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Background: The acquisition of contrast-enhanced T1 maps to calculate extracellular volume (ECV) requires contrast agent administration and is time consuming. This study investigates generative adversarial networks for contrast-free, virtual extracellular volume (vECV) by generating virtual contrast-enhanced T1 maps., Methods and Results: This retrospective study includes 2518 registered native and contrast-enhanced T1 maps from 1000 patients who underwent cardiovascular magnetic resonance at 1.5 Tesla. Recent hematocrit values of 123 patients (hold-out test) and 96 patients from a different institution (external evaluation) allowed for calculation of conventional ECV. A generative adversarial network was trained to generate virtual contrast-enhanced T1 maps from native T1 maps for vECV creation. Mean and SD of the difference per patient (ΔECV) were calculated and compared by permutation of the 2-sided t test with 10 000 resamples. For ECV and vECV, differences in area under the receiver operating characteristic curve (AUC) for discriminating hold-out test patients with normal cardiovascular magnetic resonance versus myocarditis or amyloidosis were tested with Delong's test. ECV and vECV showed a high agreement in patients with myocarditis (ΔECV: hold-out test, 2.0%±1.5%; external evaluation, 1.9%±1.7%) and normal cardiovascular magnetic resonance (ΔECV: hold-out test, 1.9%±1.4%; external evaluation, 1.5%±1.2%), but variations in amyloidosis were higher (ΔECV: hold-out test, 6.2%±6.0%; external evaluation, 15.5%±6.4%). In the hold-out test, ECV and vECV had a comparable AUC for the diagnosis of myocarditis (ECV AUC, 0.77 versus vECV AUC, 0.76; P =0.76) and amyloidosis (ECV AUC, 0.99 versus vECV AUC, 0.96; P =0.52)., Conclusions: Generation of vECV on the basis of native T1 maps is feasible. Multicenter training data are required to further enhance generalizability of vECV in amyloidosis.

Some pathologies such as cancer and dementia require multiple imaging modalities to fully diagnose and assess the extent of the disease. Magnetic resonance imaging offers this kind of polyvalence, but examinations take time and can require contrast agent injection. The flexible synthesis of these imaging sequences based on the available ones for a given patient could help reduce scan times or circumvent the need for contrast agent injection. In this work, we propose a deep learning architecture that can perform the synthesis of all missing imaging sequences from any subset of available images. The network is trained adversarially, with the generator consisting of parallel 3D U-Net encoders and decoders that optimally combines their multi-resolution representations with a fusion operation learned by an attention network trained conjointly with the generator network. We compare our synthesis performance with 3D networks using other types of fusion and a comparable number of trainable parameters, such as the mean/variance fusion. In all synthesis scenarios except one, the synthesis performance of the network using attention-guided fusion was better than the other fusion schemes. We also inspect the encoded representations and the attention network outputs to gain insights into the synthesis process, and uncover desirable behaviors such as prioritization of specific modalities, flexible construction of the representation when important modalities are missing, and modalities being selected in regions where they carry sequence-specific information. This work suggests that a better construction of the latent representation space in hetero-modal networks can be achieved by using an attention network., (© 2024 IOP Publishing Ltd. All rights, including for text and data mining, AI training, and similar technologies, are reserved.)

The authenticity of salted goose products is concerning for consumers. This study describes an integrated deep-learning framework based on a generative adversarial network and combines it with data from headspace solid phase microextraction/gas chromatography-mass spectrometry, headspace gas chromatography-ion mobility spectrometry, E-nose, E-tongue, quantitative descriptive analysis, and free amino acid and 5'-nucleotide analyses to achieve reliable discrimination of four salted goose breeds. Volatile and non-volatile compounds and sensory characteristics and intelligent sensory characteristics were analyzed. A preliminary composite dataset was generated in InfoGAN and provided to several base classifiers for training. The prediction results were fused via dynamic weighting to produce an integrated model prediction. An ablation study demonstrated that ensemble learning was indispensable to improving the generalization capability of the model. The framework has an accuracy of 95%, a root mean square error (RMSE) of 0.080, a precision of 0.9450, a recall of 0.9470, and an F1-score of 0.9460., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Medical imaging datasets for research are frequently collected from multiple imaging centers using different scanners, protocols, and settings. These variations affect data consistency and compatibility across different sources. Image harmonization is a critical step to mitigate the effects of factors like inherent differences between various vendors, hardware upgrades, protocol changes, and scanner calibration drift, as well as to ensure consistent data for medical image processing techniques. Given the critical importance and widespread relevance of this issue, a vast array of image harmonization methodologies have emerged, with deep learning-based approaches driving substantial advancements in recent times. The goal of this review paper is to examine the latest deep learning techniques employed for image harmonization by analyzing cutting-edge architectural approaches in the field of medical image harmonization, evaluating both their strengths and limitations. This paper begins by providing a comprehensive fundamental overview of image harmonization strategies, covering three critical aspects: established imaging datasets, commonly used evaluation metrics, and characteristics of different scanners. Subsequently, this paper analyzes recent structural MRI (Magnetic Resonance Imaging) harmonization techniques based on network architecture, network learning algorithm, network supervision strategy, and network output. The underlying architectures include U-Net, Generative Adversarial Networks (GANs), Variational Autoencoders (VAEs), flow-based generative models, transformer-based approaches, as well as custom-designed network architectures. This paper investigates the effectiveness of Disentangled Representation Learning (DRL) as a pivotal learning algorithm in harmonization. Lastly, the review highlights the primary limitations in harmonization techniques, specifically the lack of comprehensive quantitative comparisons across different methods. The overall aim of this review is to serve as a guide for researchers and practitioners to select appropriate architectures based on their specific conditions and requirements. It also aims to foster discussions around ongoing challenges in the field and shed light on promising future research directions with the potential for significant advancements., (© 2024. The Author(s).)

Background and Objectives: This study aims to develop and evaluate NeuNN, a system based on convolutional neural networks (CNN) and generative adversarial networks (GAN) for the automatic identification of normal neutrophils and those containing several types of inclusions or showing hypogranulation., Methods: From peripheral blood smears, a set of 5605 digital images was obtained with neutrophils belonging to seven categories: Normal neutrophils (NEU), Hypogranulated (HYP) or containing cryoglobulins (CRY), Döhle bodies (DB), Howell-Jolly body-like inclusions (HJBLI), Green-blue inclusions of death (GBI) and phagocytosed bacteria (BAC). The dataset utilized in this study has been made publicly available. The class of GBI was augmented using synthetic images generated by GAN. The NeuNN classification model is based on an EfficientNet-B7 architecture trained from scratch., Results: NeuNN achieved an overall performance of 94.3% accuracy on the test data set. Performance metrics, including sensitivity, specificity, precision, F1-Score, Jaccard index, and Matthews correlation coefficient indicated overall values of 94%, 99.1%, 94.3%, 94.3%, 89.6%, and 93.6%, respectively., Conclusions: The proposed approach, combining data augmentation and classification techniques, allows for automated identification of morphological findings in neutrophils, such us inclusions or hypogranulation. The system can be used as a support tool for clinical pathologists to detect these specific abnormalities with clinical relevance., Competing Interests: Declaration of competing interest We wish to confirm that there are no known conflicts of interest associated with this publication and there has been no significant financial support for this work that could have influenced its outcome., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition that affects an individual's behavior, speech, and social interaction. Early and accurate diagnosis of ASD is pivotal for successful intervention. The limited availability of large datasets for neuroimaging investigations, however, poses a significant challenge to the timely and precise identification of ASD. To address this problem, we propose a breakthrough approach, GARL, for ASD diagnosis using neuroimaging data. GARL innovatively integrates the power of GANs and Deep Q-Learning to augment limited datasets and enhance diagnostic precision. We utilized the Autistic Brain Imaging Data Exchange (ABIDE) I and II datasets and employed a GAN to expand these datasets, creating a more robust and diversified dataset for analysis. This approach not only captures the underlying sample distribution within ABIDE I and II but also employs deep reinforcement learning for continuous self-improvement, significantly enhancing the capability of the model to generalize and adapt. Our experimental results confirmed that GAN-based data augmentation effectively improved the performance of all prediction models on both datasets, with the combination of InfoGAN and DQN's GARL yielding the most notable improvement., (© 2024. The Author(s).)

Purpose: To evaluate CycleGAN's ability to enhance T2-weighted image (T2WI) quality., Method: A CycleGAN algorithm was used to enhance T2WI quality. 96 patients (192 scans) were identified from patients who underwent multiple axial T2WI due to poor quality on the first attempt (RAD1) and improved quality on re-acquisition (RAD2). CycleGAN algorithm gave DL classifier scores (0-1) for quality quantification and produced enhanced versions of QI1 and QI2 from RAD1 and RAD2, respectively. A subset (n = 20 patients) was selected for a blinded, multi-reader study, where four radiologists rated T2WI on a scale of 1-4 for quality. The multi-reader study presented readers with 60 image pairs (RAD1 vs RAD2, RAD1 vs QI1, and RAD2 vs QI2), allowing for selecting sequence preferences and quantifying the quality changes., Results: The DL classifier correctly discerned 71.9 % of quality classes, with 90.6 % (96/106) as poor quality and 48.8 % (42/86) as diagnostic in original sequences (RAD1, RAD2). CycleGAN images (QI1, QI2) demonstrated quantitative improvements, with consistently higher DL classifier scores than original scans (p < 0.001). In the multi-reader analysis, CycleGAN demonstrated no qualitative improvements, with diminished overall quality and motion in QI2 in most patients compared to RAD2, with noise levels remaining similar (8/20). No readers preferred QI2 to RAD2 for diagnosis., Conclusion: Despite quantitative enhancements with CycleGAN, there was no qualitative boost in T2WI diagnostic quality, noise, or motion. Expert radiologists didn't favor CycleGAN images over standard scans, highlighting the divide between quantitative and qualitative metrics., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

With the wide application of deep learning in Drug Discovery, deep generative model has shown its advantages in drug molecular generation. Generative adversarial networks can be used to learn the internal structure of molecules, but the training process may be unstable, such as gradient disappearance and model collapse, which may lead to the generation of molecules that do not conform to chemical rules or a single style. In this paper, a novel method called STAGAN was proposed to solve the difficulty of model training, by adding a new gradient penalty term in the discriminator and designing a parallel layer of batch normalization used in generator. As an illustration of method, STAGAN generated higher valid and unique molecules than previous models in training datasets from QM9 and ZINC-250K. This indicates that the proposed method can effectively solve the instability problem in the model training process, and can provide more instructive guidance for the further study of molecular graph generation., Competing Interests: Declaration of competing interest The authors declare no competing financial interest., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: In this work, we applied and validated an artificial intelligence technique known as generative adversarial networks (GANs) to create large volumes of high-fidelity synthetic anteroposterior (AP) pelvis radiographs that can enable deep learning (DL)-based image analyses, while ensuring patient privacy., Methods: AP pelvis radiographs with native hips were gathered from an institutional registry between 1998 and 2018. The data was used to train a model to create 512 × 512 pixel synthetic AP pelvis images. The network was trained on 25 million images produced through augmentation. A set of 100 random images (50/50 real/synthetic) was evaluated by 3 orthopaedic surgeons and 2 radiologists to discern real versus synthetic images. Two models (joint localization and segmentation) were trained using synthetic images and tested on real images., Results: The final model was trained on 37,640 real radiographs (16,782 patients). In a computer assessment of image fidelity, the final model achieved an "excellent" rating. In a blinded review of paired images (1 real, 1 synthetic), orthopaedic surgeon reviewers were unable to correctly identify which image was synthetic (accuracy = 55%, Kappa = 0.11), highlighting synthetic image fidelity. The synthetic and real images showed equivalent performance when they were assessed by established DL models., Conclusion: This work shows the ability to use a DL technique to generate a large volume of high-fidelity synthetic pelvis images not discernible from real imaging by computers or experts. These images can be used for cross-institutional sharing and model pretraining, further advancing the performance of DL models without risk to patient data safety., Level of Evidence: Level III., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background: Although susceptibility-weighted imaging (SWI) is the gold standard for visualizing cerebral microbleeds (CMBs) in the brain, the required phase data are not always available clinically. Having a postprocessing tool for generating SWI contrast from T2*-weighted magnitude images is therefore advantageous., Purpose: To create synthetic SWI images from clinical T2*-weighted magnitude images using deep learning and evaluate the resulting images in terms of similarity to conventional SWI images and ability to detect radiation-associated CMBs., Study Type: Retrospective., Population: A total of 145 adults (87 males/58 females; 43.9 years old) with radiation-associated CMBs were used to train (16,093 patches/121 patients), validate (484 patches/4 patients), and test (2420 patches/20 patients) our networks., Field Strength/sequence: 3D T2*-weighted, gradient-echo acquired at 3 T., Assessment: Structural similarity index (SSIM), peak signal-to-noise-ratio (PSNR), normalized mean-squared-error (nMSE), CMB counts, and line profiles were compared among magnitude, original SWI, and synthetic SWI images. Three blinded raters (J.E.V.M., M.A.M., B.B. with 8-, 6-, and 4-years of experience, respectively) independently rated and classified test-set images., Statistical Tests: Kruskall-Wallis and Wilcoxon signed-rank tests were used to compare SSIM, PSNR, nMSE, and CMB counts among magnitude, original SWI, and predicted synthetic SWI images. Intraclass correlation assessed interrater variability. P values <0.005 were considered statistically significant., Results: SSIM values of the predicted vs. original SWI (0.972, 0.995, 0.9864) were statistically significantly higher than that of the magnitude vs. original SWI (0.970, 0.994, 0.9861) for whole brain, vascular structures, and brain tissue regions, respectively; 67% (19/28) CMBs detected on original SWI images were also detected on the predicted SWI, whereas only 10 (36%) were detected on magnitude images. Overall image quality was similar between the synthetic and original SWI images, with less artifacts on the former., Conclusions: This study demonstrated that deep learning can increase the susceptibility contrast present in neurovasculature and CMBs on T2*-weighted magnitude images, without residual susceptibility-induced artifacts. This may be useful for more accurately estimating CMB burden from magnitude images alone., Evidence Level: 3., Technical Efficacy: Stage 2., (© 2023 International Society for Magnetic Resonance in Medicine.)

Early melanoma diagnosis is the most important factor in the treatment of skin cancer and can effectively reduce mortality rates. Recently, Generative Adversarial Networks have been used to augment data, prevent overfitting and improve the diagnostic capacity of models. However, its application remains a challenging task due to the high levels of inter and intra-class variance seen in skin images, limited amounts of data, and model instability. We present a more robust Progressive Growing of Adversarial Networks based on residual learning, which is highly recommended to ease the training of deep networks. The stability of the training process was increased by receiving additional inputs from preceding blocks. The architecture is able to produce plausible photorealistic synthetic 512 × 512 skin images, even with small dermoscopic and non-dermoscopic skin image datasets as problem domains. In this manner, we tackle the lack of data and the imbalance problems. Additionally, the proposed approach leverages a skin lesion boundary segmentation algorithm and transfer learning to enhance the diagnosis of melanoma. Inception score and Matthews Correlation Coefficient were used to measure the performance of the models. The architecture was evaluated qualitatively and quantitatively through the use of an extensive experimental study on sixteen datasets, illustrating its effectiveness in the diagnosis of melanoma. Finally, four state-of-the-art data augmentation techniques applied in five convolutional neural network models were significantly outperformed. The results indicated that a bigger number of trainable parameters will not necessarily obtain a better performance in melanoma diagnosis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Purpose: To determine whether a deep learning approach using generative adversarial networks (GANs) is beneficial for the classification of retinal conditions with Optical coherence tomography (OCT) images., Methods: Our study utilized 84,452 retinal OCT images obtained from a publicly available dataset (Kermany Dataset). Employing GAN, synthetic OCT images are produced to balance classes of retinal disorders. A deep learning classification model is constructed using pretrained deep neural networks (DNNs), and outcomes are evaluated using 2082 images collected from patients who visited the Department of Ophthalmology and the Department of Endocrinology and Metabolism at the Tri-service General Hospital in Taipei from January 2017 to December 2021., Results: The highest classification accuracies accomplished by deep learning machines trained on the unbalanced dataset for its training set, validation set, fivefold cross validation (CV), Kermany test set, and TSGH test set were 97.73%, 96.51%, 97.14%, 99.59%, and 81.03%, respectively. The highest classification accuracies accomplished by deep learning machines trained on the synthesis-balanced dataset for its training set, validation set, fivefold CV, Kermany test set, and TSGH test set were 98.60%, 98.41%, 98.52%, 99.38%, and 84.92%, respectively. In comparing the highest accuracies, deep learning machines trained on the synthesis-balanced dataset outperformed deep learning machines trained on the unbalanced dataset for the training set, validation set, fivefold CV, and TSGH test set., Conclusions: Overall, deep learning machines on a synthesis-balanced dataset demonstrated to be advantageous over deep learning machines trained on an unbalanced dataset for the classification of retinal conditions., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Previous studies have explored resting-state functional connectivity (rs-FC) of the amygdala in patients with autism spectrum disorder (ASD). However, it remains unclear whether there are frequency-specific FC alterations of the amygdala in ASD and whether FC in specific frequency bands can be used to distinguish patients with ASD from typical controls (TCs). Data from 306 patients with ASD and 314 age-matched and sex-matched TCs were collected from 28 sites in the Autism Brain Imaging Data Exchange database. The bilateral amygdala, defined as the seed regions, was used to perform seed-based FC analyses in the conventional, slow-5, and slow-4 frequency bands at each site. Image-based meta-analyses were used to obtain consistent brain regions across 28 sites in the three frequency bands. By combining generative adversarial networks and deep neural networks, a deep learning approach was applied to distinguish patients with ASD from TCs. The meta-analysis results showed frequency band specificity of FC in ASD, which was reflected in the slow-5 frequency band instead of the conventional and slow-4 frequency bands. The deep learning results showed that, compared with the conventional and slow-4 frequency bands, the slow-5 frequency band exhibited a higher accuracy of 74.73%, precision of 74.58%, recall of 75.05%, and area under the curve of 0.811 to distinguish patients with ASD from TCs. These findings may help us to understand the pathological mechanisms of ASD and provide preliminary guidance for the clinical diagnosis of ASD., (© 2022 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.)

Recent advances in Deep Learning have largely benefited from larger and more diverse training sets. However, collecting large datasets for medical imaging is still a challenge due to privacy concerns and labeling costs. Data augmentation makes it possible to greatly expand the amount and variety of data available for training without actually collecting new samples. Data augmentation techniques range from simple yet surprisingly effective transformations such as cropping, padding, and flipping, to complex generative models. Depending on the nature of the input and the visual task, different data augmentation strategies are likely to perform differently. For this reason, it is conceivable that medical imaging requires specific augmentation strategies that generate plausible data samples and enable effective regularization of deep neural networks. Data augmentation can also be used to augment specific classes that are underrepresented in the training set, e.g., to generate artificial lesions. The goal of this systematic literature review is to investigate which data augmentation strategies are used in the medical domain and how they affect the performance of clinical tasks such as classification, segmentation, and lesion detection. To this end, a comprehensive analysis of more than 300 articles published in recent years (2018-2022) was conducted. The results highlight the effectiveness of data augmentation across organs, modalities, tasks, and dataset sizes, and suggest potential avenues for future research., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Advances in electron microscopy (EM) such as electron tomography and focused ion-beam scanning electron microscopy provide unprecedented, three-dimensional views of cardiac ultrastructures within sample volumes ranging from hundreds of nanometres to hundreds of micrometres. The datasets from these samples are typically large, with file sizes ranging from gigabytes to terabytes and the number of image slices within the three-dimensional stack in the hundreds. A significant bottleneck with these large datasets is the time taken to extract and statistically analyse three-dimensional changes in cardiac ultrastructures. This is because of the inherently low contrast and the significant amount of structural detail that is present in EM images. These datasets often require manual annotation, which needs substantial person-hours and may result in only partial segmentation that makes quantitative analysis of the three-dimensional volumes infeasible. We present CardioVinci, a deep learning workflow to automatically segment and statistically quantify the morphologies and spatial assembly of mitochondria, myofibrils and Z-discs with minimal manual annotation. The workflow encodes a probabilistic model of the three-dimensional cardiomyocyte using a generative adversarial network. This generative model can be used to create new models of cardiomyocyte architecture that reflect variations in morphologies and cell architecture found in EM datasets. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.

Recently, artificial intelligence (AI) based on IoT sensors has been widely used, which has increased the risk of attacks targeting AI. Adversarial examples are among the most serious types of attacks in which the attacker designs inputs that can cause the machine learning system to generate incorrect outputs. Considering the architecture using multiple sensor devices, hacking even a few sensors can create a significant risk; an attacker can attack the machine learning model through the hacked sensors. Some studies demonstrated the possibility of adversarial examples on the deep neural network (DNN) model based on IoT sensors, but it was assumed that an attacker must access all features. The impact of hacking only a few sensors has not been discussed thus far. Therefore, in this study, we discuss the possibility of attacks on DNN models by hacking only a small number of sensors. In this scenario, the attacker first hacks few sensors in the system, obtains the values of the hacked sensors, and changes them to manipulate the system, but the attacker cannot obtain and change the values of the other sensors. We perform experiments using the human activity recognition model with three sensor devices attached to the chest, wrist, and ankle of a user, and demonstrate that attacks are possible by hacking a small number of sensors.

Deep learning biomechanical models perform optimally when trained with large datasets, however these can be challenging to collect in gait labs, while limited augmentation techniques are available. This study presents a data augmentation approach based on generative adversarial networks which generate synthetic motion capture (mocap) datasets of marker trajectories and ground reaction forces (GRFs). The proposed architecture, called adversarial autoencoder, consists of an encoder compressing mocap data to a latent vector, a decoder reconstructing the mocap data from the latent vector and a discriminator distinguishing random vectors from encoded latent vectors. Direct kinematics (DK) and inverse kinematics (IK) joint angles, GRFs, and inverse dynamics (ID) joint moments calculated for real and synthetic trials were compared using statistical parametric mapping to assure realistic data generation and select optimal architectural hyperparameters based on percentage average differences across the gait cycle length. We observed negligible differences for DK computed joint angles and GRFs, but not for inverse methods (IK: 29.2%, ID: 35.5%). When the same architecture was trained also including the joint angles calculated by IK, we found no significant differences in the kinematics and GRFs, and improvements in joint moments estimation (ID: 25.7%). Finally, we showed that our data augmentation approach improved the accuracy of joint kinematics (up to 23%, 0.8°) and vertical GRFs (11%) predicted by standard neural networks using a single simulated pelvic inertial measurement unit. These findings suggest that predictive deep learning models can benefit from the synthetic datasets produced with the proposed technique., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The L1000 technology, a cost-effective high-throughput transcriptomics technology, has been applied to profile a collection of human cell lines for their gene expression response to > 30,000 chemical and genetic perturbations. In total, there are currently over 3 million available L1000 profiles. Such a dataset is invaluable for the discovery of drug and target candidates and for inferring mechanisms of action for small molecules. The L1000 assay only measures the mRNA expression of 978 landmark genes while 11,350 additional genes are computationally reliably inferred. The lack of full genome coverage limits knowledge discovery for half of the human protein coding genes, and the potential for integration with other transcriptomics profiling data. Here we present a Deep Learning two-step model that transforms L1000 profiles to RNA-seq-like profiles. The input to the model are the measured 978 landmark genes while the output is a vector of 23,614 RNA-seq-like gene expression profiles. The model first transforms the landmark genes into RNA-seq-like 978 gene profiles using a modified CycleGAN model applied to unpaired data. The transformed 978 RNA-seq-like landmark genes are then extrapolated into the full genome space with a fully connected neural network model. The two-step model achieves 0.914 Pearson's correlation coefficients and 1.167 root mean square errors when tested on a published paired L1000/RNA-seq dataset produced by the LINCS and GTEx programs. The processed RNA-seq-like profiles are made available for download, signature search, and gene centric reverse search with unique case studies., (© 2022. The Author(s).)

The deterioration of infrastructure's health has become more predominant on a global scale during the 21st century. Aging infrastructure as well as those structures damaged by natural disasters have prompted the research community to improve state-of-the-art methodologies for conducting Structural Health Monitoring (SHM). The necessity for efficient SHM arises from the hazards damaged infrastructure imposes, often resulting in structural collapse, leading to economic loss and human fatalities. Furthermore, day-to-day operations in these affected areas are limited until an inspection is performed to assess the level of damage experienced by the structure and the required rehabilitation determined. However, human-based inspections are often labor-intensive, inefficient, subjective, and restricted to accessible site locations, which ultimately negatively impact our ability to collect large amounts of data from inspection sites. Though Deep-Learning (DL) methods have been heavily explored in the past decade to rectify the limitations of traditional methods and automate structural inspection, data scarcity continues to remain prevalent within the field of SHM. The absence of sufficiently large, balanced, and generalized databases to train DL-based models often results in inaccurate and biased damage predictions. Recently, Generative Adversarial Networks (GANs) have received attention from the SHM community as a data augmentation tool by which a training dataset can be expanded to improve the damage classification. However, there are no existing studies within the SHM field which investigate the performance of DL-based multiclass damage identification using synthetic data generated from GANs. Therefore, this paper investigates the performance of a convolutional neural network architecture using synthetic images generated from a GAN for multiclass damage detection of concrete surfaces. Through this study, it was determined the average classification performance of the proposed CNN on hybrid datasets decreased by 10.6% and 7.4% for validation and testing datasets when compared to the same model trained entirely on real samples. Moreover, each model's performance decreased on average by 1.6% when comparing a singular model trained with real samples and the same model trained with both real and synthetic samples for a given training configuration. The correlation between classification accuracy and the amount and diversity of synthetic data used for data augmentation is quantified and the effect of using limited data to train existing GAN architectures is investigated. It was observed that the diversity of the samples decreases and correlation increases with the increase in the number of synthetic samples.

Background: Retinal pigment epithelium (RPE) aging is an important cause of vision loss. As RPE aging is accompanied by changes in cell morphological features, an accurate segmentation of RPE cells is a prerequisite to such morphology analyses. Due the overwhelmingly large cell number, manual annotations of RPE cell borders are time-consuming. Computer based methods do not work well on cells with weak or missing borders in the impaired RPE sheet regions., Method: To address such a challenge, we develop a semi-supervised deep learning approach, namely MultiHeadGAN, to segment low contrast cells from impaired regions in RPE flatmount images. The developed deep learning model has a multi-head structure that allows model training with only a small scale of human annotated data. To strengthen model learning, we further train our model with RPE cells without ground truth cell borders by generative adversarial networks. Additionally, we develop a new shape loss to guide the network to produce closed cell borders in the segmentation results., Results: In this study, 155 annotated and 1,640 unlabeled image patches are included for model training. The testing dataset consists of 200 image patches presenting large impaired RPE regions. The average RPE segmentation performance of the developed model MultiHeadGAN is 85.4 (correct rate), 88.8 (weighted correct rate), 87.3 (precision), and 80.1 (recall), respectively. Compared with other state-of-the-art deep learning approaches, our method demonstrates its superior qualitative and quantitative performance., Conclusions: Suggested by our extensive experimental results, our developed deep learning method can accurately segment cells in RPE flatmount microscopy images and is promising to support large scale cell morphological analyses for RPE aging investigations., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Deep learning has remarkably impacted several different scientific disciplines over the last few years. For example, in image processing and analysis, deep learning algorithms were able to outperform other cutting-edge methods. Additionally, deep learning has delivered state-of-the-art results in tasks like autonomous driving, outclassing previous attempts. There are even instances where deep learning outperformed humans, for example with object recognition and gaming. Deep learning is also showing vast potential in the medical domain. With the collection of large quantities of patient records and data, and a trend towards personalized treatments, there is a great need for automated and reliable processing and analysis of health information. Patient data is not only collected in clinical centers, like hospitals and private practices, but also by mobile healthcare apps or online websites. The abundance of collected patient data and the recent growth in the deep learning field has resulted in a large increase in research efforts. In Q2/2020, the search engine PubMed returned already over 11,000 results for the search term 'deep learning', and around 90% of these publications are from the last three years. However, even though PubMed represents the largest search engine in the medical field, it does not cover all medical-related publications. Hence, a complete overview of the field of 'medical deep learning' is almost impossible to obtain and acquiring a full overview of medical sub-fields is becoming increasingly more difficult. Nevertheless, several review and survey articles about medical deep learning have been published within the last few years. They focus, in general, on specific medical scenarios, like the analysis of medical images containing specific pathologies. With these surveys as a foundation, the aim of this article is to provide the first high-level, systematic meta-review of medical deep learning surveys., Competing Interests: Declaration of Competing Interest The authors declare no competing financial interests., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)

Automated synthesis of histology images has several potential applications including the development of data-efficient deep learning algorithms. In the field of computational pathology, where histology images are large in size and visual context is crucial, synthesis of large high-resolution images via generative modeling is an important but challenging task due to memory and computational constraints. To address this challenge, we propose a novel framework called SAFRON (Stitching Across the FROntier Network) to construct realistic, large high-resolution tissue images conditioned on input tissue component masks. The main novelty in the framework is integration of stitching in its loss function which enables generation of images of arbitrarily large sizes after training on relatively small image patches while preserving morphological features with minimal boundary artifacts. We have used the proposed framework for generating, to the best of our knowledge, the largest-sized synthetic histology images to date (up to 11K×8K pixels). Compared to existing approaches, our framework is efficient in terms of the memory required for training and computations needed for synthesizing large high-resolution images. The quality of generated images was assessed quantitatively using Frechet Inception Distance as well as by 7 trained pathologists, who assigned a realism score to a set of images generated by SAFRON. The average realism score across all pathologists for synthetic images was as high as that of real images. We also show that training with additional synthetic data generated by SAFRON can significantly boost prediction performance of gland segmentation and cancer detection algorithms in colorectal cancer histology images., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

Deep learning (DL) is being successfully applied across multiple domains, yet these models learn in a most artificial way: they require large quantities of labeled data to grasp even simple concepts. Thus, the main bottleneck is often access to supervised data. Here, we highlight a trend in a potential solution to this challenge: synthetic data. Synthetic data are becoming accessible due to progress in rendering pipelines, generative adversarial models, and fusion models. Moreover, advancements in domain adaptation techniques help close the statistical gap between synthetic and real data. Paradoxically, this artificial solution is also likely to enable more natural learning, as seen in biological systems, including continual, multimodal, and embodied learning. Complementary to this, simulators and deep neural networks (DNNs) will also have a critical role in providing insight into the cognitive and neural functioning of biological systems. We also review the strengths of, and opportunities and novel challenges associated with, synthetic data., Competing Interests: Declaration of interests None declared by authors., (Published by Elsevier Ltd.)

The antibody drug field has continually sought improvements to methods for candidate discovery and engineering. Historically, most such methods have been laboratory-based, but informatics methods have recently started to make an impact. Deep learning, a subfield of machine learning, is rapidly gaining prominence in the biomedical research. Recent advances in microfluidics technologies and next-generation sequencing have not only revolutionized therapeutic antibody discovery, but also contributed to a vast amount of antibody repertoire sequencing data, providing opportunities for deep learning-based applications. Previously, we used microfluidics, yeast display, and deep sequencing to generate a panel of binder and non-binder antibody sequences to the cancer immunotherapy targets PD-1 and CTLA-4. Here we encoded the antibody light and heavy chain complementarity-determining regions (CDR3s) into antibody images, then built and trained convolutional neural network models to classify binders and non-binders. To improve model interpretability, we performed in silico mutagenesis to identify CDR3 residues that were important for binder classification. We further built generative deep learning models using generative adversarial network models to produce synthetic antibodies against PD-1 and CTLA-4. Our models generated variable length CDR3 sequences that resemble real sequences. Overall, our study demonstrates that deep learning methods can be leveraged to mine and learn patterns in antibody sequences, offering insights into antibody engineering, optimization, and discovery.

In the past few years, de novo molecular design has increasingly been using generative models from the emergent field of Deep Learning, proposing novel compounds that are likely to possess desired properties or activities. De novo molecular design finds applications in different fields ranging from drug discovery and materials sciences to biotechnology. A panoply of deep generative models, including architectures as Recurrent Neural Networks, Autoencoders, and Generative Adversarial Networks, can be trained on existing data sets and provide for the generation of novel compounds. Typically, the new compounds follow the same underlying statistical distributions of properties exhibited on the training data set Additionally, different optimization strategies, including transfer learning, Bayesian optimization, reinforcement learning, and conditional generation, can direct the generation process toward desired aims, regarding their biological activities, synthesis processes or chemical features. Given the recent emergence of these technologies and their relevance, this work presents a systematic and critical review on deep generative models and related optimization methods for targeted compound design, and their applications.

Emerging research shows that circular RNA (circRNA) plays a crucial role in the diagnosis, occurrence and prognosis of complex human diseases. Compared with traditional biological experiments, the computational method of fusing multi-source biological data to identify the association between circRNA and disease can effectively reduce cost and save time. Considering the limitations of existing computational models, we propose a semi-supervised generative adversarial network (GAN) model SGANRDA for predicting circRNA-disease association. This model first fused the natural language features of the circRNA sequence and the features of disease semantics, circRNA and disease Gaussian interaction profile kernel, and then used all circRNA-disease pairs to pre-train the GAN network, and fine-tune the network parameters through labeled samples. Finally, the extreme learning machine classifier is employed to obtain the prediction result. Compared with the previous supervision model, SGANRDA innovatively introduced circRNA sequences and utilized all the information of circRNA-disease pairs during the pre-training process. This step can increase the information content of the feature to some extent and reduce the impact of too few known associations on the model performance. SGANRDA obtained AUC scores of 0.9411 and 0.9223 in leave-one-out cross-validation and 5-fold cross-validation, respectively. Prediction results on the benchmark dataset show that SGANRDA outperforms other existing models. In addition, 25 of the top 30 circRNA-disease pairs with the highest scores of SGANRDA in case studies were verified by recent literature. These experimental results demonstrate that SGANRDA is a useful model to predict the circRNA-disease association and can provide reliable candidates for biological experiments., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Although contrast agents would be beneficial, they are seldom used in four-dimensional (4D) flow magnetic resonance imaging (MRI) due to potential side effects and contraindications., Purpose: To develop and evaluate a deep learning architecture to generate high blood-tissue contrast in noncontrast 4D flow MRI by emulating the use of an external contrast agent., Study Type: Retrospective., Subjects: Of 222 data sets, 141 were used for neural network (NN) training (69 with and 72 without contrast agent). Evaluation was performed on the remaining 81 noncontrast data sets., Field Strength/sequences: Gradient echo or echo-planar 4D flow MRI at 1.5 T and 3 T., Assessment: A cyclic generative adversarial NN was trained to perform image translation between noncontrast and contrast data. Evaluation was performed quantitatively using contrast-to-noise ratio (CNR), signal-to-noise ratio (SNR), structural similarity index (SSIM), mean squared error (MSE) of edges, and Dice coefficient of segmentations. Three observers performed a qualitative assessment of blood-tissue contrast, noise, presence of artifacts, and image structure visualization., Statistical Tests: The Wilcoxon rank-sum test evaluated statistical significance. Kendall's concordance coefficient assessed interobserver agreement., Results: Contrast in the regions of interest (ROIs) in the NN enhanced images increased by 88%, CNR increased by 63%, and SNR improved by 48% (all P < 0.001). The SSIM was 0.82 ± 0.01, and the MSE of edges was 0.09 ± 0.01 (range [0,1]). Segmentations based on the generated images resulted in a Dice similarity increase of 15.25%. The observers managed to differentiate between contrast MR images and our results; however, they preferred the NN enhanced images in 76.7% of cases. This percentage increased to 93.3% for phase-contrast MR angiograms created from the NN enhanced data. Visual grading scores were blood-tissue contrast = 4.30 ± 0.74, noise = 3.12 ± 0.98, and presence of artifacts = 3.63 ± 0.76. Image structures within and without the ROIs resulted in scores of 3.42 ± 0.59 and 3.07 ± 0.71, respectively (P < 0.001)., Data Conclusion: The proposed approach improves blood-tissue contrast in MR images and could be used to improve data quality, visualization, and postprocessing of cardiovascular 4D flow data. EVIDENCE LEVEL: 3 TECHNICAL EFFICACY: Stage 1., (© 2021 The Authors. Journal of Magnetic Resonance Imaging published by Wiley Periodicals LLC. on behalf of International Society for Magnetic Resonance in Medicine.)

The purpose of this study was to simultaneously predict the drug release and skin permeation of Piroxicam (PX) topical films based on Chitosan (CTS), Xanthan gum (XG) and its Carboxymethyl derivatives (CMXs) as matrix systems. These films were prepared by the solvent casting method, using Tween 80 (T80) as a permeation enhancer. All of the prepared films were assessed for their physicochemical parameters, their in vitro drug release and ex vivo skin permeation studies. Moreover, deep learning models and machine learning models were applied to predict the drug release and permeation rates. The results indicated that all of the films exhibited good consistency and physicochemical properties. Furthermore, it was noticed that when T80 was used in the optimal formulation (F8) based on CTS-CMX3, a satisfactory drug release pattern was found where 99.97% of PX was released and an amount of 1.18 mg/cm 2 was permeated after 48 h. Moreover, Generative Adversarial Network (GAN) efficiently enhanced the performance of deep learning models and DNN was chosen as the best predictive approach with MSE values equal to 0.00098 and 0.00182 for the drug release and permeation kinetics, respectively. DNN precisely predicted PX dissolution profiles with f 2 values equal to 99.99 for all the formulations., (Copyright © 2021 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.)

The goal of monaural speech enhancement is to separate clean speech from noisy speech. Recently, many studies have employed generative adversarial networks (GAN) to deal with monaural speech enhancement tasks. When using generative adversarial networks for this task, the output of the generator is a speech waveform or a spectrum, such as a magnitude spectrum, a mel-spectrum or a complex-valued spectrum. The spectra generated by current speech enhancement methods in the time-frequency domain usually lack details, such as consonants and harmonics with low energy. In this paper, we propose a new type of adversarial training framework for spectrum generation, named μ-law spectrum generative adversarial networks (μ-law SGAN). We introduce a trainable μ-law spectrum compression layer (USCL) into the proposed discriminator to compress the dynamic range of the spectrum. As a result, the compressed spectrum can display more detailed information. In addition, we use the spectrum transformed by USCL to regularize the generator's training, so that the generator can pay more attention to the details of the spectrum. Experimental results on the open dataset Voice Bank + DEMAND show that μ-law SGAN is an effective generative adversarial architecture for speech enhancement. Moreover, visual spectrogram analysis suggests that μ-law SGAN pays more attention to the enhancement of low energy harmonics and consonants., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The applicability of generative adversarial networks (GANs) capable of unsupervised anomaly detection (AnoGAN) was investigated in the management of quality of 1 H-MRS human brain spectra at 3.0 T. The AnoGAN was trained in an unsupervised manner solely on simulated normal brain spectra and used for filtering out abnormal spectra with a broad range of abnormalities, which were simulated by including abnormal ranges of SNR, linewidth and metabolite concentrations and spectral artifacts such as ghost, residual water, and lipid. The AnoGAN was able to filter out those spectra with SNR less than ~11-12 dB with an accuracy of ~80% or higher (assuming a normal SNR range to be 15-18 dB). It also detected with an accuracy of ~80% or higher those spectra, in which NAA levels were reduced by ~25-30% or more from the lower bound and elevated by ~20-30% or more from the upper bound of the normal concentration range (7.5-17 mmol/L), while the concentrations of the rest of the metabolites were all within the normal ranges. Despite the fact that those spectra contaminated with ghost, residual water or lipid have never been involved in the training or optimization of the AnoGAN, they were correctly classified as abnormal regardless of the types of the artifacts, depending solely on their intensity. Although the current version of our AnoGAN requires further technical improvement particularly for the detection of linewidth-associated abnormality and validation on in vivo data, our unsupervised deep learning-based approach could be an option in addition to those previously reported supervised deep learning-based approaches in the binary classification of spectral quality with an extended abnormal spectra regime., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Deep learning methods have already enjoyed an unprecedented success in medical imaging problems. Similar success has been evidenced when it comes to the detection of COVID-19 from medical images, therefore deep learning approaches are considered good candidates for detecting this disease, in collaboration with radiologists and/or physicians. In this paper, we propose a new approach to detect COVID-19 via exploiting a conditional generative adversarial network to generate synthetic images for augmenting the limited amount of data available. Additionally, we propose two deep learning models following a lightweight architecture, commensurating with the overall amount of data available. Our experiments focused on both binary classification for COVID-19 vs Normal cases and multi-classification that includes a third class for bacterial pneumonia. Our models achieved a competitive performance compared to other studies in literature and also a ResNet8 model. Our best performing binary model achieved 98.7% accuracy, 100% sensitivity and 98.3% specificity, while our three-class model achieved 98.3% accuracy, 99.3% sensitivity and 98.1% specificity. Moreover, via adopting a testing protocol proposed in literature, our models proved to be more robust and reliable in COVID-19 detection than a baseline ResNet8, making them good candidates for detecting COVID-19 from posteroanterior chest X-ray images., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The generative adversarial network (GAN) is a good example of a strong-performing, neural network-based generative model, even though it does have some drawbacks of its own. Mode collapsing and the difficulty in finding the optimal network structure are two of the most concerning issues. In this paper, we address these two issues at the same time by proposing a neuro-evolutionary approach with an agile evaluation method for the fast evolution of robust deep architectures that avoid mode collapsing. The computation of Pareto set approximations with GANs is chosen as a suitable benchmark to evaluate the quality of our approach. Furthermore, we demonstrate the consistency, scalability, and generalization capabilities of the proposed method, which shows its potential applications to many areas. We finally readdress the issue of designing this kind of models by analyzing the characteristics of the best performing GAN specifications, and conclude with a set of general guidelines. This results in a reduction of the many-dimensional problem of structural manual design or automated search., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background and Objective: Retinal imaging has two major modalities, traditional fundus photography (TFP) and ultra-widefield fundus photography (UWFP). This study demonstrates the feasibility of a state-of-the-art deep learning-based domain transfer from UWFP to TFP., Methods: A cycle-consistent generative adversarial network (CycleGAN) was used to automatically translate the UWFP to the TFP domain. The model was based on an unpaired dataset including anonymized 451 UWFP and 745 TFP images. To apply CycleGAN to an independent dataset, we randomly divided the data into training (90%) and test (10%) datasets. After automated image registration and masking dark frames, the generator and discriminator networks were trained. Additional twelve publicly available paired TFP and UWFP images were used to calculate the intensity histograms and structural similarity (SSIM) indices., Results: We observed that all UWFP images were successfully translated into TFP-style images by CycleGAN, and the main structural information of the retina and optic nerve was retained. The model did not generate fake features in the output images. Average histograms demonstrated that the intensity distribution of the generated output images provided a good match to the ground truth images, with an average SSIM level of 0.802., Conclusions: Our approach enables automated synthesis of TFP images directly from UWFP without a manual pre-conditioning process. The generated TFP images might be useful for clinicians in investigating posterior pole and for researchers in integrating TFP and UWFP databases. This is also likely to save scan time and will be more cost-effective for patients by avoiding additional examinations for an accurate diagnosis., Competing Interests: Declaration of Competing Interest Ik Hee Ryu and Jin Kuk Kim are executives of VISUWORKS, Inc. The remaining authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020. Published by Elsevier B.V.)

Background: For the growing patient population with congenital heart disease (CHD), improving clinical workflow, accuracy of diagnosis, and efficiency of analyses are considered unmet clinical needs. Cardiovascular magnetic resonance (CMR) imaging offers non-invasive and non-ionizing assessment of CHD patients. However, although CMR data facilitates reliable analysis of cardiac function and anatomy, clinical workflow mostly relies on manual analysis of CMR images, which is time consuming. Thus, an automated and accurate segmentation platform exclusively dedicated to pediatric CMR images can significantly improve the clinical workflow, as the present work aims to establish., Methods: Training artificial intelligence (AI) algorithms for CMR analysis requires large annotated datasets, which are not readily available for pediatric subjects and particularly in CHD patients. To mitigate this issue, we devised a novel method that uses a generative adversarial network (GAN) to synthetically augment the training dataset via generating synthetic CMR images and their corresponding chamber segmentations. In addition, we trained and validated a deep fully convolutional network (FCN) on a dataset, consisting of [Formula: see text] pediatric subjects with complex CHD, which we made publicly available. Dice metric, Jaccard index and Hausdorff distance as well as clinically-relevant volumetric indices are reported to assess and compare our platform with other algorithms including U-Net and cvi42, which is used in clinics., Results: For congenital CMR dataset, our FCN model yields an average Dice metric of [Formula: see text] and [Formula: see text] for LV at end-diastole and end-systole, respectively, and [Formula: see text] and [Formula: see text] for RV at end-diastole and end-systole, respectively. Using the same dataset, the cvi42, resulted in [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] for LV and RV at end-diastole and end-systole, and the U-Net architecture resulted in [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] for LV and RV at end-diastole and end-systole, respectively., Conclusions: The chambers' segmentation results from our fully-automated method showed strong agreement with manual segmentation and no significant statistical difference was found by two independent statistical analyses. Whereas cvi42 and U-Net segmentation results failed to pass the t-test. Relying on these outcomes, it can be inferred that by taking advantage of GANs, our method is clinically relevant and can be used for pediatric and congenital CMR segmentation and analysis.

Purpose: To assess whether a generative adversarial network (GAN) could synthesize realistic optical coherence tomography (OCT) images that satisfactorily serve as the educational images for retinal specialists, and the training datasets for the classification of various retinal disorders using deep learning (DL)., Methods: The GANs architecture was adopted to synthesize high-resolution OCT images trained on a publicly available OCT dataset, including urgent referrals (37,206 OCT images from eyes with choroidal neovascularization, and 11,349 OCT images from eyes with diabetic macular edema) and nonurgent referrals (8617 OCT images from eyes with drusen, and 51,140 OCT images from normal eyes). Four hundred real and synthetic OCT images were evaluated by two retinal specialists (with over 10 years of clinical retinal experience) to assess image quality. We further trained two DL models on either real or synthetic datasets and compared the performance of urgent versus nonurgent referrals diagnosis tested on a local (1000 images from the public dataset) and clinical validation dataset (278 images from Shanghai Shibei Hospital)., Results: The image quality of real versus synthetic OCT images was similar as assessed by two retinal specialists. The accuracy of discrimination of real versus synthetic OCT images was 59.50% for retinal specialist 1 and 53.67% for retinal specialist 2. For the local dataset, the DL model trained on real (DL&#95;Model&#95;R) and synthetic OCT images (DL&#95;Model&#95;S) had an area under the curve (AUC) of 0.99, and 0.98, respectively. For the clinical dataset, the AUC was 0.94 for DL&#95;Model&#95;R and 0.90 for DL&#95;Model&#95;S., Conclusions: The GAN synthetic OCT images can be used by clinicians for educational purposes and for developing DL algorithms., Translational Relevance: The medical image synthesis based on GANs is promising in humans and machines to fulfill clinical tasks., Competing Interests: Disclosure: C. Zheng, None; X. Xie, None; K. Zhou, None; B. Chen, None; J. Chen, None; H. Ye, None; W. Li, None; T. Qiao, None; S. Gao, None; J. Yang, None; J. Liu, None, (Copyright 2020 The Authors.)

Purpose: Cone-beam computed tomography (CBCT) offers advantages over conventional fan-beam CT in that it requires a shorter time and less exposure to obtain images. However, CBCT images suffer from low soft-tissue contrast, noise, and artifacts compared to conventional fan-beam CT images. Therefore, it is essential to improve the image quality of CBCT., Methods: In this paper, we propose a synthetic approach to translate CBCT images with deep neural networks. Our method requires only unpaired and unaligned CBCT images and planning fan-beam CT (PlanCT) images for training. The CBCT images and PlanCT images may be obtained from other patients as long as they are acquired with the same scanner settings. Once trained, three-dimensionally reconstructed CBCT images can be directly translated into high-quality PlanCT-like images., Results: We demonstrate the effectiveness of our method with images obtained from 20 prostate patients, and provide a statistical and visual comparison. The image quality of the translated images shows substantial improvement in voxel values, spatial uniformity, and artifact suppression compared to those of the original CBCT. The anatomical structures of the original CBCT images were also well preserved in the translated images., Conclusions: Our method produces visually PlanCT-like images from CBCT images while preserving anatomical structures., (© 2019 American Association of Physicists in Medicine.)

Purpose: Accurate tumor segmentation is a requirement for magnetic resonance (MR)-based radiotherapy. Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed., Methods: Eighty-one T2-weighted MRI scans from 28 patients with non-small cell lung cancers (nine with pretreatment and weekly MRI and the remainder with pre-treatment MRI scans) were analyzed. Cross-modality model encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning network. This model was used to translate 377 expert segmented non-small cell lung cancer CT scans from the Cancer Imaging Archive into pseudo MRI that served as additional training set. This method was benchmarked against shallow learning using random forest, standard data augmentation, and three state-of-the art adversarial learning-based cross-modality data (pseudo MR) augmentation methods. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdorff distance metrics, and volume ratio., Results: The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of (0.75 ± 0.12) and the lowest Hausdorff distance of (9.36 mm ± 6.00 mm) on the test dataset using a U-Net structure. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37)., Conclusions: A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality information using a model that explicitly incorporates knowledge of tumors in modality translation to augment segmentation training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods., (© 2019 American Association of Physicists in Medicine.)

Conventional neural networks have been demonstrated to be a powerful framework for background subtraction in video acquired by static cameras. Indeed, the well-known Self-Organizing Background Subtraction (SOBS) method and its variants based on neural networks have long been the leading methods on the large-scale CDnet 2012 dataset during a long time. Convolutional neural networks, which are used in deep learning, have been recently and excessively employed for background initialization, foreground detection, and deep learned features. The top background subtraction methods currently used in CDnet 2014 are based on deep neural networks, and have demonstrated a large performance improvement in comparison to conventional unsupervised approaches based on multi-feature or multi-cue strategies. Furthermore, since the seminal work of Braham and Van Droogenbroeck in 2016, a large number of studies on convolutional neural networks applied to background subtraction have been published, and a continual gain of performance has been achieved. In this context, we provide the first review of deep neural network concepts in background subtraction for novices and experts in order to analyze this success and to provide further directions. To do so, we first surveyed the background initialization and background subtraction methods based on deep neural networks concepts, and also deep learned features. We then discuss the adequacy of deep neural networks for the task of background subtraction. Finally, experimental results are presented for the CDnet 2014 dataset., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Adversarial networks were developed to complete powerful image-processing tasks on the basis of example images provided to train the networks. These networks are relatively new in the field of deep learning and have proved to have unique strengths that can potentially benefit radiology. Specifically, adversarial networks have the potential to decrease radiation exposure to patients through minimizing repeat imaging due to artifact, decreasing acquisition time, and generating higher quality images from low-dose or no-dose studies. The authors provide an overview of a specific type of adversarial network called a "generalized adversarial network" and review its uses in current medical imaging research., (Copyright © 2019 American College of Radiology. Published by Elsevier Inc. All rights reserved.)

An accurate estimation of three-dimensional (3D) temperature fields in channel flows is challenging but critical for many important applications such as heat exchangers, radiation energy collectors, and enhanced geothermal systems. In this paper, we demonstrate the possibility of inferring temperature fields from concentration fields for laminar convection flows in a 3D channel using a machine learning (ML) approach. The study involves generation of data using 3D numerical simulations, application of deep learning methodology using conditional generative adversarial networks (cGANs), and analysis of how dataset selection affects model performance. The model is also tested for applicability in different convection scenarios. Results show that cGANs can successfully infer temperature fields from concentration fields, and the reconstruction accuracy is sensitive to the training dataset selected. In this study, we demonstrate how ML can be used to overcome the limitations of traditional heat and mass analogy functions widely used in heat transfer research. [ABSTRACT FROM AUTHOR]

4D MRI with high spatiotemporal resolution is desired for image-guided liver radiotherapy. Acquiring densely sampled k-space data is time-consuming. Accelerated acquisition with sparse sampling is desirable but often causes degraded image quality or long reconstruction time. We propose the Reconstruct Paired Conditional Generative Adversarial Network (Re-Con-GAN) for shortening the 4D MRI reconstruction time while maintaining the reconstruction quality. Methods: Patients underwent free-breathing liver 4D MRI were included in the study. Fully- and retrospectively under-sampled data at 3, 6 and 10 times (3x, 6x and 10x) were first reconstructed using the nuFFT algorithm. Re-Con-GAN then trained input and output in pairs. Three types of networks, ResNet9, UNet and reconstruction swin transformer, were explored as generators. PatchGAN was selected as the discriminator. Re-Con-GAN processed the data (3D+t) as temporal slices (2D+t). A total of 48 patients with 12332 temporal slices were split into training (37 patients with 10721 slices) and test (11 patients with 1611 slices). Compressed sensing (CS) reconstruction with spatiotemporal sparsity constraint was used as a benchmark. Reconstructed image quality was further evaluated with a liver gross tumor volume (GTV) localization task using Mask-RCNN trained from a separate 3D static liver MRI dataset (70 patients; 103 GTV contours).Results: Re-Con-GAN consistently achieved comparable/better PSNR, SSIM, and RMSE scores compared to CS/UNet models. The inference time of Re-Con-GAN, UNet and CS are 0.15s, 0.16s, and 120s. The GTV detection task showed that Re-Con-GAN and CS, compared to UNet, better improved the dice score (3x Re-Con-GAN 80.98%; 3x CS 80.74%; 3x UNet 79.88%) of unprocessed under-sampled images (3x 69.61%). Conclusion: A generative network with adversarial training is proposed with promising and efficient reconstruction results demonstrated on an in-house dataset. The rapid and qualitative reconstruction of 4D liver MR has the potential to facilitate online adaptive MR-guided radiotherapy for liver cancer.

Summary: Wireless body sensor network (WBSN) is essential for monitoring patients' health problems and offers a low‐cost option for various healthcare applications. In this manuscript, a Novel Health Monitoring Approach for WBSNs (DIWGAN‐WBSN) is proposed, which uses Dual Interactive Wasserstein Generative Adversarial Network (DIWGAN) optimized with War Strategy Optimization Algorithm (WSOA). After sensing the aforementioned attribute information, it is the responsibility of WBSN nodes to transfer the sensed data to the sink node. The Volcano Eruption Algorithm (VEA) is applied to select the optimum cluster heads in WBSN. The results from VEA are fed to the target node; it consists of DIWGAN to classify the health records and to portray the patient's health status. Generally, DIWGAN does not adopt any optimization methods for measuring the ideal parameters and guaranteeing accurate health monitoring and risk assessment. So the proposed WSOA is considered to enhance the DIWGAN. The proposed method is activated in MATLAB; its efficacy is estimated under performance metrics, like precision, specificity, accuracy, and energy utilization. The proposed approach attains 23.9%, 21.34%, and 51.09% higher accuracy; 21.45%, 13.94%, and 20.6% higher precision; 31.32%, 29.61%, and 11.03% higher specificity; and 20.9%, 19.87%, and 24.6% lower energy utilization for HD classification using the Cleveland database than the existing methods like back propagation neural network‐based risk detection in WBSN for health monitoring, random forest algorithm–based health monitoring in WBSN, and ensemble deep learning and feature fusion for health monitoring using WBSN methods, respectively. [ABSTRACT FROM AUTHOR]

The current quantitative retrieval of Aerosol Optical Depth (AOD) typically uses Top-of-atmosphere (TOA) reflectance data obtained by the scale and offset terms of radiometric calibration. Errors can be introduced during the conversion of Digital Number (DN) values to TOA reflectance, restraining the accurate retrieval of AOD. Particularly when surface reflectance is high, conversion errors can significantly distort the retrieval of Aerosol Optical Depth (AOD), given the minimal impact of aerosols on the radiation detected by satellite sensors. To counteract this, we introduce an innovative retrieval algorithm that harnesses a Generative Adversarial Network (GANN), a deep learning (DL) model, to accurately derive AOD from the scaled digital number (DN) values of multi-spectral satellite imagery. The DL technology enables the use of scaled DN values for AOD retrieval, bypassing the conversion errors associated with TOA reflectance since it relies on a sample learning approach instead of radiative transfer calculations. To ensure the number and representativeness of training samples, a total of 37,103 samples from different underlying surfaces from 2014 to 2018 were obtained using a space-time matching strategy. Our K-cross validation demonstrates that employing DN values for AOD retrieval promises to yield higher accuracy compared to using TOA reflectance. Independent 2019 data were used to estimate GANN, MCD19A2 and MOD04_3K aerosol products. Our model showed superior performance compared to the other products in terms of a higher correlation (R = 0.8184) with AERONET AOD and obtaining more reliable retrievals (7601). The sensitivity experiment suggests that GANN exhibits limitations in areas characterized by high aerosol loads and heterogeneity. Our study can give a novel insight into AOD retrieval based on multi-spectral satellite and DL models. [ABSTRACT FROM AUTHOR]

This study proposes a synthetic data generation model to create a classification framework for cerebellar ataxia patients using trajectory data from the visuomotor adaptation task. The classification objectives include patients with cerebellar ataxia, age-matched normal individuals, and young healthy subjects. Synthetic data for the three classes is generated based on class conditions and random noise by leveraging a combination of conditional adversarial generative neural networks and reconstruction networks. This synthetic data, alongside real data, is utilized as training data for the patient classification model to enhance classification accuracy. The fidelity of the synthetic data is assessed visually to measure the validity and diversity of the generated data qualitatively while quantitatively evaluating distribution similarity to real data. Furthermore, the clinical efficacy of the patient classification model employing synthetic data is demonstrated by showcasing improved classification accuracy through a comparative analysis between results obtained using solely real data and those obtained when both real and synthetic data are utilized. This methodological approach holds promise in addressing data insufficiency in the digital healthcare domain, employing deep learning methodologies, and developing early disease diagnosis tools. [ABSTRACT FROM AUTHOR]

Cyber-physical system is one of the essential components of wireless sensor network (WSN). WSN conjointly senses, collects, analyzes and communicates data on recognized items at service part before transmitting this data to the owner of the network. Blackhole, Grayhole, Flooding, Scheduling are the common WSN attacks that rapidly damage the system. Intrusion detection systems, such as WSN have drawbacks, like less detection rates, high computation costs and high percentage of false alarms, because sensor nodes have limited resources. Therefore, a Self Attention Generative Adversarial Capsule Network as an intrusion detection scheme for WSN (SAGACN-ID-WSN) is proposed in this paper to address the aforementioned issues. Initially, the data are amassed from WSN-DS dataset. Then, the data are sent for pre-processing. The input data are preprocessed using the Guided Box Filtering (GBF) method. Then, the preprocessed data are provided to the Atomic Orbital Search (AOS), Tasmanian Devil Optimization (TDO) and Ebola Optimization Search (EOS) algorithms for feature selection. The attacks are divided into four categories: normal, Grayhole attack, Black hole attack, flooding attack, and scheduling attack. The proposed ID-WSN is implemented in Network simulator 2 (NS-2) utilizing the dataset of WSN-DS. The metrics, like accuracy, precision, recall, F-measure, ROC and computational time are analyzed. The proposed SAGACN-ID-WSN technique attains 25.5%, 20.12% and 20.7% high accuracy, 51.136%, 59.04% and 32.81%; higher precision, 2.292%, 1.51% and 3.915% lower error rate compared to the existing models, like Dataset for Intrusion Detection Systems in WSN (SLGBM-ID-WSN), multi-layer machine learning-based ID-WSN (NB-RF-ID-WSN), deep learning and entity embedding-base intrusion detection systems in WSN, respectively. [ABSTRACT FROM AUTHOR]

Background: Bioactive peptides are important bioactive molecules composed of short-chain amino acids that play various crucial roles in the body, such as regulating physiological processes and promoting immune responses and antibacterial effects. Due to their significance, bioactive peptides have broad application potential in drug development, food science, and biotechnology. Among them, understanding their biological mechanisms will contribute to new ideas for drug discovery and disease treatment. Results: This study employs generative adversarial capsule networks (CapsuleGAN), gated recurrent units (GRU), and convolutional neural networks (CNN) as base classifiers to achieve ensemble learning through voting methods, which not only obtains high-precision prediction results on the angiotensin-converting enzyme (ACE) inhibitory peptides dataset and the anticancer peptides (ACP) dataset but also demonstrates effective model performance. For this method, we first utilized the protein language model—evolutionary scale modeling (ESM-2)—to extract relevant features for the ACE inhibitory peptides and ACP datasets. Following feature extraction, we trained three deep learning models—CapsuleGAN, GRU, and CNN—while continuously adjusting the model parameters throughout the training process. Finally, during the voting stage, different weights were assigned to the models based on their prediction accuracy, allowing full utilization of the model's performance. Experimental results show that on the ACE inhibitory peptide dataset, the balanced accuracy is 0.926, the Matthews correlation coefficient (MCC) is 0.831, and the area under the curve is 0.966; on the ACP dataset, the accuracy (ACC) is 0.779, and the MCC is 0.558. The experimental results on both datasets are superior to existing methods, demonstrating the effectiveness of the experimental approach. Conclusion: In this study, CapsuleGAN, GRU, and CNN were successfully employed as base classifiers to implement ensemble learning, which not only achieved good results in the prediction of two datasets but also surpassed existing methods. The ability to predict peptides with strong ACE inhibitory activity and ACPs more accurately and quickly is significant, and this work provides valuable insights for predicting other functional peptides. The source code and dataset for this experiment are publicly available at https://github.com/Zhou-Jianren/bioactive-peptides. [ABSTRACT FROM AUTHOR]

Background Purpose Methods Results Conclusion Automatic primary gross tumor volume (GTVp) segmentation for nasopharyngeal carcinoma (NPC) is a quite challenging task because of the existence of similar visual characteristics between tumors and their surroundings, especially on computed tomography (CT) images with severe low contrast resolution. Therefore, most recently proposed methods based on radiomics or deep learning (DL) is difficult to achieve good results on CT datasets.A peritumoral radiomics‐guided generative adversarial network (PRG‐GAN) was proposed to address this challenge.A total of 157 NPC patients with CT images was collected and divided into training, validation, and testing cohorts of 108, 9, and 30 patients, respectively. The proposed model was based on a standard GAN consisting of a generator network and a discriminator network. Morphological dilation on the initial segmentation results from GAN was first conducted to delineate annular peritumoral region, in which radiomics features were extracted as priori guide knowledge. Then, radiomics features were fused with semantic features by the discriminator's fully connected layer to achieve the voxel‐level classification and segmentation. The dice similarity coefficient (DSC), 95% Hausdorff distance (HD95), and average symmetric surface distance (ASSD) were used to evaluate the segmentation performance using a paired samples t‐test with Bonferroni correction and Cohen's d (d) effect sizes. A two‐sided p‐value of less than 0.05 was considered statistically significant.The model‐generated predictions had a high overlap ratio with the ground truth. The average DSC, HD95, and ASSD were significantly improved from 0.80 ± 0.12, 4.65 ± 4.71  mm, and 1.35 ± 1.15  mm of GAN to 0.85 ± 0.18 (p = 0.001, d = 0.71), 4.15 ± 7.56 mm (p = 0.002, d = 0.67), and 1.11 ± 1.65 mm (p < 0.001, d = 0.46) of PRG‐GAN, respectively.Integrating radiomics features into GAN is promising to solve unclear border limitations and increase the delineation accuracy of GTVp for patients with NPC. [ABSTRACT FROM AUTHOR]

Viral oncoproteins play crucial roles in transforming normal cells into cancer cells, representing a significant factor in the etiology of various cancers. Traditionally, identifying these oncoproteins is both time-consuming and costly. With advancements in computational biology, bioinformatics tools based on machine learning have emerged as effective methods for predicting biological activities. Here, for the first time, we propose an innovative approach that combines Generative Adversarial Networks (GANs) with supervised learning methods to enhance the accuracy and generalizability of viral oncoprotein prediction. Our methodology evaluated multiple machine learning models, including Random Forest, Multilayer Perceptron, Light Gradient Boosting Machine, eXtreme Gradient Boosting, and Support Vector Machine. In ten-fold cross-validation on our training dataset, the GAN-enhanced Random Forest model demonstrated superior performance metrics: 0.976 accuracy, 0.976 F1 score, 0.977 precision, 0.976 sensitivity, and 1.0 AUC. During independent testing, this model achieved 0.982 accuracy, 0.982 F1 score, 0.982 precision, 0.982 sensitivity, and 1.0 AUC. These results establish our new tool, VirOncoTarget, accessible via a web application. We anticipate that VirOncoTarget will be a valuable resource for researchers, enabling rapid and reliable viral oncoprotein prediction and advancing our understanding of their role in cancer biology. [ABSTRACT FROM AUTHOR]

Background: Recent advancements in generative artificial intelligence (AI) for image generation have presented significant opportunities for medical imaging, offering a promising way to generate realistic virtual medical images while ensuring patient privacy. The generation of a large number of virtual medical images through AI has the potential to augment training datasets for discriminative AI models, particularly in fields with limited data availability, such as neuroimaging. Current studies on generative AI in neuroimaging have mainly focused on disease discrimination; however, its potential for simulating complex phenomena in psychiatric disorders remains unknown. In this study, as examples of a simulation, we aimed to present a novel generative AI model that transforms magnetic resonance imaging (MRI) images of healthy individuals into images that resemble those of patients with schizophrenia (SZ) and explore its application. Methods: We used anonymized public datasets from the Center for Biomedical Research Excellence (SZ, 71 patients; healthy subjects [HSs], 71 patients) and the Autism Brain Imaging Data Exchange (autism spectrum disorder [ASD], 79 subjects; HSs, 105 subjects). We developed a model to transform MRI images of HSs into MRI images of SZ using cycle generative adversarial networks. The efficacy of the transformation was evaluated using voxel-based morphometry to assess the differences in brain region volumes and the accuracy of age prediction pre- and post-transformation. In addition, the model was examined for its applicability in simulating disease comorbidities and disease progression. Results: The model successfully transformed HS images into SZ images and identified brain volume changes consistent with existing case-control studies. We also applied this model to ASD MRI images, where simulations comparing SZ with and without ASD backgrounds highlighted the differences in brain structures due to comorbidities. Furthermore, simulating disease progression while preserving individual characteristics showcased the model's ability to reflect realistic disease trajectories. Discussion: The results suggest that our generative AI model can capture subtle changes in brain structures associated with SZ, providing a novel tool for visualizing brain changes in different diseases. The potential of this model extends beyond clinical diagnosis to advances in the simulation of disease mechanisms, which may ultimately contribute to the refinement of therapeutic strategies. [ABSTRACT FROM AUTHOR]