EliasHossain/CancerAbstracts huggingface dataset:
Category: Generic
Railway defects can result in substantial economic and human losses. Among all defects, surface defects are the most common and prominent type, and various optical-based non-destructive testing (NDT) methods have been employed to detect them. In NDT, reliable and accurate interpretation of test data is vital for effective defect detection. Among the many sources of errors, human errors are the most unpredictable and frequent. Artificial intelligence (AI) has the potential to address this challenge; however, the lack of sufficient railway images with diverse types of defects is the major obstacle to training the AI models through supervised learning. To overcome this obstacle, this research proposes the RailGAN model, which enhances the basic CycleGAN model by introducing a pre-sampling stage for railway tracks. Two pre-sampling techniques are tested for the RailGAN model: image-filtration, and U-Net. By applying both techniques to 20 real-time railway images, it is demonstrated that U-Net produces more consistent results in image segmentation across all images and is less affected by the pixel intensity values of the railway track. Comparison of the RailGAN model with U-Net and the original CycleGAN model on real-time railway images reveals that the original CycleGAN model generates defects in the irrelevant background, while the RailGAN model produces synthetic defect patterns exclusively on the railway surface. The artificial images generated by the RailGAN model closely resemble real cracks on railway tracks and are suitable for training neural-network-based defect identification algorithms. The effectiveness of the RailGAN model can be evaluated by training a defect identification algorithm with the generated dataset and applying it to real defect images. The proposed RailGAN model has the potential to improve the accuracy of NDT for railway defects, which can ultimately lead to increased safety and reduced economic losses. The method is currently performed offline, but further study is planned to achieve real-time defect detection in the future.
Category: Generic
Recent advances in computer vision have shown promising results in image generation. Diffusion probabilistic models have generated realistic images from textual input, as demonstrated by DALL-E 2, Imagen, and Stable Diffusion. However, their use in medicine, where imaging data typically comprises three-dimensional volumes, has not been systematically evaluated. Synthetic images may play a crucial role in privacy-preserving artificial intelligence and can also be used to augment small datasets. We show that diffusion probabilistic models can synthesize high-quality medical data for magnetic resonance imaging (MRI) and computed tomography (CT). For quantitative evaluation, two radiologists rated the quality of the synthesized images regarding "realistic image appearance", "anatomical correctness", and "consistency between slices". Furthermore, we demonstrate that synthetic images can be used in self-supervised pre-training and improve the performance of breast segmentation models when data is scarce (Dice scores, 0.91 [without synthetic data], 0.95 [with synthetic data]).
Category: Generic
In this paper, we address the task of semantic-guided image generation. One challenge common to most existing image-level generation methods is the difficulty in generating small objects and detailed local textures. To address this, in this work we consider generating images using local context. As such, we design a local class-specific generative network using semantic maps as guidance, which separately constructs and learns subgenerators for different classes, enabling it to capture finer details. To learn more discriminative class-specific feature representations for the local generation, we also propose a novel classification module. To combine the advantages of both global image-level and local class-specific generation, a joint generation network is designed with an attention fusion module and a dual-discriminator structure embedded. Lastly, we propose a novel semantic-aware upsampling method, which has a larger receptive field and can take far-away pixels that are semantically related for feature upsampling, enabling it to better preserve semantic consistency for instances with the same semantic labels. Extensive experiments on two image generation tasks show the superior performance of the proposed method. State-of-the-art results are established by large margins on both tasks and on nine challenging public benchmarks. The source code and trained models are available at https://github.com/Ha0Tang/LGGAN.
Category: Generic
Deep learning models have been used in several domains, however, adjusting is still required to be applied in sensitive areas such as medical imaging. As the use of technology in the medical domain is needed because of the time limit, the level of accuracy assures trustworthiness. Because of privacy concerns, machine learning applications in the medical field are unable to use medical data. For example, the lack of brain MRI images makes it difficult to classify brain tumors using image-based classification. The solution to this challenge was achieved through the application of Generative Adversarial Network (GAN)-based augmentation techniques. Deep Convolutional GAN (DCGAN) and Vanilla GAN are two examples of GAN architectures used for image generation. In this paper, a framework, denoted as BrainGAN, for generating and classifying brain MRI images using GAN architectures and deep learning models was proposed. Consequently, this study proposed an automatic way to check that generated images are satisfactory. It uses three models: CNN, MobileNetV2, and ResNet152V2. Training the deep transfer models with images made by Vanilla GAN and DCGAN, and then evaluating their performance on a test set composed of real brain MRI images. From the results of the experiment, it was found that the ResNet152V2 model outperformed the other two models. The ResNet152V2 achieved 99.09% accuracy, 99.12% precision, 99.08% recall, 99.51% area under the curve (AUC), and 0.196 loss based on the brain MRI images generated by DCGAN architecture.
Category: Generic
Computed Tomography (CT) has become an important clinical imaging modality, as well as the leading source of radiation dose from medical imaging procedures. Modern CT exams are usually led by two quick orthogonal localization scans, which are used for patient positioning and diagnostic scan parameter definition. These two localization scans contribute to the patient dose but are not used for diagnosis purposes. In this study, we investigate the possibility of using deep learning models to reconstruct one localization scan image from the other, thus reducing the patient dose and simplifying the clinical workflow.
Category: Generic
Predicting brain aging can help in the early detection and prognosis of neurodegenerative diseases. Longitudinal cohorts of healthy subjects scanned through magnetic resonance imaging (MRI) have been essential to understand the structural brain changes due to aging. However, these cohorts suffer from missing data due to logistic issues in the recruitment of subjects. This paper proposes a methodology for filling up missing data in longitudinal cohorts with anatomically plausible images that capture the subject-specific aging process. The proposed methodology is developed within the framework of diffeomorphic registration. First, two novel modules are introduced within Synthmorph, a fast, state-of-the-art deep learning-based diffeomorphic registration method, to simulate the aging process between the first and last available MRI scan for each subject in three-dimensional (3D). The use of image registration also makes the generated images plausible by construction. Second, we used six image similarity measurements to rearrange the generated images to the specific age range. Finally, we estimated the age of every generated image by using the assumption of linear brain decay in healthy subjects. The methodology was evaluated on 2662 T1-weighted MRI scans from 796 healthy participants from 3 different longitudinal cohorts: Alzheimer's Disease Neuroimaging Initiative, Open Access Series of Imaging Studies-3, and Group of Neuropsychological Studies of the Canary Islands (GENIC). In total, we generated 7548 images to simulate the access of a scan per subject every 6 months in these cohorts. We evaluated the quality of the synthetic images using six quantitative measurements and a qualitative assessment by an experienced neuroradiologist with state-of-the-art results. The assumption of linear brain decay was accurate in these cohorts (R<sup>2</sup> [.924, .940]). The experimental results show that the proposed methodology can produce anatomically plausible aging predictions that can be used to enhance longitudinal datasets. Compared to deep learning-based generative methods, diffeomorphic registration is more likely to preserve the anatomy of the different structures of the brain, which makes it more appropriate for its use in clinical applications. The proposed methodology is able to efficiently simulate anatomically plausible 3D MRI scans of brain aging of healthy subjects from two images scanned at two different time points.
Category: Generic
Multimodal images such as magnetic resonance imaging (MRI) and positron emission tomography (PET) could provide complementary information about the brain and have been widely investigated for the diagnosis of neurodegenerative disorders such as Alzheimer's disease (AD). However, multimodal brain images are often incomplete in clinical practice. It is still challenging to make use of multimodality for disease diagnosis with missing data. In this paper, we propose a deep learning framework with the multi-level guided generative adversarial network (MLG-GAN) and multimodal transformer (Mul-T) for incomplete image generation and disease classification, respectively. First, MLG-GAN is proposed to generate the missing data, guided by multi-level information from voxels, features, and tasks. In addition to voxel-level supervision and task-level constraint, a feature-level auto-regression branch is proposed to embed the features of target images for an accurate generation. With the complete multimodal images, we propose a Mul-T network for disease diagnosis, which can not only combine the global and local features but also model the latent interactions and correlations from one modality to another with the cross-modal attention mechanism. Comprehensive experiments on three independent datasets (i.e., ADNI-1, ADNI-2, and OASIS-3) show that the proposed method achieves superior performance in the tasks of image generation and disease diagnosis compared to state-of-the-art methods.
Category: Generic
Recently, deep learning-based methods have been established to denoise the low-count positron emission tomography (PET) images and predict their standard-count image counterparts, which could achieve reduction of injected dosage and scan time, and improve image quality for equivalent lesion detectability and clinical diagnosis. In clinical settings, the majority scans are still acquired using standard injection dose with standard scan time. In this work, we applied a 3D U-Net network to reduce the noise of standard-count PET images to obtain the virtual-high-count (VHC) PET images for identifying the potential benefits of the obtained VHC PET images.
Category: Generic
Generative adversarial networks (GANs) and their variants as an effective method for generating visually appealing images have shown great potential in different medical imaging applications during past decades. However, some issues remain insufficiently investigated: many models still suffer from model collapse, vanishing gradients, and convergence failure. Considering the fact that medical images differ from typical RGB images in terms of complexity and dimensionality, we propose an adaptive generative adversarial network, namely MedGAN, to mitigate these issues. Specifically, we first use Wasserstein loss as a convergence metric to measure the convergence degree of the generator and the discriminator. Then, we adaptively train MedGAN based on this metric. Finally, we generate medical images based on MedGAN and use them to build few-shot medical data learning models for disease classification and lesion localization. On demodicosis, blister, molluscum, and parakeratosis datasets, our experimental results verify the advantages of MedGAN in model convergence, training speed, and visual quality of generated samples. We believe this approach can be generalized to other medical applications and contribute to radiologists' efforts for disease diagnosis. The source code can be downloaded at https://github.com/geyao-c/MedGAN.
Category: Generic
Deep-learning (DL) based CT image generation methods are often evaluated using RMSE and SSIM. By contrast, conventional model-based image reconstruction (MBIR) methods are often evaluated using image properties such as resolution, noise, bias. Calculating such image properties requires time consuming Monte Carlo (MC) simulations. For MBIR, linearized analysis using first order Taylor expansion has been developed to characterize noise and resolution without MC simulations. This inspired us to investigate if linearization can be applied to DL networks to enable efficient characterization of resolution and noise. We used FBPConvNet as an example DL network and performed extensive numerical evaluations, including both computer simulations and real CT data. Our results showed that network linearization works well under normal exposure settings. For such applications, linearization can characterize image noise and resolutions without running MC simulations. We provide with this work the computational tools to implement network linearization. The efficiency and ease of implementation of network linearization can hopefully popularize the physics-related image quality measures for DL applications. Our methodology is general; it allows flexible compositions of DL nonlinear modules and linear operators such as filtered-backprojection (FBP). For the latter, we develop a generic method for computing the covariance images that is needed for network linearization.
Category: Generic
The synthesis of high-resolution remote sensing images based on text descriptions has great potential in many practical application scenarios. Although deep neural networks have achieved great success in many important remote sensing tasks, generating realistic remote sensing images from text descriptions is still very difficult. To address this challenge, we propose a novel text-to-image modern Hopfield network (Txt2Img-MHN). The main idea of Txt2Img-MHN is to conduct hierarchical prototype learning on both text and image embeddings with modern Hopfield layers. Instead of directly learning concrete but highly diverse text-image joint feature representations for different semantics, Txt2Img-MHN aims to learn the most representative prototypes from text-image embeddings, achieving a coarse-to-fine learning strategy. These learned prototypes can then be utilized to represent more complex semantics in the text-to-image generation task. To better evaluate the realism and semantic consistency of the generated images, we further conduct zero-shot classification on real remote sensing data using the classification model trained on synthesized images. Despite its simplicity, we find that the overall accuracy in the zero-shot classification may serve as a good metric to evaluate the ability to generate an image from text. Extensive experiments on the benchmark remote sensing text-image dataset demonstrate that the proposed Txt2Img-MHN can generate more realistic remote sensing images than existing methods. Code and pre-trained models are available online (https://github.com/YonghaoXu/Txt2Img-MHN).
Category: Generic
Research on coal foreign object detection based on deep learning is of great significance to safe, efficient, and green production of coal mines. However, the foreign object image dataset is scarce due to collection conditions, which brings an enormous challenge to coal foreign object detection. To achieve augmentation of foreign object datasets, a high-quality coal foreign object image generation method based on improved StyleGAN is proposed. Firstly, the dual self-attention module is introduced into the generator to strengthen the long-distance dependence of features between spatial and channel, refine the details of the generated images, accurately distinguish the front background information, and improve the quality of the generated images. Secondly, the depthwise separable convolution is introduced into the discriminator to solve the problem of low efficiency caused by the large number of parameters of multi-stage convolutional networks, to realize the lightweight model, and to accelerate the training speed. Experimental results show that the improved model has significant advantages over several classical GANS and original StyleGAN in terms of quality and diversity of the generated images, with an average improvement of 2.52 in IS and a decrease of 5.80 in FID for each category. As for the model complexity, the parameters and training time of the improved model are reduced to 44.6% and 58.8% of the original model without affecting the generated images quality. Finally, the results of applying different data augmentation methods to the foreign object detection task show that our image generation method is more effective than the traditional methods, and that, under the optimal conditions, it improves AP<sub>box</sub> by 5.8% and AP<sub>mask</sub> by 4.5%.
Category: Generic
The advent of computed tomography significantly improves patients' health regarding diagnosis, prognosis, and treatment planning and verification. However, tomographic imaging escalates concomitant radiation doses to patients, inducing potential secondary cancer by 4%. We demonstrate the feasibility of a data-driven approach to synthesize volumetric images using patients' surface images, which can be obtained from a zero-dose surface imaging system. This study includes 500 computed tomography (CT) image sets from 50 patients. Compared to the ground truth CT, the synthetic images result in the evaluation metric values of 26.9 4.1 Hounsfield units, 39.1 1.0 dB, and 0.965 0.011 regarding the mean absolute error, peak signal-to-noise ratio, and structural similarity index measure. This approach provides a data integration solution that can potentially enable real-time imaging, which is free of radiation-induced risk and could be applied to image-guided medical procedures.
Category: Generic
The purpose of this study was to develop a method for generating synthetic MR images of macrotrabecular-massive hepatocellular carcinoma (MTM-HCC).
Category: Generic
The metabolic heterogeneity and metabolic interplay between cells are known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we are yet to establish systematic understanding of the intra-tissue metabolic heterogeneity and cooperative mechanisms. To mitigate this knowledge gap, we developed a novel computational method, namely, single-cell flux estimation analysis (scFEA), to infer the cell-wise fluxome from single-cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a systematically reconstructed human metabolic map as a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network-based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multilayer neural networks to capitulate the nonlinear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq data set with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this data set showed the consistency between predicted flux and the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics data sets and identified context- and cell group-specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analyses including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.
Category: Generic
In this paper, we investigate the problem of graph neural network quantization. Despite the great success on convolutional neural networks, directly applying current network quantization approaches to graph neural networks faces two challenges. First, the fixed-scale parameter in the current methods cannot flexibly fit diverse tasks and network architectures. Second, the variations of node degree in a graph leads to uneven responses, limiting the accuracy of the quantizer. To address these two challenges, we introduce learnable scale parameters that can be optimized jointly with the graph networks. In addition, we propose degree-aware normalization to process nodes with different degrees. Experiments on different tasks, baselines, and datasets demonstrate the superiority of our method against previous state-of-the-art ones.
Category: Generic
Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional graph representations. Graph neural networks (GNNs) are currently the most popular model in graph embedding approaches. However, standard GNNs in the neighborhood aggregation paradigm suffer from limited discriminative power in distinguishing high-order graph structures as opposed to low-order structures. To capture high-order structures, researchers have resorted to motifs and developed motif-based GNNs. However, the existing motif-based GNNs still often suffer from less discriminative power on high-order structures. To overcome the above limitations, we propose motif GNN (MGNN), a novel framework to better capture high-order structures, hinging on our proposed motif redundancy minimization operator and injective motif combination. First, MGNN produces a set of node representations with respect to each motif. The next phase is our proposed redundancy minimization among motifs which compares the motifs with each other and distills the features unique to each motif. Finally, MGNN performs the updating of node representations by combining multiple representations from different motifs. In particular, to enhance the discriminative power, MGNN uses an injective function to combine the representations with respect to different motifs. We further show that our proposed architecture increases the expressive power of GNNs with a theoretical analysis. We demonstrate that MGNN outperforms state-of-the-art methods on seven public benchmarks on both the node classification and graph classification tasks.