Elucidating genetic and molecular basis of altered higher-order brain structure-function coupling in major depressive disorder.

Previous studies have shown that major depressive disorder (MDD) patients exhibit structural and functional impairments, but few studies have investigated changes in higher-order coupling between structure and function. Here, we systematically investigated the effect of MDD on higher-order coupling between structural connectivity (SC) and functional connectivity (FC). Each brain region was mapped into embedding vector by the node2vec algorithm. We used support vector machine (SVM) with the brain region embedding vector to distinguish MDD patients from health controls (HCs) and identify the most discriminative brain regions. Our study revealed that MDD patients had decreased higher-order coupling in connections between the most discriminative brain regions and local connections in rich-club organization and increased higher-order coupling in connections between the ventral attentional network and limbic network compared with HCs. Interestingly, transcriptome-neuroimaging association analysis demonstrated the correlations between regional rSC-FC coupling variations between MDD patients and HCs and α/ß-hydrolase domain-containing 6 (ABHD6), ß 1,3-N-acetylglucosaminyltransferase-9(ß3GNT9), transmembrane protein 45B (TMEM45B), the correlation between regional dSC-FC coupling variations and retinoic acid early transcript 1E antisense RNA 1(RAET1E-AS1), and the correlations between regional iSC-FC coupling variations and ABHD6, ß3GNT9, katanin-like 2 protein (KATNAL2). In addition, correlation analysis with neurotransmitter receptor/transporter maps found that the rSC-FC and iSC-FC coupling variations were both correlated with neuroendocrine transporter (NET) expression, and the dSC-FC coupling variations were correlated with metabotropic glutamate receptor 5 (mGluR5). Further mediation analysis explored the relationship between genes, neurotransmitter receptor/transporter and MDD related higher-order coupling variations. These findings indicate that specific genetic and molecular factors underpin the observed disparities in higher-order SC-FC coupling between MDD patients and HCs. Our study confirmed that higher-order coupling between SC and FC plays an important role in diagnosing MDD. The identification of new biological evidence for MDD etiology holds promise for the development of innovative antidepressant therapies.

Dielectric Metasurface for Synchronously Spiral Phase Contrast and Bright-Field Imaging.

Spiral phase contrast imaging and bright-field imaging are two widely used modes in microscopy, providing distinct morphological information about objects. However, conventional microscopes are always unable to operate with these two modes at the same time and need additional optical elements to switch between them. Here, we present a microscopy setup that incorporates a dielectric metasurface capable of achieving spiral phase contrast imaging and bright-field imaging synchronously. The metasurface not only can focus the light for diffraction-limited imaging but also can perform a two-dimensional spatial differentiation operation by imparting an orbital angular momentum to the incident light field. This allows two spatially separated images to be simultaneously obtained, one containing high-frequency edge information and the other showing the entirety of the object. Combined with the advantages of planar architecture and ultrathin thickness of the metasurface, this approach is expected to provide support in the fields of microscopy, biomedicine, and materials science.

Deep co-supervision and attention fusion strategy for automatic COVID-19 lung infection segmentation on CT images.

Due to the irregular shapes,various sizes and indistinguishable boundaries between the normal and infected tissues, it is still a challenging task to accurately segment the infected lesions of COVID-19 on CT images. In this paper, a novel segmentation scheme is proposed for the infections of COVID-19 by enhancing supervised information and fusing multi-scale feature maps of different levels based on the encoder-decoder architecture. To this end, a deep collaborative supervision (Co-supervision) scheme is proposed to guide the network learning the features of edges and semantics. More specifically, an Edge Supervised Module (ESM) is firstly designed to highlight low-level boundary features by incorporating the edge supervised information into the initial stage of down-sampling. Meanwhile, an Auxiliary Semantic Supervised Module (ASSM) is proposed to strengthen high-level semantic information by integrating mask supervised information into the later stage. Then an Attention Fusion Module (AFM) is developed to fuse multiple scale feature maps of different levels by using an attention mechanism to reduce the semantic gaps between high-level and low-level feature maps. Finally, the effectiveness of the proposed scheme is demonstrated on four various COVID-19 CT datasets. The results show that the proposed three modules are all promising. Based on the baseline (ResUnet), using ESM, ASSM, or AFM alone can respectively increase Dice metric by 1.12%, 1.95%,1.63% in our dataset, while the integration by incorporating three models together can rise 3.97%. Compared with the existing approaches in various datasets, the proposed method can obtain better segmentation performance in some main metrics, and can achieve the best generalization and comprehensive performance.

A Robust Real Time Direction-of-Arrival Estimation Method for Sequential Movement Events of Vehicles.

Parameters estimation of sequential movement events of vehicles is facing the challenges of noise interferences and the demands of portable implementation. In this paper, we propose a robust direction-of-arrival (DOA) estimation method for the sequential movement events of vehicles based on a small Micro-Electro-Mechanical System (MEMS) microphone array system. Inspired by the incoherent signal-subspace method (ISM), the method that is proposed in this work employs multiple sub-bands, which are selected from the wideband signals with high magnitude-squared coherence to track moving vehicles in the presence of wind noise. The field test results demonstrate that the proposed method has a better performance in emulating the DOA of a moving vehicle even in the case of severe wind interference than the narrowband multiple signal classification (MUSIC) method, the sub-band DOA estimation method, and the classical two-sided correlation transformation (TCT) method.

Seismic target classification using a wavelet packet manifold in unattended ground sensors systems.

One of the most challenging problems in target classification is the extraction of a robust feature, which can effectively represent a specific type of targets. The use of seismic signals in unattended ground sensor (UGS) systems makes this problem more complicated, because the seismic target signal is non-stationary, geology-dependent and with high-dimensional feature space. This paper proposes a new feature extraction algorithm, called wavelet packet manifold (WPM), by addressing the neighborhood preserving embedding (NPE) algorithm of manifold learning on the wavelet packet node energy (WPNE) of seismic signals. By combining non-stationary information and low-dimensional manifold information, WPM provides a more robust representation for seismic target classification. By using a K nearest neighbors classifier on the WPM signature, the algorithm of wavelet packet manifold classification (WPMC) is proposed. Experimental results show that the proposed WPMC can not only reduce feature dimensionality, but also improve the classification accuracy up to 95.03%. Moreover, compared with state-of-the-art methods, WPMC is more suitable for UGS in terms of recognition ratio and computational complexity.

PPNet: Pyramid pooling based network for polyp segmentation.

Colonoscopy is the gold standard method for investigating the gastrointestinal tract. Localizing the polyps in colonoscopy images plays a vital role when doing a colonoscopy screening, and it is also quite important for the following treatment, e.g., polyp resection. Many deep learning-based methods have been applied for solving the polyp segmentation issue. However, precisely polyp segmentation is still an open issue. Considering the effectiveness of the Pyramid Pooling Transformer (P2T) in modeling long-range dependencies and capturing robust contextual features, as well as the power of pyramid pooling in extracting features, we propose a pyramid pooling based network for polyp segmentation, namely PPNet. We first adopt the P2T as the encoder for extracting more powerful features. Next, a pyramid feature fusion module (PFFM) combining the channel attention scheme is utilized for learning a global contextual feature, in order to guide the information transition in the decoder branch. Aiming to enhance the effectiveness of PPNet on feature extraction during the decoder stage layer by layer, we introduce the memory-keeping pyramid pooling module (MPPM) into each side branch of the encoder, and transmit the corresponding feature to each lower-level side branch. Experimental results conducted on five public colorectal polyp segmentation datasets are given and discussed. Our method performs better compared with several state-of-the-art polyp extraction networks, which demonstrate the effectiveness of the mechanism of pyramid pooling for colorectal polyp segmentation.

PLSNet: Position-aware GCN-based autism spectrum disorder diagnosis via FC learning and ROIs sifting.

Brain function connectivity, derived from functional magnetic resonance imaging (fMRI), has enjoyed high popularity in the studies of Autism Spectrum Disorder (ASD) diagnosis. Albeit rapid progress has been made, most studies still suffer from several knotty issues: (1) the hardship of modeling the sophisticated brain neuronal connectivity; (2) the mismatch of identically graph node setup to the variations of different brain regions; (3) the dimensionality explosion resulted from excessive voxels in each fMRI sample; (4) the poor interpretability giving rise to unpersuasive diagnosis. To ameliorate these issues, we propose a position-aware graph-convolution-network-based model, namely PLSNet, with superior accuracy and compelling built-in interpretability for ASD diagnosis. Specifically, a time-series encoder is designed for context-rich feature extraction, followed by a function connectivity generator to model the correlation with long range dependencies. In addition, to discriminate the brain nodes with different locations, the position embedding technique is adopted, giving a unique identity to each graph region. We then embed a rarefying method to sift the salient nodes during message diffusion, which would also benefit the reduction of the dimensionality complexity. Extensive experiments conducted on Autism Brain Imaging Data Exchange demonstrate that our PLSNet achieves state-of-the-art performance. Notably, on CC200 atlas, PLSNet reaches an accuracy of 76.4% and a specificity of 78.6%, overwhelming the previous state-of-the-art with 2.5% and 6.5% under five-fold cross-validation policy. Moreover, the most salient brain regions predicted by PLSNet are closely consistent with the theoretical knowledge in the medical domain, providing potential biomarkers for ASD clinical diagnosis. Our code is available at https://github.com/CodeGoat24/PLSNet.

Adaptively Customizing Activation Functions for Various Layers.

To enhance the nonlinearity of neural networks and increase their mapping abilities between the inputs and response variables, activation functions play a crucial role to model more complex relationships and patterns in the data. In this work, a novel methodology is proposed to adaptively customize activation functions only by adding very few parameters to the traditional activation functions such as Sigmoid, Tanh, and rectified linear unit (ReLU). To verify the effectiveness of the proposed methodology, some theoretical and experimental analysis on accelerating the convergence and improving the performance is presented, and a series of experiments are conducted based on various network models (such as AlexNet, VggNet, GoogLeNet, ResNet and DenseNet), and various datasets (such as CIFAR10, CIFAR100, miniImageNet, PASCAL VOC, and COCO). To further verify the validity and suitability in various optimization strategies and usage scenarios, some comparison experiments are also implemented among different optimization strategies (such as SGD, Momentum, AdaGrad, AdaDelta, and ADAM) and different recognition tasks such as classification and detection. The results show that the proposed methodology is very simple but with significant performance in convergence speed, precision, and generalization, and it can surpass other popular methods such as ReLU and adaptive functions such as Swish in almost all experiments in terms of overall performance.

TaskDrop: A competitive baseline for continual learning of sentiment classification.

In this paper, we study the multi-task sentiment classification problem in the continual learning setting, i.e., a model is sequentially trained to classify the sentiment of reviews of products in a particular category. The use of common sentiment words in reviews of different product categories leads to large cross-task similarity, which differentiates it from continual learning in other domains. This knowledge sharing nature renders forgetting reduction focused approaches less effective for the problem under consideration. Unlike existing approaches, where task-specific masks are learned with specifically presumed training objectives, we propose an approach called Task-aware Dropout (TaskDrop) to randomly sample a binary mask for each task. While the standard dropout generates and applies random masks for each training instance per epoch for regularization, random masks in TaskDrop are used for model capacity allocation and reuse to each coming task. We conducted experimental studies on Amazon review data and made comparison to various baselines and state-of-the-art approaches. Our empirical results show that regardless of simplicity, TaskDrop overall achieved competitive performance, especially after relatively long term learning. This demonstrates that the proposed random capacity allocation mechanism works well for continual sentiment classification.

Colorectal polyp region extraction using saliency detection network with neutrosophic enhancement.

Colorectal polyp recognition is crucial for early colorectal cancer detection and treatment. Colonoscopy is always employed for colorectal polyp scanning. However, one out of four polyps may be ignored, due to the similarity of polyp and normal tissue. In this paper, we present a novel method called NeutSS-PLP for polyp region extraction in colonoscopy images using a short connected saliency detection network with neutrosophic enhancement. We first utilize the neutrosophic theory to enhance the quality of specular reflections detection in the colonoscopy images. We develop the local and global threshold criteria in the single-valued neutrosophic set (SVNS) domain and define the corresponding T (Truth), I (Indeterminacy), and F (Falsity) functions for each criterion. The well-built neutrosophic images are processed and employed for specular reflection detection and suppressing. Next, we introduce two-level short connections into the saliency detection network, aiming to take advantage of the multi-level and multi-scale features extracted from different stages of the network. Experimental results conducted on two public colorectal polyp datasets achieve 0.877 and 0.9135 mIoU for polyp extraction respectively, and our method performs better compared with several state-of-the-art saliency networks and semantic segmentation networks, which demonstrate the effectiveness of applying the saliency detection mechanism for colorectal polyp region extraction.

Generative Adversarial Networks in Medical Image augmentation: A review.

OBJECT: With the development of deep learning, the number of training samples for medical image-based diagnosis and treatment models is increasing. Generative Adversarial Networks (GANs) have attracted attention in medical image processing due to their excellent image generation capabilities and have been widely used in data augmentation. In this paper, a comprehensive and systematic review and analysis of medical image augmentation work are carried out, and its research status and development prospects are reviewed. METHOD: This paper reviews 105 medical image augmentation related papers, which mainly collected by ELSEVIER, IEEE Xplore, and Springer from 2018 to 2021. We counted these papers according to the parts of the organs corresponding to the images, and sorted out the medical image datasets that appeared in them, the loss function in model training, and the quantitative evaluation metrics of image augmentation. At the same time, we briefly introduce the literature collected in three journals and three conferences that have received attention in medical image processing. RESULT: First, we summarize the advantages of various augmentation models, loss functions, and evaluation metrics. Researchers can use this information as a reference when designing augmentation tasks. Second, we explore the relationship between augmented models and the amount of the training set, and tease out the role that augmented models may play when the quality of the training set is limited. Third, the statistical number of papers shows that the development momentum of this research field remains strong. Furthermore, we discuss the existing limitations of this type of model and suggest possible research directions. CONCLUSION: We discuss GAN-based medical image augmentation work in detail. This method effectively alleviates the challenge of limited training samples for medical image diagnosis and treatment models. It is hoped that this review will benefit researchers interested in this field.

Medical image augmentation for lesion detection using a texture-constrained multichannel progressive GAN.

Lesion detectors based on deep learning can assist doctors in diagnosing diseases. However, the performance of current detectors is likely to be unsatisfactory due to the scarcity of training samples. Therefore, it is beneficial to use image generation to augment the training set of a detector. However, when the imaging texture of the medical image is relatively delicate, the synthesized image generated by an existing method may be too poor in quality to meet the training requirements of the detectors. In this regard, a medical image augmentation method, namely, a texture-constrained multichannel progressive generative adversarial network (TMP-GAN), is proposed in this work. TMP-GAN uses joint training of multiple channels to effectively avoid the typical shortcomings of the current generation methods. It also uses an adversarial learning-based texture discrimination loss to further improve the fidelity of the synthesized images. In addition, TMP-GAN employs a progressive generation mechanism to steadily improve the accuracy of the medical image synthesizer. Experiments on the publicly available dataset CBIS-DDMS and our pancreatic tumor dataset show that the precision/recall/F1-score of the detector trained on the TMP-GAN augmented dataset improves by 2.59%/2.70%/2.77% and 2.44%/2.06%/2.36%, respectively, compared to the optimal results of other data augmentation methods. The FROC curve of the detector is also better than the curve from the contrast-augmented trained dataset. Therefore, we believe the proposed TMP-GAN is a practical technique to efficiently implement lesion detection case studies.

An adaptive learning method of anchor shape priors for biological cells detection and segmentation.

BACKGROUND AND OBJECTIVE: Owing to the variable shapes, large size difference, uneven grayscale and dense distribution among biological cells in an image, it is still a challenging task for the standard Mask R-CNN to accurately detect and segment cells. Especially, the state-of-the-art anchor-based methods fail to generate the anchors of sufficient scales effectively according to the various sizes and shapes of cells, thereby hardly covering all scales of cells. METHODS: We propose an adaptive approach to learn the anchor shape priors from data samples, and the aspect ratios and the number of anchor boxes can be dynamically adjusted by using ISODATA clustering algorithm instead of human prior knowledge in this work. To solve the identification difficulties for small objects owing to the multiple down-samplings in a deep learning-based method, a densification strategy of candidate anchors is presented to enhance the effects of identifying tinny size cells. Finally, a series of comparative experiments are conducted on various datasets to select appropriate a network structure and verify the effectiveness of the proposed methods. RESULTS: The results show that the ResNet-50-FPN combining the ISODATA method and densification strategy can obtain better performance than other methods in multiple metrics (including AP, Precision, Recall, Dice and PQ) for various biological cell datasets, such as U373, GoTW1, SIM+ and T24. CONCLUSIONS: Our adaptive algorithm could effectively learn the anchor shape priors from the various sizes and shapes of cells. It is promising and encouraging for a real-world anchor-based detection and segmentation application of biomedical engineering in the future.

A machine and human reader study on AI diagnosis model safety under attacks of adversarial images.

While active efforts are advancing medical artificial intelligence (AI) model development and clinical translation, safety issues of the AI models emerge, but little research has been done. We perform a study to investigate the behaviors of an AI diagnosis model under adversarial images generated by Generative Adversarial Network (GAN) models and to evaluate the effects on human experts when visually identifying potential adversarial images. Our GAN model makes intentional modifications to the diagnosis-sensitive contents of mammogram images in deep learning-based computer-aided diagnosis (CAD) of breast cancer. In our experiments the adversarial samples fool the AI-CAD model to output a wrong diagnosis on 69.1% of the cases that are initially correctly classified by the AI-CAD model. Five breast imaging radiologists visually identify 29%-71% of the adversarial samples. Our study suggests an imperative need for continuing research on medical AI model's safety issues and for developing potential defensive solutions against adversarial attacks.

Broadband generation of perfect Poincaré beams via dielectric spin-multiplexed metasurface.

The term Poincaré beam, which describes the space-variant polarization of a light beam carrying spin angular momentum (SAM) and orbital angular momentum (OAM), plays an important role in various optical applications. Since the radius of a Poincaré beam conventionally depends on the topological charge number, it is difficult to generate a stable and high-quality Poincaré beam by two optical vortices with different topological charge numbers, as the Poincaré beam formed in this way collapses upon propagation. Here, based on an all-dielectric metasurface platform, we experimentally demonstrate broadband generation of a generalized perfect Poincaré beam (PPB), whose radius is independent of the topological charge number. By utilizing a phase-only modulation approach, a single-layer spin-multiplexed metasurface is shown to achieve all the states of PPBs on the hybrid-order Poincaré Sphere for visible light. Furthermore, as a proof-of-concept demonstration, a metasurface encoding multidimensional SAM and OAM states in the parallel channels of elliptical and circular PPBs is implemented for optical information encryption. We envision that this work will provide a compact and efficient platform for generation of PPBs for visible light, and may promote their applications in optical communications, information encryption, optical data storage and quantum information sciences.

Whole Volume Apparent Diffusion Coefficient (ADC) Histogram as a Quantitative Imaging Biomarker to Differentiate Breast Lesions: Correlation with the Ki-67 Proliferation Index.

OBJECTIVES: To evaluate the value of the whole volume apparent diffusion coefficient (ADC) histogram in distinguishing between benign and malignant breast lesions and differentiating different molecular subtypes of breast cancers and to assess the correlation between ADC histogram parameters and Ki-67 expression in breast cancers. METHODS: The institutional review board approved this retrospective study. Between September 2016 and February 2019, 189 patients with 84 benign lesions and 105 breast cancers underwent magnetic resonance imaging (MRI). Volumetric ADC histograms were created by placing regions of interest (ROIs) on the whole lesion. The relationships between the ADC parameters and Ki-67 were analysed using Spearman's correlation analysis. RESULTS: Of the 189 breast lesions included, there were significant differences in patient age (P < 0.001) and lesion size (P = 0.006) between the benign and malignant lesions. The results also demonstrated significant differences in all ADC histogram parameters between benign and malignant lesions (all P < 0.001). The median and mean ADC histogram parameters performed better than the other ADC histogram parameters (AUCs were 0.943 and 0.930, respectively). The receiver operating characteristic (ROC) analysis revealed that the 10th percentile ADC value and entropy could determine the human epidermal growth factor receptor 2 (HER-2) status (both P = 0.001) and estrogen receptor (ER)/progesterone receptor (PR) status (P = 0.020 and P = 0.041, respectively). Among all breast cancer lesions, 35 tumours in the low-proliferation group (Ki - 67 < 14%) and 70 tumours in the high-proliferation group (Ki - 67 ≥ 14) were analysed with ROC curves and correlation analyses. The ROC analysis revealed that entropy and skewness could determine the Ki-67 status (P = 0.007 and P < 0.001, respectively), and there were weak correlations between ADC entropy (r = 0.383) and skewness (r = 0.209) and the Ki-67 index. CONCLUSION: The volumetric ADC histogram could serve as an imaging marker to determine breast lesion characteristics and may be a supplemental method in predicting tumour proliferation in breast cancer.