them and promoting semantic complementarity. Experimental results based on CTA volumes from 1,068 patients demonstrate our framework outperforms state-of-the-art methods, advancing the clinical application of intelligent CAD-RADS.

Data distribution gaps often pose significant challenges to the use of deep segmentation models. However, retraining models for each distribution is expensive and time-consuming. In clinical contexts, device-embedded algorithms and networks, typically unretrainable and unaccessable post-manufacture, exacerbate this issue. Generative translation methods offer a solution to mitigate the gap by transferring data across domains. However, existing methods mainly focus on intensity distributions while ignoring the gaps due to structure disparities. In this paper, we formulate a new image-to-image translation task to reduce structural gaps. We propose a simple, yet powerful Structure-Unbiased Adversarial (SUA) network which accounts for both intensity and structural differences between the training and test sets for segmentation. It consists of a spatial transformation block followed by an intensity distribution rendering module. The spatial transformation block is proposed to reduce the structural gaps between the two images. The intensity distribution rendering module then renders the deformed structure to an image with the target intensity distribution. Experimental results show that the proposed SUA method has the capability to transfer both intensity distribution and structural content between multiple pairs of datasets and is superior to prior arts in closing the gaps for improving segmentation.

Unsupervised image registration commonly adopts U-Net style networks to predict dense displacement fields in the full-resolution spatial domain. For high-resolution volumetric image data, this process is however resource-intensive and time-consuming. To tackle this problem, we propose the Fourier-Net, replacing the expansive path in a U-Net style network with a parameter-free model-driven decoder. Specifically, instead of our Fourier-Net learning to output a full-resolution displacement field in the spatial domain, we learn its low-dimensional representation in a band-limited Fourier domain. This representation is then decoded by our devised model-driven decoder (consisting of a zero padding layer and an inverse discrete Fourier transform layer) to the dense, full-resolution displacement field in the spatial domain. These changes allow our unsupervised Fourier-Net to contain fewer parameters and computational operations, resulting in faster inference speeds. Fourier-Net is then evaluated on two public 3D brain datasets against various state-of-the-art approaches. For example, when compared to a recent transformer-based method, named TransMorph, our Fourier-Net, which only uses 2.2% of its parameters and 6.66% of the multiply-add operations, achieves a 0.5% higher Dice score and an 11.48 times faster inference speed. Code is available at https://github.com/xi-jia/Fourier-Net.

In this work, we investigate image registration in a variational framework and focus on regularization generality and solver efficiency. We first propose a variational model combining the state-of-the-art sum of absolute differences (SAD) and a new arbitrary order total variation regularization term. The main advantage is that this variational model preserves discontinuities in the resultant deformation while being robust to outlier noise. It is however non-trivial to optimize the model due to its non-convexity, non-differentiabilities, and generality in the derivative order. To tackle these, we propose to first apply linearization to the problem to formulate a convex objective function and then break down the resultant convex optimization into several point-wise, closed-form subproblems using a fast, over-relaxed alternating direction method of multipliers (ADMM). With our proposed algorithm, we show that solving higher-order variational formulations is similar to solving their lower-order counterparts. Extensive experiments show that our ADMM is significantly more efficient than both the subgradient and primal-dual algorithms particularly when higher-order derivatives are used, and that our new models outperform state-of-the-art methods based on deep learning and free-form deformation. Our code implemented in both Matlab and Pytorch is publicly available at https://github.com/j-duan/AOTV.

MOTIVATION: Nanopore sequencing is one of the leading third-generation sequencing technologies. A number of computational tools have been developed to facilitate the processing and analysis of the Nanopore data. Previously, we have developed DeepSimulator1.0 (DS1.0), which is the first simulator for Nanopore sequencing to produce both the raw electrical signals and the reads. However, although DS1.0 can produce high-quality reads, for some sequences, the divergence between the simulated raw signals and the real signals can be large. Furthermore, the Nanopore sequencing technology has evolved greatly since DS1.0 was released. It is thus necessary to update DS1.0 to accommodate those changes. RESULTS: We propose DeepSimulator1.5 (DS1.5), all three modules of which have been updated substantially from DS1.0. As for the sequence generator, we updated the sample read length distribution to reflect the newest real reads' features. In terms of the signal generator, which is the core of DeepSimulator, we added one more pore model, the context-independent pore model, which is much faster than the previous context-dependent one. Furthermore, to make the generated signals more similar to the real ones, we added a low-pass filter to post-process the pore model signals. Regarding the basecaller, we added the support for the newest official basecaller, Guppy, which can support both GPU and CPU. In addition, multiple optimizations, related to multiprocessing control, memory and storage management, have been implemented to make DS1.5 a much more amenable and lighter simulator than DS1.0. AVAILABILITY AND IMPLEMENTATION: The main program and the data are available at https://github.com/lykaust15/DeepSimulator. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

COVID-19 has caused a global pandemic and become the most urgent threat to the entire world. Tremendous efforts and resources have been invested in developing diagnosis, prognosis and treatment strategies to combat the disease. Although nucleic acid detection has been mainly used as the gold standard to confirm this RNA virus-based disease, it has been shown that such a strategy has a high false negative rate, especially for patients in the early stage, and thus CT imaging has been applied as a major diagnostic modality in confirming positive COVID-19. Despite the various, urgent advances in developing artificial intelligence (AI)-based computer-aided systems for CT-based COVID-19 diagnosis, most of the existing methods can only perform classification, whereas the state-of-the-art segmentation method requires a high level of human intervention. In this paper, we propose a fully-automatic, rapid, accurate, and machine-agnostic method that can segment and quantify the infection regions on CT scans from different sources. Our method is founded upon two innovations: 1) the first CT scan simulator for COVID-19, by fitting the dynamic change of real patients' data measured at different time points, which greatly alleviates the data scarcity issue; and 2) a novel deep learning algorithm to solve the large-scene-small-object problem, which decomposes the 3D segmentation problem into three 2D ones, and thus reduces the model complexity by an order of magnitude and, at the same time, significantly improves the segmentation accuracy. Comprehensive experimental results over multi-country, multi-hospital, and multi-machine datasets demonstrate the superior performance of our method over the existing ones and suggest its important application value in combating the disease.