Sensitivity of deep learning applied to spatial image steganalysis.
Ontology highlight
ABSTRACT:
SUBMITTER: Tabares-Soto R
PROVIDER: S-EPMC8444093 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Medical image classification is a novel technology that presents a new challenge. It is essential that pathological images are automatically and correctly classified to enable doctors to provide precise treatment. Convolutional neural networks have demonstrated their effectiveness in classifying images in deep learning, which may have dozens or hundreds of layers, to illustrate the relationship between them in terms of their different neural network features. Convolutional layers consisting of small kernels take weights as input and guide them through an activation function as output. The main advantage of using convolutional neural networks (CNNs) instead of traditional neural networks is that they reduce the model parameters for greater accuracy. However, many studies have simply been focused on finding the best CNN model and classification results from a single medical image classification. Therefore, we applied a common deep learning network model in an attempt to identify the best model framework by training and validating different model parameters to classify medical images. After conducting experiments on six publicly available databases of pathological images, including colorectal cancer tissue, chest X-rays, common skin lesions, diabetic retinopathy, pediatric chest X-ray, and breast ultrasound image datasets, we were able to confirm that the recognition accuracy of the Inception V3 method was significantly better than that of other existing deep learning models.
| S-EPMC9600639 | biostudies-literature
Project description:Graph-based deep learning has shown great promise in cancer histopathology image analysis by contextualizing complex morphology and structure across whole slide images to make high quality downstream outcome predictions (ex: prognostication). These methods rely on informative representations (i.e., embeddings) of image patches comprising larger slides, which are used as node attributes in slide graphs. Spatial omics data, including spatial transcriptomics, is a novel paradigm offering a wealth of detailed information. Pairing this data with corresponding histological imaging localized at 50-micron resolution, may facilitate the development of algorithms which better appreciate the morphological and molecular underpinnings of carcinogenesis. Here, we explore the utility of leveraging spatial transcriptomics data with a contrastive crossmodal pretraining mechanism to generate deep learning models that can extract molecular and histological information for graph-based learning tasks. Performance on cancer staging, lymph node metastasis prediction, survival prediction, and tissue clustering analyses indicate that the proposed methods bring improvement to graph based deep learning models for histopathological slides compared to leveraging histological information from existing schemes, demonstrating the promise of mining spatial omics data to enhance deep learning for pathology workflows.
| S-EPMC10783797 | biostudies-literature
Project description:Recovery from acute kidney injury can vary widely in patients and in animal models. Immunofluorescence staining can provide spatial information about heterogeneous injury responses, but often only a fraction of stained tissue is analyzed. Deep learning can expand analysis to larger areas and sample numbers by substituting for time-intensive manual or semi-automated quantification techniques. Here we report one approach to leverage deep learning tools to quantify heterogenous responses to kidney injury that can be deployed without specialized equipment or programming expertise. We first demonstrated that deep learning models generated from small training sets accurately identified a range of stains and structures with performance similar to that of trained human observers. We then showed this approach accurately tracks the evolution of folic acid induced kidney injury in mice and highlights spatially clustered tubules that fail to repair. We then demonstrated that this approach captures the variation in recovery across a robust sample of kidneys after ischemic injury. Finally, we showed markers of failed repair after ischemic injury were correlated both spatially within and between animals and that failed repair was inversely correlated with peritubular capillary density. Combined, we demonstrate the utility and versatility of our approach to capture spatially heterogenous responses to kidney injury.
| S-EPMC10115810 | biostudies-literature
Project description:Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually-tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep learning models for cell segmentation and spot detection with a probabilistic gene decoder to quantify single-cell gene expression accurately. Polaris offers a unifying, turnkey solution for analyzing spatial transcriptomics data from MERFSIH, seqFISH, or ISS experiments. Polaris is available through the DeepCell software library (https://github.com/vanvalenlab/deepcell-spots) and https://www.deepcell.org.
| S-EPMC10508757 | biostudies-literature
Project description:PurposeImage quality of positron emission tomography (PET) is limited by various physical degradation factors. Our study aims to perform PET image denoising by utilizing prior information from the same patient. The proposed method is based on unsupervised deep learning, where no training pairs are needed.MethodsIn this method, the prior high-quality image from the patient was employed as the network input and the noisy PET image itself was treated as the training label. Constrained by the network structure and the prior image input, the network was trained to learn the intrinsic structure information from the noisy image and output a restored PET image. To validate the performance of the proposed method, a computer simulation study based on the BrainWeb phantom was first performed. A 68Ga-PRGD2 PET/CT dataset containing 10 patients and a 18F-FDG PET/MR dataset containing 30 patients were later on used for clinical data evaluation. The Gaussian, non-local mean (NLM) using CT/MR image as priors, BM4D, and Deep Decoder methods were included as reference methods. The contrast-to-noise ratio (CNR) improvements were used to rank different methods based on Wilcoxon signed-rank test.ResultsFor the simulation study, contrast recovery coefficient (CRC) vs. standard deviation (STD) curves showed that the proposed method achieved the best performance regarding the bias-variance tradeoff. For the clinical PET/CT dataset, the proposed method achieved the highest CNR improvement ratio (53.35% ± 21.78%), compared with the Gaussian (12.64% ± 6.15%, P = 0.002), NLM guided by CT (24.35% ± 16.30%, P = 0.002), BM4D (38.31% ± 20.26%, P = 0.002), and Deep Decoder (41.67% ± 22.28%, P = 0.002) methods. For the clinical PET/MR dataset, the CNR improvement ratio of the proposed method achieved 46.80% ± 25.23%, higher than the Gaussian (18.16% ± 10.02%, P < 0.0001), NLM guided by MR (25.36% ± 19.48%, P < 0.0001), BM4D (37.02% ± 21.38%, P < 0.0001), and Deep Decoder (30.03% ± 20.64%, P < 0.0001) methods. Restored images for all the datasets demonstrate that the proposed method can effectively smooth out the noise while recovering image details.ConclusionThe proposed unsupervised deep learning framework provides excellent image restoration effects, outperforming the Gaussian, NLM methods, BM4D, and Deep Decoder methods.
| S-EPMC7814987 | biostudies-literature
Project description:Artificial intelligence, deep convolutional neural networks, and deep learning are all niche terms that are increasingly appearing in scientific presentations as well as in the general media. In this review, we focus on deep learning and how it is applied to microscopy image data of cells and tissue samples. Starting with an analogy to neuroscience, we aim to give the reader an overview of the key concepts of neural networks, and an understanding of how deep learning differs from more classical approaches for extracting information from image data. We aim to increase the understanding of these methods, while highlighting considerations regarding input data requirements, computational resources, challenges, and limitations. We do not provide a full manual for applying these methods to your own data, but rather review previously published articles on deep learning in image cytometry, and guide the readers toward further reading on specific networks and methods, including new methods not yet applied to cytometry data. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
| S-EPMC6590257 | biostudies-literature
Project description:Cassava is the third largest source of carbohydrates for human food in the world but is vulnerable to virus diseases, which threaten to destabilize food security in sub-Saharan Africa. Novel methods of cassava disease detection are needed to support improved control which will prevent this crisis. Image recognition offers both a cost effective and scalable technology for disease detection. New deep learning models offer an avenue for this technology to be easily deployed on mobile devices. Using a dataset of cassava disease images taken in the field in Tanzania, we applied transfer learning to train a deep convolutional neural network to identify three diseases and two types of pest damage (or lack thereof). The best trained model accuracies were 98% for brown leaf spot (BLS), 96% for red mite damage (RMD), 95% for green mite damage (GMD), 98% for cassava brown streak disease (CBSD), and 96% for cassava mosaic disease (CMD). The best model achieved an overall accuracy of 93% for data not used in the training process. Our results show that the transfer learning approach for image recognition of field images offers a fast, affordable, and easily deployable strategy for digital plant disease detection.
| S-EPMC5663696 | biostudies-literature
Project description:In recent years, deep learning (DL) networks have been widely used in super-resolution (SR) and exhibit improved performance. In this paper, an image quality assessment (IQA)-guided single image super-resolution (SISR) method is proposed in DL architecture, in order to achieve a nice tradeoff between perceptual quality and distortion measure of the SR result. Unlike existing DL-based SR algorithms, an IQA net is introduced to extract perception features from SR results, calculate corresponding loss fused with original absolute pixel loss, and guide the adjustment of SR net parameters. To solve the problem of heterogeneous datasets used by IQA and SR networks, an interactive training model is established via cascaded network. We also propose a pairwise ranking hinge loss method to overcome the shortcomings of insufficient samples during training process. The performance comparison between our proposed method with recent SISR methods shows that the former achieves a better tradeoff between perceptual quality and distortion measure than the latter. Extensive benchmark experiments and analyses also prove that our method provides a promising and opening architecture for SISR, which is not confined to a specific network model.
| S-EPMC7595386 | biostudies-literature
Project description:Digitalisation has opened a wealth of new data opportunities by revolutionizing how images are captured. Although the cost of data generation is no longer a major concern, the data management and processing have become a bottleneck. Any successful visual trait system requires automated data structuring and a data retrieval model to manage, search, and retrieve unstructured and complex image data. This paper investigates a highly scalable and computationally efficient image retrieval system for real-time content-based searching through large-scale image repositories in the domain of remote sensing and plant biology. Images are processed independently without considering any relevant context between sub-sets of images. We utilize a deep Convolutional Neural Network (CNN) model as a feature extractor to derive deep feature representations from the imaging data. In addition, we propose an effective scheme to optimize data structure that can facilitate faster querying at search time based on the hierarchically nested structure and recursive similarity measurements. A thorough series of tests were carried out for plant identification and high-resolution remote sensing data to evaluate the accuracy and the computational efficiency of the proposed approach against other content-based image retrieval (CBIR) techniques, such as the bag of visual words (BOVW) and multiple feature fusion techniques. The results demonstrate that the proposed scheme is effective and considerably faster than conventional indexing structures.
| S-EPMC8320911 | biostudies-literature
Project description:Background and aimsEarly diagnosis of aortic stenosis (AS) is critical to prevent morbidity and mortality but requires skilled examination with Doppler imaging. This study reports the development and validation of a novel deep learning model that relies on two-dimensional (2D) parasternal long axis videos from transthoracic echocardiography without Doppler imaging to identify severe AS, suitable for point-of-care ultrasonography.Methods and resultsIn a training set of 5257 studies (17 570 videos) from 2016 to 2020 [Yale-New Haven Hospital (YNHH), Connecticut], an ensemble of three-dimensional convolutional neural networks was developed to detect severe AS, leveraging self-supervised contrastive pretraining for label-efficient model development. This deep learning model was validated in a temporally distinct set of 2040 consecutive studies from 2021 from YNHH as well as two geographically distinct cohorts of 4226 and 3072 studies, from California and other hospitals in New England, respectively. The deep learning model achieved an area under the receiver operating characteristic curve (AUROC) of 0.978 (95% CI: 0.966, 0.988) for detecting severe AS in the temporally distinct test set, maintaining its diagnostic performance in geographically distinct cohorts [0.952 AUROC (95% CI: 0.941, 0.963) in California and 0.942 AUROC (95% CI: 0.909, 0.966) in New England]. The model was interpretable with saliency maps identifying the aortic valve, mitral annulus, and left atrium as the predictive regions. Among non-severe AS cases, predicted probabilities were associated with worse quantitative metrics of AS suggesting an association with various stages of AS severity.ConclusionThis study developed and externally validated an automated approach for severe AS detection using single-view 2D echocardiography, with potential utility for point-of-care screening.
| S-EPMC11004929 | biostudies-literature