Bronchoalveolar lavage fluid (BALF) is a liquid obtained from the alveoli and bronchi, often used to study pulmonary diseases. So far, proteomic analyses have identified over three thousand proteins in BALF. However, the comprehensive characterization of these proteins remains challenging due to their complexity and technological limitations. This paper presented a novel deep learning framework called SecProGNN, designed to predict secretory proteins in BALF. Firstly, SecProGNN represented proteins as graph-structured data, with amino acids connected based on their interactions. Then, these graphs were processed through graph neural networks (GNNs) model to extract graph features. Finally, the extracted feature vectors were fed into a multi-layer perceptron (MLP) module to predict BALF secreted proteins. Additionally, by utilizing SecProGNN, we investigated potential biomarkers for lung adenocarcinoma and identified 16 promising candidates that may be secreted into BALF.

The generation of synthetic data using physics-based modeling provides a solution to limited or lacking real-world training samples in deep learning methods for rapid quantitative magnetic resonance imaging (qMRI). However, synthetic data distribution differs from real-world data, especially under complex imaging conditions, resulting in gaps between domains and limited generalization performance in real scenarios. Recently, a single-shot qMRI method, multiple overlapping-echo detachment imaging (MOLED), was proposed, quantifying tissue transverse relaxation time ( $\text {T}_{{2}}$ ) in the order of milliseconds with the help of a trained network. Previous works leveraged a Bloch-based simulator to generate synthetic data for network training, which leaves the domain gap between synthetic and real-world scenarios and results in limited generalization. In this study, we proposed a $\text {T}_{{2}}$ mapping method via MOLED from the perspective of domain adaptation, which obtained accurate mapping performance without real-label training and reduced the cost of sequence research at the same time. Experiments demonstrate that our method outshined in the restoration of MR anatomical structures.

The primary challenge faced by reconstruction-based anomaly detection (AD) methods is that neural networks exhibit strong generalization, resulting in a high probability and accuracy of anomaly reconstruction. Several existing methods attempt to alleviate this problem by randomly masking partial image regions and reconstructing the image from partial inpaintings. However, local masking in spatial space is not guaranteed to remove anomalous regions during the testing phase and poses the risk of normal regions being inaccurately reconstructed. Hence, we explore an approach to compress the global information of the image while ensuring the loss of partial anomaly information renders it difficult to reconstruct. Inspired by the fact that each Fourier coefficient contains global information of the image, we propose an adaptive Fourier space compression (AFSC) method. Specifically, the Fourier coefficients of the input image are sparsely sampled by binary masks obtained from the AFSC module (AFSCm). In AFSCm, the masks are jointly optimized with the reconstruction network subject to sparsity constraint. The learned masks are forced to selectively retain part of the global information that is favourable to recovering normal images. In addition, we introduce an efficient Fourier convolution module that enables the network to accurately reconstruct normal regions under conditions of losing partial information. Experimental results on three benchmarks of industrial scenarios demonstrate our method (without external prior) achieves competitive results compared with recent methods.

The goal of hyperspectral image fusion (HIF) is to reconstruct high spatial resolution hyperspectral images (HR-HSI) via fusing low spatial resolution hyperspectral images (LR-HSI) and high spatial resolution multispectral images (HR-MSI) without loss of spatial and spectral information. Most existing HIF methods are designed based on the assumption that the observation models are known, which is unrealistic in many scenarios. To address this blind HIF problem, we propose a deep learning-based method that optimizes the observation model and fusion processes iteratively and alternatively during the reconstruction to enforce bidirectional data consistency, which leads to better spatial and spectral accuracy. However, general deep neural network inherently suffers from information loss, preventing us to achieve this bidirectional data consistency. To settle this problem, we enhance the blind HIF algorithm by making part of the deep neural network invertible via applying a slightly modified spectral normalization to the weights of the network. Furthermore, in order to reduce spatial distortion and feature redundancy, we introduce a Content-Aware ReAssembly of FEatures module and an SE-ResBlock model to our network. The former module helps to boost the fusion performance, while the latter make our model more compact. Experiments demonstrate that our model performs favorably against compared methods in terms of both nonblind HIF fusion and semiblind HIF fusion.

Underwater images suffer from degradation due to light scattering and absorption. It remains challenging to restore such degraded images using deep neural networks since real-world paired data is scarcely available while synthetic paired data cannot approximate real-world data perfectly. In this paper, we propose an UnSupervised Underwater Image Restoration method (USUIR) by leveraging the homology property between a raw underwater image and a re-degraded image. Specifically, USUIR first estimates three latent components of the raw underwater image, i.e., the global background light, the transmission map, and the scene radiance (the clean image). Then, a re-degraded image is generated by randomly mixing up the estimated scene radiance and the raw underwater image. We demonstrate that imposing a homology constraint between the raw underwater image and the re-degraded image is equivalent to minimizing the restoration error and hence can be used for the unsupervised restoration. Extensive experiments show that USUIR achieves promising performance in both inference time and restoration quality.

Synthesizing a subject-specific pathology-free image from a pathological image is valuable for algorithm development and clinical practice. In recent years, several approaches based on the Generative Adversarial Network (GAN) have achieved promising results in pseudo-healthy synthesis. However, the discriminator (i.e., a classifier) in the GAN cannot accurately identify lesions and further hampers from generating admirable pseudo-healthy images. To address this problem, we present a new type of discriminator, the segmentor, to accurately locate the lesions and improve the visual quality of pseudo-healthy images. Then, we apply the generated images into medical image enhancement and utilize the enhanced results to cope with the low contrast problem existing in medical image segmentation. Furthermore, a reliable metric is proposed by utilizing two attributes of label noise to measure the health of synthetic images. Comprehensive experiments on the T2 modality of BraTS demonstrate that the proposed method substantially outperforms the state-of-the-art methods. The method achieves better performance than the existing methods with only 30% of the training data. The effectiveness of the proposed method is also demonstrated on the LiTS and the T1 modality of BraTS. The code and the pre-trained model of this study are publicly available at https://github.com/Au3C2/Generator-Versus-Segmentor.

The identification of lesion within medical image data is necessary for diagnosis, treatment and prognosis. Segmentation and classification approaches are mainly based on supervised learning with well-paired image-level or voxel-level labels. However, labeling the lesion in medical images is laborious requiring highly specialized knowledge. We propose a medical image synthesis model named abnormal-to-normal translation generative adversarial network (ANT-GAN) to generate a normal-looking medical image based on its abnormal-looking counterpart without the need for paired training data. Unlike typical GANs, whose aim is to generate realistic samples with variations, our more restrictive model aims at producing a normal-looking image corresponding to one containing lesions, and thus requires a special design. Being able to provide a "normal" counterpart to a medical image can provide useful side information for medical imaging tasks like lesion segmentation or classification validated by our experiments. In the other aspect, the ANT-GAN model is also capable of producing highly realistic lesion-containing image corresponding to the healthy one, which shows the potential in data augmentation verified in our experiments.

The segmentation of brain tissue in MRI is valuable for extracting brain structure to aid diagnosis, treatment and tracking the progression of different neurologic diseases. Medical image data are volumetric and some neural network models for medical image segmentation have addressed this using a 3D convolutional architecture. However, this volumetric spatial information has not been fully exploited to enhance the representative ability of deep networks, and these networks have not fully addressed the practical issues facing the analysis of multimodal MRI data. In this paper, we propose a spatially-weighted 3D network (SW-3D-UNet) for brain tissue segmentation of single-modality MRI, and extend it using multimodality MRI data. We validate our model on the MRBrainS13 and MALC12 datasets. This unpublished model ranked first on the leaderboard of the MRBrainS13 Challenge.

Compressed sensing (CS) theory can accelerate multi-contrast magnetic resonance imaging (MRI) by sampling fewer measurements within each contrast. However, conventional optimization-based reconstruction models suffer several limitations, including a strict assumption of shared sparse support, time-consuming optimization, and "shallow" models with difficulties in encoding the patterns contained in massive MRI data. In this paper, we propose the first deep learning model for multi-contrast CS-MRI reconstruction. We achieve information sharing through feature sharing units, which significantly reduces the number of model parameters. The feature sharing unit combines with a data fidelity unit to comprise an inference block, which are then cascaded with dense connections, allowing for efficient information transmission across different depths of the network. Experiments on various multi-contrast MRI datasets show that the proposed model outperforms both state-of-the-art single-contrast and multi-contrast MRI methods in accuracy and efficiency. We demonstrate that improved reconstruction quality can bring benefits to subsequent medical image analysis. Furthermore, the robustness of the proposed model to misregistration shows its potential in real MRI applications.

Compressed sensing magnetic resonance imaging (CS-MRI) is an active research topic in the field of inverse problems. Conventional CS-MRI algorithms usually exploit the sparse nature of MRI in an iterative manner. These optimization-based CS-MRI methods are often time-consuming at test time, and are based on fixed transform bases or shallow dictionaries, which limits modeling capacity. Recently, deep models have been introduced to the CS-MRI problem. One main challenge for CS-MRI methods based on deep learning is the trade off between model performance and network size. We propose a recursive dilated network (RDN) for CS-MRI that achieves good performance while reducing the number of network parameters. We adopt dilated convolutions in each recursive block to aggregate multi-scale information within the MRI. We also adopt a modified shortcut strategy to help features flow into deeper layers. Experimental results show that the proposed RDN model achieves state-of-the-art performance in CS-MRI while using far fewer parameters than previously required.

BACKGROUND: In recent decades, detecting protein complexes (PCs) from protein-protein interaction networks (PPINs) has been an active area of research. There are a large number of excellent graph clustering methods that work very well for identifying PCs. However, most of existing methods usually overlook the inherent core-attachment organization of PCs. Therefore, these methods have three major limitations we should concern. Firstly, many methods have ignored the importance of selecting seed, especially without considering the impact of overlapping nodes as seed nodes. Thus, there may be false predictions. Secondly, PCs are generally supposed to be dense subgraphs. However, the subgraphs with high local modularity structure usually correspond to PCs. Thirdly, a number of available methods lack handling noise mechanism, and miss some peripheral proteins. In summary, all these challenging issues are very important for predicting more biological overlapping PCs. RESULTS: In this paper, to overcome these weaknesses, we propose a clustering method by core-attachment and local modularity structure, named CALM, to detect overlapping PCs from weighted PPINs with noises. Firstly, we identify overlapping nodes and seed nodes. Secondly, for a node, we calculate the support function between a node and a cluster. In CALM, a cluster which initially consists of only a seed node, is extended by adding its direct neighboring nodes recursively according to the support function, until this cluster forms a locally optimal modularity subgraph. Thirdly, we repeat this process for the remaining seed nodes. Finally, merging and removing procedures are carried out to obtain final predicted clusters. The experimental results show that CALM outperforms other classical methods, and achieves ideal overall performance. Furthermore, CALM can match more complexes with a higher accuracy and provide a better one-to-one mapping with reference complexes in all test datasets. Additionally, CALM is robust against the high rate of noise PPIN. CONCLUSIONS: By considering core-attachment and local modularity structure, CALM could detect PCs much more effectively than some representative methods. In short, CALM could potentially identify previous undiscovered overlapping PCs with various density and high modularity.

Compressed sensing theory facilitates the fast magnetic resonance imaging by reducing the required number of measurements for reconstruction. Conventional compressed sensing magnetic resonance imaging(CSMRI) method utilize the partial k-space measurements as a whole without considering their intrinsic property. Some recent researches have shown the advantage of dealing the high and low frequency image content separately. Based on this, we propose a novel CSMRI algorithm based on total variation regularization with k-space decomposition. First we decompose k-space into high frequency band and low frequency band, then we reconstruct the corresponding high and low MR images which will be used for integration later. All the steps can be unified into a objective function. We will show that the proposed objective function can be split into several subproblems to solve iteratively using ADMM technique. The experimental results show that the proposed method outperforms the conventional CSMRI method. Besides, the proposed method can be extended to other image processing applications as well.

Compressed sensing utilizes the sparsity of Magnetic resonance (MR) images to obtain accurate reconstructions from undersampled k-space data. In this paper, a novel nonlocal dynamic MRI reconstruction method with low-rank regularization is developed to exploit the spatiotemporal structural sparsity of a MRI sequence. The nonlocal prior and low rank prior are combined organically by grouping similar patches in both spatial and temporal domain. The low-rank regularization can be approximated by nuclear norm minimization solved by a singular value thresholding (SVT) method with adaptive thresholds estimation. The objective function is divided into several sub-problems that are easier to solve by alternative direction multiplier method (ADMM). Extensive experiments show that the new method outperforms commonly used classical dynamic MRI reconstruction algorithms.