The role of generative adversarial networks in brain MRI: a scoping review.
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SUBMITTER: Ali H
PROVIDER: S-EPMC9167371 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:PurposeComplementary information obtained from multiple contrasts of tissue facilitates physicians assessing, diagnosing and planning treatment of a variety of diseases. However, acquiring multiple contrasts magnetic resonance images (MRI) for every patient using multiple pulse sequences is time-consuming and expensive, where, medical image synthesis has been demonstrated as an effective alternative. The purpose of this study is to develop a unified framework for multimodal MR image synthesis.MethodsA unified generative adversarial network consisting of only a single generator and a single discriminator was developed to learn the mappings among images of four different modalities. The generator took an image and its modality label as inputs and learned to synthesize the image in the target modality, while the discriminator was trained to distinguish between real and synthesized images and classify them to their corresponding modalities. The network was trained and tested using multimodal brain MRI consisting of four different contrasts which are T1-weighted (T1), T1-weighted and contrast-enhanced (T1c), T2-weighted (T2), and fluid-attenuated inversion recovery (Flair). Quantitative assessments of our proposed method were made through computing normalized mean absolute error (NMAE), peak signal-to-noise ratio (PSNR), structural similarity index measurement (SSIM), visual information fidelity (VIF), and naturalness image quality evaluator (NIQE).ResultsThe proposed model was trained and tested on a cohort of 274 glioma patients with well-aligned multi-types of MRI scans. After the model was trained, tests were conducted by using each of T1, T1c, T2, Flair as a single input modality to generate its respective rest modalities. Our proposed method shows high accuracy and robustness for image synthesis with arbitrary MRI modality that is available in the database as input. For example, with T1 as input modality, the NMAEs for the generated T1c, T2, Flair respectively are 0.034 ± 0.005, 0.041 ± 0.006, and 0.041 ± 0.006, the PSNRs respectively are 32.353 ± 2.525 dB, 30.016 ± 2.577 dB, and 29.091 ± 2.795 dB, the SSIMs are 0.974 ± 0.059, 0.969 ± 0.059, and 0.959 ± 0.059, the VIF are 0.750 ± 0.087, 0.706 ± 0.097, and 0.654 ± 0.062, and NIQE are 1.396 ± 0.401, 1.511 ± 0.460, and 1.259 ± 0.358, respectively.ConclusionsWe proposed a novel multimodal MR image synthesis method based on a unified generative adversarial network. The network takes an image and its modality label as inputs and synthesizes multimodal images in a single forward pass. The results demonstrate that the proposed method is able to accurately synthesize multimodal MR images from a single MR image.
| S-EPMC7796974 | biostudies-literature
Project description:BackgroundResearch on the diagnosis of COVID-19 using lung images is limited by the scarcity of imaging data. Generative adversarial networks (GANs) are popular for synthesis and data augmentation. GANs have been explored for data augmentation to enhance the performance of artificial intelligence (AI) methods for the diagnosis of COVID-19 within lung computed tomography (CT) and X-ray images. However, the role of GANs in overcoming data scarcity for COVID-19 is not well understood.ObjectiveThis review presents a comprehensive study on the role of GANs in addressing the challenges related to COVID-19 data scarcity and diagnosis. It is the first review that summarizes different GAN methods and lung imaging data sets for COVID-19. It attempts to answer the questions related to applications of GANs, popular GAN architectures, frequently used image modalities, and the availability of source code.MethodsA search was conducted on 5 databases, namely PubMed, IEEEXplore, Association for Computing Machinery (ACM) Digital Library, Scopus, and Google Scholar. The search was conducted from October 11-13, 2021. The search was conducted using intervention keywords, such as "generative adversarial networks" and "GANs," and application keywords, such as "COVID-19" and "coronavirus." The review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines for systematic and scoping reviews. Only those studies were included that reported GAN-based methods for analyzing chest X-ray images, chest CT images, and chest ultrasound images. Any studies that used deep learning methods but did not use GANs were excluded. No restrictions were imposed on the country of publication, study design, or outcomes. Only those studies that were in English and were published from 2020 to 2022 were included. No studies before 2020 were included.ResultsThis review included 57 full-text studies that reported the use of GANs for different applications in COVID-19 lung imaging data. Most of the studies (n=42, 74%) used GANs for data augmentation to enhance the performance of AI techniques for COVID-19 diagnosis. Other popular applications of GANs were segmentation of lungs and superresolution of lung images. The cycleGAN and the conditional GAN were the most commonly used architectures, used in 9 studies each. In addition, 29 (51%) studies used chest X-ray images, while 21 (37%) studies used CT images for the training of GANs. For the majority of the studies (n=47, 82%), the experiments were conducted and results were reported using publicly available data. A secondary evaluation of the results by radiologists/clinicians was reported by only 2 (4%) studies.ConclusionsStudies have shown that GANs have great potential to address the data scarcity challenge for lung images in COVID-19. Data synthesized with GANs have been helpful to improve the training of the convolutional neural network (CNN) models trained for the diagnosis of COVID-19. In addition, GANs have also contributed to enhancing the CNNs' performance through the superresolution of the images and segmentation. This review also identified key limitations of the potential transformation of GAN-based methods in clinical applications.
| S-EPMC9246088 | biostudies-literature
Project description:BackgroundDifficulties in detecting brain lesions in acute ischemic stroke (AIS) have convinced researchers to use computed tomography (CT) to scan for and magnetic resonance imaging (MRI) to search for these lesions. This work aimed to develop a generative adversarial network (GAN) model for CT-to-MR image synthesis and evaluate reader performance with synthetic MRI (syn-MRI) in detecting brain lesions in suspected patients.MethodsPatients with primarily suspected AIS were randomly assigned to the training (n=140) or testing (n=53) set. Emergency CT and follow-up MR images in the training set were used to develop a GAN model to generate syn-MR images from the CT data in the testing set. The standard reference was the manual segmentations of follow-up MR images. Image similarity was evaluated between syn-MRI and the ground truth using a 4-grade visual rating scale, the peak signal-to-noise ratio (PSNR), and the structural similarity index measure (SSIM). Reader performance with syn-MRI and CT was evaluated and compared on a per-patient (patient detection) and per-lesion (lesion detection) basis. Paired t-tests or Wilcoxon signed-rank tests were used to compare reader performance in lesion detection between the syn-MRI and CT data.ResultsGrade 2-4 brain lesions were observed on syn-MRI in 92.5% (49/53) of the patients, while the remaining syn-MRI data showed no lesions compared to the ground truth. The GAN model exhibited a weak PSNR of 24.30 dB but a favorable SSIM of 0.857. Compared with CT, syn-MRI led to an increase in the overall sensitivity from 38% (57/150) to 82% (123/150) in patient detection and from 4% (68/1,620) to 16% (262/1,620) in lesion detection (R=0.32, corrected P<0.001), but the specificity in patient detection decreased from 67% (6/9) to 33% (3/9). An additional 75% (70/93) of patients and 15% (77/517) of lesions missed on CT were detected on syn-MRI.ConclusionsThe GAN model holds potential for generating synthetic MR images from noncontrast CT data and thus could help sensitively detect individuals among patients with suspected AIS. However, the image similarity performance of the model needs to be improved, and further expert discrimination is strongly recommended.
| S-EPMC8848363 | biostudies-literature
Project description:Generative adversarial networks (GANs) have been recently applied to medical imaging on different modalities (MRI, CT, X-ray, etc). However there are not many applications on ultrasound modality as a data augmentation technique applied to downstream classification tasks. This study aims to explore and evaluate the generation of synthetic ultrasound fetal brain images via GANs and apply them to improve fetal brain ultrasound plane classification. State of the art GANs stylegan2-ada were applied to fetal brain image generation and GAN-based data augmentation classifiers were compared with baseline classifiers. Our experimental results show that using data generated by both GANs and classical augmentation strategies allows for increasing the accuracy and area under the curve score.
| S-EPMC8659720 | biostudies-literature
Project description:MotivationThe application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning approaches require data from across this space to train models. Because of this, previous approaches have typically been limited to inferring relationships among unrooted quartets of taxa, where there are only three possible topologies. Here, we explore the potential of generative adversarial networks (GANs) to address this limitation. GANs consist of a generator and a discriminator: at each step, the generator aims to create data that is similar to real data, while the discriminator attempts to distinguish generated and real data. By using an evolutionary model as the generator, we use GANs to make evolutionary inferences. Since a new model can be considered at each iteration, heuristic searches of complex model spaces are possible. Thus, GANs offer a potential solution to the challenges of applying machine learning in phylogenetics.ResultsWe developed phyloGAN, a GAN that infers phylogenetic relationships among species. phyloGAN takes as input a concatenated alignment, or a set of gene alignments, and infers a phylogenetic tree either considering or ignoring gene tree heterogeneity. We explored the performance of phyloGAN for up to 15 taxa in the concatenation case and 6 taxa when considering gene tree heterogeneity. Error rates are relatively low in these simple cases. However, run times are slow and performance metrics suggest issues during training. Future work should explore novel architectures that may result in more stable and efficient GANs for phylogenetics.Availability and implementationphyloGAN is available on github: https://github.com/meganlsmith/phyloGAN/.
| S-EPMC10500083 | biostudies-literature
Project description:Recent years have witnessed a rapidly expanding use of artificial intelligence and machine learning in medical imaging. Generative adversarial networks (GANs) are techniques to synthesize images based on artificial neural networks and deep learning. In addition to the flexibility and versatility inherent in deep learning on which the GANs are based, the potential problem-solving ability of the GANs has attracted attention and is being vigorously studied in the medical and molecular imaging fields. Here this narrative review provides a comprehensive overview for GANs and discuss their usefulness in medical and molecular imaging on the following topics: (I) data augmentation to increase training data for AI-based computer-aided diagnosis as a solution for the data-hungry nature of such training sets; (II) modality conversion to complement the shortcomings of a single modality that reflects certain physical measurement principles, such as from magnetic resonance (MR) to computed tomography (CT) images or vice versa; (III) de-noising to realize less injection and/or radiation dose for nuclear medicine and CT; (IV) image reconstruction for shortening MR acquisition time while maintaining high image quality; (V) super-resolution to produce a high-resolution image from low-resolution one; (VI) domain adaptation which utilizes knowledge such as supervised labels and annotations from a source domain to the target domain with no or insufficient knowledge; and (VII) image generation with disease severity and radiogenomics. GANs are promising tools for medical and molecular imaging. The progress of model architectures and their applications should continue to be noteworthy.
| S-EPMC8246192 | biostudies-literature
Project description:IntroductionAcquisition and pre-processing pipelines for diffusion-weighted imaging (DWI) volumes are resource- and time-consuming. Generating synthetic DWI scalar maps from commonly acquired brain MRI sequences such as fluid-attenuated inversion recovery (FLAIR) could be useful for supplementing datasets. In this work we design and compare GAN-based image translation models for generating DWI scalar maps from FLAIR MRI for the first time.MethodsWe evaluate a pix2pix model, two modified CycleGANs using paired and unpaired data, and a convolutional autoencoder in synthesizing DWI fractional anisotropy (FA) and mean diffusivity (MD) from whole FLAIR volumes. In total, 420 FLAIR and DWI volumes (11,957 images) from multi-center dementia and vascular disease cohorts were used for training/testing. Generated images were evaluated using two groups of metrics: (1) human perception metrics including peak signal-to-noise ratio (PSNR) and structural similarity (SSIM), (2) structural metrics including a newly proposed histogram similarity (Hist-KL) metric and mean squared error (MSE).ResultsPix2pix demonstrated the best performance both quantitatively and qualitatively with mean PSNR, SSIM, and MSE metrics of 23.41 dB, 0.8, 0.004, respectively for MD generation, and 24.05 dB, 0.78, 0.004, respectively for FA generation. The new histogram similarity metric demonstrated sensitivity to differences in fine details between generated and real images with mean pix2pix MD and FA Hist-KL metrics of 11.73 and 3.74, respectively. Detailed analysis of clinically relevant regions of white matter (WM) and gray matter (GM) in the pix2pix images also showed strong significant (p < 0.001) correlations between real and synthetic FA values in both tissue types (R = 0.714 for GM, R = 0.877 for WM).Discussion/conclusionOur results show that pix2pix's FA and MD models had significantly better structural similarity of tissue structures and fine details than other models, including WM tracts and CSF spaces, between real and generated images. Regional analysis of synthetic volumes showed that synthetic DWI images can not only be used to supplement clinical datasets, but demonstrates potential utility in bypassing or correcting registration in data pre-processing.
| S-EPMC10436214 | biostudies-literature
Project description:We developed a deep learning-based super-resolution model for prostate MRI. 2D T2-weighted turbo spin echo (T2w-TSE) images are the core anatomical sequences in a multiparametric MRI (mpMRI) protocol. These images have coarse through-plane resolution, are non-isotropic, and have long acquisition times (approximately 10-15 min). The model we developed aims to preserve high-frequency details that are normally lost after 3D reconstruction. We propose a novel framework for generating isotropic volumes using generative adversarial networks (GAN) from anisotropic 2D T2w-TSE and single-shot fast spin echo (ssFSE) images. The CycleGAN model used in this study allows the unpaired dataset mapping to reconstruct super-resolution (SR) volumes. Fivefold cross-validation was performed. The improvements from patch-to-volume reconstruction (PVR) to SR are 80.17%, 63.77%, and 186% for perceptual index (PI), RMSE, and SSIM, respectively; the improvements from slice-to-volume reconstruction (SVR) to SR are 72.41%, 17.44%, and 7.5% for PI, RMSE, and SSIM, respectively. Five ssFSE cases were used to test for generalizability; the perceptual quality of SR images surpasses the in-plane ssFSE images by 37.5%, with 3.26% improvement in SSIM and a higher RMSE by 7.92%. SR images were quantitatively assessed with radiologist Likert scores. Our isotropic SR volumes are able to reproduce high-frequency detail, maintaining comparable image quality to in-plane TSE images in all planes without sacrificing perceptual accuracy. The SR reconstruction networks were also successfully applied to the ssFSE images, demonstrating that high-quality isotropic volume achieved from ultra-fast acquisition is feasible.
| S-EPMC8555005 | biostudies-literature
Project description:The constant demand for novel functional materials calls for efficient strategies to accelerate the materials discovery, and crystal structure prediction is one of the most fundamental tasks along that direction. In addressing this challenge, generative models can offer new opportunities since they allow for the continuous navigation of chemical space via latent spaces. In this work, we employ a crystal representation that is inversion-free based on unit cell and fractional atomic coordinates and build a generative adversarial network for crystal structures. The proposed model is applied to generate the Mg-Mn-O ternary materials with the theoretical evaluation of their photoanode properties for high-throughput virtual screening (HTVS). The proposed generative HTVS framework predicts 23 new crystal structures with reasonable calculated stability and band gap. These findings suggest that the generative model can be an effective way to explore hidden portions of the chemical space, an area that is usually unreachable when conventional substitution-based discovery is employed.
| S-EPMC7453563 | biostudies-literature
Project description:Skin cancer is a serious condition that requires accurate diagnosis and treatment. One way to assist clinicians in this task is using computer-aided diagnosis tools that automatically segment skin lesions from dermoscopic images. We propose a novel adversarial learning-based framework called Efficient-GAN (EGAN) that uses an unsupervised generative network to generate accurate lesion masks. It consists of a generator module with a top-down squeeze excitation-based compound scaled path, an asymmetric lateral connection-based bottom-up path, and a discriminator module that distinguishes between original and synthetic masks. A morphology-based smoothing loss is also implemented to encourage the network to create smooth semantic boundaries of lesions. The framework is evaluated on the International Skin Imaging Collaboration Lesion Dataset. It outperforms the current state-of-the-art skin lesion segmentation approaches with a Dice coefficient, Jaccard similarity, and accuracy of 90.1%, 83.6%, and 94.5%, respectively. We also design a lightweight segmentation framework called Mobile-GAN (MGAN) that achieves comparable performance as EGAN but with an order of magnitude lower number of training parameters, thus resulting in faster inference times for low compute resource settings.
| S-EPMC10439152 | biostudies-literature