scholarly journals Multi-omics Data Integration by Generative Adversarial Network

2021 ◽  
Author(s):  
Khandakar Tanvir Ahmed ◽  
Jiao Sun ◽  
Jeongsik Yong ◽  
Wei Zhang
Keyword(s):  
Large Scale ◽  
Synthetic Data ◽  
Interaction Network ◽  
Vital Role ◽  
The Cancer Genome Atlas ◽  
Survival Prediction ◽  
Omics Data ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Cancer Outcome

Accurate 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 (GAN) 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. Large-scale experiments on The Cancer Genome Atlas (TCGA) breast cancer and ovarian cancer datasets validate that (1) the model can effectively integrate two omics data (i.e., mRNA and microRNA expression data) and their interaction network (i.e., 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. (2) 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.

scholarly journals Generative adversarial network for glioblastoma ensures morphologic variations and improves diagnostic model for isocitrate dehydrogenase mutant type

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ji Eun Park ◽  
Dain Eun ◽  
Ho Sung Kim ◽  
Da Hyun Lee ◽  
Ryoung Woo Jang ◽  
...  
Keyword(s):  
Isocitrate Dehydrogenase ◽  
Synthetic Data ◽  
Diagnostic Model ◽  
Generative Adversarial Network ◽  
Classification Rate ◽  
Mutant Type ◽  
Clinical Model ◽  
The Real ◽  
Adversarial Network ◽  
Synthetic Images

AbstractGenerative adversarial network (GAN) creates synthetic images to increase data quantity, but whether GAN ensures meaningful morphologic variations is still unknown. We investigated whether GAN-based synthetic images provide sufficient morphologic variations to improve molecular-based prediction, as a rare disease of isocitrate dehydrogenase (IDH)-mutant glioblastomas. GAN was initially trained on 500 normal brains and 110 IDH-mutant high-grade astocytomas, and paired contrast-enhanced T1-weighted and FLAIR MRI data were generated. Diagnostic models were developed from real IDH-wild type (n = 80) with real IDH-mutant glioblastomas (n = 38), or with synthetic IDH-mutant glioblastomas, or augmented by adding both real and synthetic IDH-mutant glioblastomas. Turing tests showed synthetic data showed reality (classification rate of 55%). Both the real and synthetic data showed that a more frontal or insular location (odds ratio [OR] 1.34 vs. 1.52; P = 0.04) and distinct non-enhancing tumor margins (OR 2.68 vs. 3.88; P < 0.001), which become significant predictors of IDH-mutation. In an independent validation set, diagnostic accuracy was higher for the augmented model (90.9% [40/44] and 93.2% [41/44] for each reader, respectively) than for the real model (84.1% [37/44] and 86.4% [38/44] for each reader, respectively). The GAN-based synthetic images yield morphologically variable, realistic-seeming IDH-mutant glioblastomas. GAN will be useful to create a realistic training set in terms of morphologic variations and quality, thereby improving diagnostic performance in a clinical model.

scholarly journals Denoising large-scale biological data using network filters

2021 ◽  
Author(s):  
Andrew J Kavran ◽  
Aaron Clauset
Keyword(s):  
Large Scale ◽  
Synthetic Data ◽  
Interaction Network ◽  
Learning Task ◽  
Biological Data ◽  
Data Sets ◽  
Proteomics Data ◽  
Life History Variation ◽  
Wide Range ◽  
Underlying Processes

Abstract Background: Large-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation.Results: We describe a general method for automatically reducing noise in large-scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or “filtered” to better recover an underlying biological signal. Similar to the process of denoising an image, a single network filter may be applied to an entire system, or the system may be first decomposed into distinct modules and a different filter applied to each. Applied to synthetic data with known network structure and signal, network filters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancerous tissues, network filtering prior to training increases accuracy up to 43% compared to using unfiltered data.Conclusions: Network filters are a general way to denoise biological data and can account for both correlation and anti-correlation between different measurements. Furthermore, we find that partitioning a network prior to filtering can significantly reduce errors in networks with heterogenous data and correlation patterns, and this approach outperforms existing diffusion based methods. Our results on proteomics data indicate the broad potential utility of network filters to applications in systems biology.

scholarly journals Financial Thought Experiment: A GAN-based Approach to Vast Robust Portfolio Selection

2020 ◽  
Author(s):  
Chi Seng Pun ◽  
Lei Wang ◽  
Hoi Ying Wong
Keyword(s):  
Stock Market ◽  
Thought Experiment ◽  
Empirical Studies ◽  
Synthetic Data ◽  
Risk Minimization ◽  
Portfolio Risk ◽  
Generative Adversarial Network ◽  
Day Trading ◽  
Adversarial Network ◽  
Robust Portfolio

Modern day trading practice resembles a thought experiment, where investors imagine various possibilities of future stock market and invest accordingly. Generative adversarial network (GAN) is highly relevant to this trading practice in two ways. First, GAN generates synthetic data by a neural network that is technically indistinguishable from the reality, which guarantees the reasonableness of the experiment. Second, GAN generates multitudes of fake data, which implements half of the experiment. In this paper, we present a new architecture of GAN and adapt it to portfolio risk minimization problem by adding a regression network to GAN (implementing the second half of the experiment). The new architecture is termed GANr. Battling against two distinctive networks: discriminator and regressor, GANr's generator aims to simulate a stock market that is close to the reality while allow for all possible scenarios. The resulting portfolio resembles a robust portfolio with data-driven ambiguity. Our empirical studies show that GANr portfolio is more resilient to bleak financial scenarios than CLSGAN and LASSO portfolios.

scholarly journals Group Lasso Regularized Deep Learning for Cancer Prognosis from Multi-Omics and Clinical Features

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 240 ◽  
Author(s):  
Gangcai Xie ◽  
Chengliang Dong ◽  
Yinfei Kong ◽  
Jiang Zhong ◽  
Mingyao Li ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prior Knowledge ◽  
Clinical Features ◽  
Large Scale ◽  
Real Data ◽  
Group Lasso ◽  
Cancer Prognosis ◽  
Survival Prediction ◽  
Omics Data ◽  
Patients With Cancer

Accurate prognosis of patients with cancer is important for the stratification of patients, the optimization of treatment strategies, and the design of clinical trials. Both clinical features and molecular data can be used for this purpose, for instance, to predict the survival of patients censored at specific time points. Multi-omics data, including genome-wide gene expression, methylation, protein expression, copy number alteration, and somatic mutation data, are becoming increasingly common in cancer studies. To harness the rich information in multi-omics data, we developed GDP (Group lass regularized Deep learning for cancer Prognosis), a computational tool for survival prediction using both clinical and multi-omics data. GDP integrated a deep learning framework and Cox proportional hazard model (CPH) together, and applied group lasso regularization to incorporate gene-level group prior knowledge into the model training process. We evaluated its performance in both simulated and real data from The Cancer Genome Atlas (TCGA) project. In simulated data, our results supported the importance of group prior information in the regularization of the model. Compared to the standard lasso regularization, we showed that group lasso achieved higher prediction accuracy when the group prior knowledge was provided. We also found that GDP performed better than CPH for complex survival data. Furthermore, analysis on real data demonstrated that GDP performed favorably against other methods in several cancers with large-scale omics data sets, such as glioblastoma multiforme, kidney renal clear cell carcinoma, and bladder urothelial carcinoma. In summary, we demonstrated that GDP is a powerful tool for prognosis of patients with cancer, especially when large-scale molecular features are available.

scholarly journals GANai: Standardizing CT Images using Generative Adversarial Network with Alternative Improvement

2018 ◽  
Author(s):  
Gongbo Liang ◽  
Sajjad Fouladvand ◽  
Jie Zhang ◽  
Michael A. Brooks ◽  
Nathan Jacobs ◽  
...  
Keyword(s):  
Large Scale ◽  
Model Performance ◽  
Image Synthesis ◽  
Ct Images ◽  
Image Features ◽  
Training Data ◽  
Ct Image ◽  
Generative Adversarial Network ◽  
Training Strategy ◽  
Adversarial Network

AbstractComputed tomography (CT) is a widely-used diag-reproducibility regarding radiomic features, such as intensity, nostic image modality routinely used for assessing anatomical tissue characteristics. However, non-standardized imaging pro-tocols are commonplace, which poses a fundamental challenge in large-scale cross-center CT image analysis. One approach to address the problem is to standardize CT images using generative adversarial network models (GAN). GAN learns the data distribution of training images and generate synthesized images under the same distribution. However, existing GAN models are not directly applicable to this task mainly due to the lack of constraints on the mode of data to generate. Furthermore, they treat every image equally, but in real applications, some images are more difficult to standardize than the others. All these may lead to the lack-of-detail problem in CT image synthesis. We present a new GAN model called GANai to mitigate the differences in radiomic features across CT images captured using non-standard imaging protocols. Given source images, GANai composes new images by specifying a high-level goal that the image features of the synthesized images should be similar to those of the standard images. GANai introduces an alternative improvement training strategy to alternatively and steadily improve model performance. The new training strategy enables a series of technical improvements, including phase-specific loss functions, phase-specific training data, and the adoption of ensemble learning, leading to better model performance. The experimental results show that GANai is significantly better than the existing state-of-the-art image synthesis algorithms on CT image standardization. Also, it significantly improves the efficiency and stability of GAN model training.

scholarly journals IMAGE TO POINT CLOUD TRANSLATION USING CONDITIONAL GENERATIVE ADVERSARIAL NETWORK FOR AIRBORNE LIDAR DATA

2021 ◽  
Vol V-2-2021 ◽  
pp. 169-174
Author(s):  
T. Shinohara ◽  
H. Xiu ◽  
M. Matsuoka
Keyword(s):  
Point Cloud ◽  
Large Scale ◽  
Point Clouds ◽  
Airborne Lidar ◽  
Real Point ◽  
3D Point Cloud ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
3D Point Clouds ◽  
Latent Features

Abstract. This study introduces a novel image to a 3D point-cloud translation method with a conditional generative adversarial network that creates a large-scale 3D point cloud. This can generate supervised point clouds observed via airborne LiDAR from aerial images. The network is composed of an encoder to produce latent features of input images, generator to translate latent features to fake point clouds, and discriminator to classify false or real point clouds. The encoder is a pre-trained ResNet; to overcome the difficulty of generating 3D point clouds in an outdoor scene, we use a FoldingNet with features from ResNet. After a fixed number of iterations, our generator can produce fake point clouds that correspond to the input image. Experimental results show that our network can learn and generate certain point clouds using the data from the 2018 IEEE GRSS Data Fusion Contest.

scholarly journals Cross-Modality Person Re-Identification with Generative Adversarial Training

2018 ◽  
Author(s):  
Pingyang Dai ◽  
Rongrong Ji ◽  
Haibin Wang ◽  
Qiong Wu ◽  
Yuyu Huang
Keyword(s):  
Large Scale ◽  
Characteristic Curve ◽  
Metric Learning ◽  
Feature Representation ◽  
Superior Performance ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Discriminative Feature ◽  
Adversarial Training ◽  
Rgb Images

Person re-identification (Re-ID) is an important task in video surveillance which automatically searches and identifies people across different cameras. Despite the extensive Re-ID progress in RGB cameras, few works have studied the Re-ID between infrared and RGB images, which is essentially a cross-modality problem and widely encountered in real-world scenarios. The key challenge lies in two folds, i.e., the lack of discriminative information to re-identify the same person between RGB and infrared modalities, and the difficulty to learn a robust metric towards such a large-scale cross-modality retrieval. In this paper, we tackle the above two challenges by proposing a novel cross-modality generative adversarial network (termed cmGAN). To handle the issue of insufficient discriminative information, we leverage the cutting-edge generative adversarial training to design our own discriminator to learn discriminative feature representation from different modalities. To handle the issue of large-scale cross-modality metric learning, we integrates both identification loss and cross-modality triplet loss, which minimize inter-class ambiguity while maximizing cross-modality similarity among instances. The entire cmGAN can be trained in an end-to-end manner by using standard deep neural network framework. We have quantized the performance of our work in the newly-released SYSU RGB-IR Re-ID benchmark, and have reported superior performance, i.e., Cumulative Match Characteristic curve (CMC) and Mean Average Precision (MAP), over the state-of-the-art works [Wu et al., 2017], respectively.

scholarly journals GAN-GL: Generative Adversarial Networks for Glacial Lake Mapping

2021 ◽  
Vol 13 (22) ◽  
pp. 4728
Author(s):  
Hang Zhao ◽  
Meimei Zhang ◽  
Fang Chen
Keyword(s):  
Large Scale ◽  
Glacial Lake ◽  
Background Information ◽  
Generative Adversarial Networks ◽  
High Mountain ◽  
Landsat 8 ◽  
Glacial Lakes ◽  
Ancillary Data ◽  
Generative Adversarial Network ◽  
Adversarial Network

Remote sensing is a powerful tool that provides flexibility and scalability for monitoring and investigating glacial lakes in High Mountain Asia (HMA). However, existing methods for mapping glacial lakes are designed based on a combination of several spectral features and ancillary data (such as the digital elevation model, DEM) to highlight the lake extent and suppress background information. These methods, however, suffer from either the inevitable requirement of post-processing work or the high costs of additional data acquisition. Signifying a key advancement in the deep learning models, a generative adversarial network (GAN) can capture multi-level features and learn the mapping rules in source and target domains using a minimax game between a generator and discriminator. This provides a new and feasible way to conduct large-scale glacial lake mapping. In this work, a complete glacial lake dataset was first created, containing approximately 4600 patches of Landsat-8 OLI images edited in three ways—random cropping, density cropping, and uniform cropping. Then, a GAN model for glacial lake mapping (GAN-GL) was constructed. The GAN-GL consists of two parts—a generator that incorporates a water attention module and an image segmentation module to produce the glacial lake masks, and a discriminator which employs the ResNet-152 backbone to ascertain whether a given pixel belonged to a glacial lake. The model was evaluated using the created glacial lake dataset, delivering a good performance, with an F1 score of 92.17% and IoU of 86.34%. Moreover, compared to the mapping results derived from the global–local iterative segmentation algorithm and random forest for the entire Eastern Himalayas, our proposed model was superior regarding the segmentation of glacial lakes under complex and diverse environmental conditions, in terms of accuracy (precision = 93.19%) and segmentation efficiency. Our model was also very good at detecting small glacial lakes without assistance from ancillary data or human intervention.

scholarly journals AI Radar Sensor: Creating Radar Depth Sounder Images Based on Generative Adversarial Network

Sensors ◽  
2019 ◽  
Vol 19 (24) ◽  
pp. 5479 ◽  
Author(s):  
Maryam Rahnemoonfar ◽  
Jimmy Johnson ◽  
John Paden
Keyword(s):  
Data Augmentation ◽  
Synthetic Data ◽  
Detection Algorithm ◽  
Contour Detection ◽  
Training Data ◽  
Generative Adversarial Network ◽  
Radar Images ◽  
Adversarial Network ◽  
Radar Imagery

Significant resources have been spent in collecting and storing large and heterogeneous radar datasets during expensive Arctic and Antarctic fieldwork. The vast majority of data available is unlabeled, and the labeling process is both time-consuming and expensive. One possible alternative to the labeling process is the use of synthetically generated data with artificial intelligence. Instead of labeling real images, we can generate synthetic data based on arbitrary labels. In this way, training data can be quickly augmented with additional images. In this research, we evaluated the performance of synthetically generated radar images based on modified cycle-consistent adversarial networks. We conducted several experiments to test the quality of the generated radar imagery. We also tested the quality of a state-of-the-art contour detection algorithm on synthetic data and different combinations of real and synthetic data. Our experiments show that synthetic radar images generated by generative adversarial network (GAN) can be used in combination with real images for data augmentation and training of deep neural networks. However, the synthetic images generated by GANs cannot be used solely for training a neural network (training on synthetic and testing on real) as they cannot simulate all of the radar characteristics such as noise or Doppler effects. To the best of our knowledge, this is the first work in creating radar sounder imagery based on generative adversarial network.

scholarly journals Multifeature Named Entity Recognition in Information Security Based on Adversarial Learning

2019 ◽  
Vol 2019 ◽  
pp. 1-9
Author(s):  
Han Zhang ◽  
Yuanbo Guo ◽  
Tao Li
Keyword(s):  
Information Security ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Generative Adversarial Network ◽  
Adversarial Learning ◽  
New Approach ◽  
Named Entity ◽  
Adversarial Network ◽  
Security Research

In order to obtain high quality and large-scale labelled data for information security research, we propose a new approach that combines a generative adversarial network with the BiLSTM-Attention-CRF model to obtain labelled data from crowd annotations. We use the generative adversarial network to find common features in crowd annotations and then consider them in conjunction with the domain dictionary feature and sentence dependency feature as additional features to be introduced into the BiLSTM-Attention-CRF model, which is then used to carry out named entity recognition in crowdsourcing. Finally, we create a dataset to evaluate our models using information security data. The experimental results show that our model has better performance than the other baseline models.

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