Stain-free identification of tissue pathology using a generative adversarial network to infer nanomechanical signatures.
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ABSTRACT:
SUBMITTER: Neary-Zajiczek L
PROVIDER: S-EPMC8577366 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Drug design is an important area of study for pharmaceutical businesses. However, low efficacy, off-target delivery, time consumption, and high cost are challenges and can create barriers that impact this process. Deep Learning models are emerging as a promising solution to perform de novo drug design, i.e., to generate drug-like molecules tailored to specific needs. However, stereochemistry was not explicitly considered in the generated molecules, which is inevitable in targeted-oriented molecules. This paper proposes a framework based on Feedback Generative Adversarial Network (GAN) that includes optimization strategy by incorporating Encoder-Decoder, GAN, and Predictor deep models interconnected with a feedback loop. The Encoder-Decoder converts the string notations of molecules into latent space vectors, effectively creating a new type of molecular representation. At the same time, the GAN can learn and replicate the training data distribution and, therefore, generate new compounds. The feedback loop is designed to incorporate and evaluate the generated molecules according to the multiobjective desired property at every epoch of training to ensure a steady shift of the generated distribution towards the space of the targeted properties. Moreover, to develop a more precise set of molecules, we also incorporate a multiobjective optimization selection technique based on a non-dominated sorting genetic algorithm. The results demonstrate that the proposed framework can generate realistic, novel molecules that span the chemical space. The proposed Encoder-Decoder model correctly reconstructs 99% of the datasets, including stereochemical information. The model's ability to find uncharted regions of the chemical space was successfully shown by optimizing the unbiased GAN to generate molecules with a high binding affinity to the Kappa Opioid and Adenosine [Formula: see text] receptor. Furthermore, the generated compounds exhibit high internal and external diversity levels 0.88 and 0.94, respectively, and uniqueness.
| S-EPMC9233801 | biostudies-literature
Project description:MotivationAccurate disease phenotype prediction plays an important role in the treatment of heterogeneous diseases like cancer in the era of precision medicine. With the advent of high throughput technologies, more comprehensive multi-omics data is now available that can effectively link the genotype to phenotype. However, the interactive relation of multi-omics datasets makes it particularly challenging to incorporate different biological layers to discover the coherent biological signatures and predict phenotypic outcomes. In this study, we introduce omicsGAN, a generative adversarial network model to integrate two omics data and their interaction network. The model captures information from the interaction network as well as the two omics datasets and fuse them to generate synthetic data with better predictive signals.ResultsLarge-scale experiments on The Cancer Genome Atlas breast cancer, lung cancer and ovarian cancer datasets validate that (i) the model can effectively integrate two omics data (e.g. mRNA and microRNA expression data) and their interaction network (e.g. microRNA-mRNA interaction network). The synthetic omics data generated by the proposed model has a better performance on cancer outcome classification and patients survival prediction compared to original omics datasets. (ii) The integrity of the interaction network plays a vital role in the generation of synthetic data with higher predictive quality. Using a random interaction network does not allow the framework to learn meaningful information from the omics datasets; therefore, results in synthetic data with weaker predictive signals.Availability and implementationSource code is available at: https://github.com/CompbioLabUCF/omicsGAN.Supplementary informationSupplementary data are available at Bioinformatics online.
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Project description:Trillions of microbes inhabit the human body and have a profound effect on human health. The recent development of metagenome-wide association studies and other quantitative analysis methods accelerate the discovery of the associations between human microbiome and diseases. To assess the strengths and limitations of these analytical tools, simulating realistic microbiome datasets is critically important. However, simulating the real microbiome data is challenging because it is difficult to model their correlation structure using explicit statistical models. To address the challenge of simulating realistic microbiome data, we designed a novel simulation framework termed MB-GAN, by using a generative adversarial network (GAN) and utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from them. In practice, MB-GAN showed the following advantages. First, MB-GAN avoids explicit statistical modeling assumptions, and it only requires real datasets as inputs. Second, unlike the traditional GANs, MB-GAN is easily applicable and can converge efficiently. By applying MB-GAN to a case-control gut microbiome study of 396 samples, we demonstrated that the simulated data and the original data had similar first-order and second-order properties, including sparsity, diversities, and taxa-taxa correlations. These advantages are suitable for further microbiome methodology development where high-fidelity microbiome data are needed.
| S-EPMC7931821 | biostudies-literature
Project description:In this paper, we propose the quantum semi-supervised generative adversarial network (qSGAN). The system is composed of a quantum generator and a classical discriminator/classifier (D/C). The goal is to train both the generator and the D/C, so that the latter may get a high classification accuracy for a given dataset. Hence the qSGAN needs neither any data loading nor to generate a pure quantum state, implying that qSGAN is much easier to implement than many existing quantum algorithms. Also the generator can serve as a stronger adversary than a classical one thanks to its rich expressibility, and it is expected to be robust against noise. These advantages are demonstrated in a numerical simulation.
| S-EPMC8490428 | biostudies-literature
Project description:PurposeDynamic contrast-enhanced computed tomography (CT) is widely used to provide dynamic tissue contrast for diagnostic investigation and vascular identification. However, the phase information of contrast injection is typically recorded manually by technicians, which introduces missing or mislabeling. Hence, imaging-based contrast phase identification is appealing, but challenging, due to large variations among different contrast protocols, vascular dynamics, and metabolism, especially for clinically acquired CT scans. The purpose of this study is to perform imaging-based phase identification for dynamic abdominal CT using a proposed adversarial learning framework across five representative contrast phases.MethodsA generative adversarial network (GAN) is proposed as a disentangled representation learning model. To explicitly model different contrast phases, a low dimensional common representation and a class specific code are fused in the hidden layer. Then, the low dimensional features are reconstructed following a discriminator and classifier. 36 350 slices of CT scans from 400 subjects are used to evaluate the proposed method with fivefold cross-validation with splits on subjects. Then, 2216 slices images from 20 independent subjects are employed as independent testing data, which are evaluated using multiclass normalized confusion matrix.ResultsThe proposed network significantly improved correspondence (0.93) over VGG, ResNet50, StarGAN, and 3DSE with accuracy scores 0.59, 0.62, 0.72, and 0.90, respectively (P < 0.001 Stuart-Maxwell test for normalized multiclass confusion matrix).ConclusionWe show that adversarial learning for discriminator can be benefit for capturing contrast information among phases. The proposed discriminator from the disentangled network achieves promising results.
| S-EPMC9053868 | biostudies-literature
Project description:Generative adversarial networks (GANs) have been used to obtain super-resolution (SR) videos that have improved visual perception quality and more coherent details. However, the latest methods perform poorly in areas with dense textures. To better recover the areas with dense textures in video frames and improve the visual perception quality and coherence in videos, this paper proposes a multiresolution mixture generative adversarial network for video super-resolution (MRMVSR). We propose a multiresolution mixture network (MRMNet) as the generative network that can simultaneously generate multiresolution feature maps. In MRMNet, the high-resolution (HR) feature maps can continuously extract information from low-resolution (LR) feature maps to supplement information. In addition, we propose a residual fluctuation loss function for video super-resolution. The residual fluctuation loss function is used to reduce the overall residual fluctuation on SR and HR video frames to avoid a scenario where local differences are too large. Experimental results on the public benchmark dataset show that our method outperforms the state-of-the-art methods for the majority of the test sets.
| S-EPMC7351143 | biostudies-literature
Project description:PurposeTo explore whether generative adversarial networks (GANs) can enable synthesis of realistic medical images that are indiscernible from real images, even by domain experts.Materials and methodsIn this retrospective study, progressive growing GANs were used to synthesize mammograms at a resolution of 1280 × 1024 pixels by using images from 90 000 patients (average age, 56 years ± 9) collected between 2009 and 2019. To evaluate the results, a method to assess distributional alignment for ultra-high-dimensional pixel distributions was used, which was based on moment plots. This method was able to reveal potential sources of misalignment. A total of 117 volunteer participants (55 radiologists and 62 nonradiologists) took part in a study to assess the realism of synthetic images from GANs.ResultsA quantitative evaluation of distributional alignment shows 60%-78% mutual-information score between the real and synthetic image distributions, and 80%-91% overlap in their support, which are strong indications against mode collapse. It also reveals shape misalignment as the main difference between the two distributions. Obvious artifacts were found by an untrained observer in 13.6% and 6.4% of the synthetic mediolateral oblique and craniocaudal images, respectively. A reader study demonstrated that real and synthetic images are perceptually inseparable by the majority of participants, even by trained breast radiologists. Only one out of the 117 participants was able to reliably distinguish real from synthetic images, and this study discusses the cues they used to do so.ConclusionOn the basis of these findings, it appears possible to generate realistic synthetic full-field digital mammograms by using a progressive GAN architecture up to a resolution of 1280 × 1024 pixels.Supplemental material is available for this article.© RSNA, 2020.
| S-EPMC8043361 | biostudies-literature
Project description:Background The study aims to evaluate the accuracy of the generative adversarial networks (GAN) for reconstructing bony midfacial defects. Methods According to anatomy, the bony midface was divided into five subunit structural regions and artificial defects are manually created on the corresponding CT images. GAN is trained to reconstruct artificial defects to their previous normal shape and tested. The clinical defects are reconstructed by the trained GAN, where the midspan defects were used for qualitative evaluation and the unilateral defects were used for quantitative evaluation. The cosine similarity and the mean error are used to evaluate the accuracy of reconstruction. The Mann–Whitney U test is used to detect whether reconstruction errors were consistent in artificial and unilateral clinical defects. Results This study included 518 normal CT data, with 415 in training set and 103 in testing set, and 17 real patient data, with 2 midspan defects and 15 unilateral defects. Reconstruction of midspan clinical defects assessed by experts is acceptable. The cosine similarity in the reconstruction of artificial defects and unilateral clinical defects is 0.97 ± 0.01 and 0.96 ± 0.01, P = 0.695. The mean error in the reconstruction of artificial defects and unilateral clinical defects is 0.59 ± 0.31 mm and 0.48 ± 0.08 mm, P = 0.09. Conclusion GAN-based virtual reconstruction technology has reached a high accuracy in testing set, and statistical tests suggest that it can achieve similar results in real patient data. This study has preliminarily solved the problem of bony midfacial defect without reference. Supplementary Information The online version contains supplementary material available at 10.1186/s13005-022-00325-2.
| S-EPMC9235085 | biostudies-literature
Project description:Transforming optical facial images into sketches while preserving realism and facial features poses a significant challenge. The current methods that rely on paired training data are costly and resource-intensive. Furthermore, they often fail to capture the intricate features of faces, resulting in substandard sketch generation. To address these challenges, we propose the novel hierarchical contrast generative adversarial network (HCGAN). Firstly, HCGAN consists of a global sketch synthesis module that generates sketches with well-defined global features and a local sketch refinement module that enhances the ability to extract features in critical areas. Secondly, we introduce local refinement loss based on the local sketch refinement module, refining sketches at a granular level. Finally, we propose an association strategy called "warmup-epoch" and local consistency loss between the two modules to ensure HCGAN is effectively optimized. Evaluations of the CUFS and SKSF-A datasets demonstrate that our method produces high-quality sketches and outperforms existing state-of-the-art methods in terms of fidelity and realism. Compared to the current state-of-the-art methods, HCGAN reduces FID by 12.6941, 4.9124, and 9.0316 on three datasets of CUFS, respectively, and by 7.4679 on the SKSF-A dataset. Additionally, it obtained optimal scores for content fidelity (CF), global effects (GE), and local patterns (LP). The proposed HCGAN model provides a promising solution for realistic sketch synthesis under unpaired data training.
| S-EPMC11322990 | biostudies-literature
Project description:Hi-C is commonly used to study three-dimensional genome organization. However, due to the high sequencing cost and technical constraints, the resolution of most Hi-C datasets is coarse, resulting in a loss of information and biological interpretability. Here we develop DeepHiC, a generative adversarial network, to predict high-resolution Hi-C contact maps from low-coverage sequencing data. We demonstrated that DeepHiC is capable of reproducing high-resolution Hi-C data from as few as 1% downsampled reads. Empowered by adversarial training, our method can restore fine-grained details similar to those in high-resolution Hi-C matrices, boosting accuracy in chromatin loops identification and TADs detection, and outperforms the state-of-the-art methods in accuracy of prediction. Finally, application of DeepHiC to Hi-C data on mouse embryonic development can facilitate chromatin loop detection. We develop a web-based tool (DeepHiC, http://sysomics.com/deephic) that allows researchers to enhance their own Hi-C data with just a few clicks.
| S-EPMC7055922 | biostudies-literature