Unsupervised learning of cross-modal mappings in multi-omics data for survival stratification of gastric cancer

2021 ◽  
Author(s):  
Jianmin Xu ◽  
Binghua Xu ◽  
Yipeng Li ◽  
Zhijian Su ◽  
Yueping Yao
Keyword(s):  
Gastric Cancer ◽  
Neural Networks ◽  
Clustering Analysis ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
P Value ◽  
Omics Data ◽  
Omics Integration ◽  
Tenfold Cross Validation ◽  
Independent Confirmation

Aims: This study presents a survival stratification model based on multi-omics integration using bidirectional deep neural networks (BiDNNs) in gastric cancer. Methods: Based on the survival-related representation features yielded by BiDNNs through integrating transcriptomics and epigenomics data, K-means clustering analysis was performed to cluster tumor samples into different survival subgroups. The BiDNNs-based model was validated using tenfold cross-validation and in two independent confirmation cohorts. Results: Using the BiDNNs-based survival stratification model, patients were grouped into two survival subgroups with log-rank p-value = 9.05E-05. The subgroups classification was robustly validated in tenfold cross-validation (C-index = 0.65 ± 0.02) and in two confirmation cohorts (E-GEOD-26253, C-index = 0.609; E-GEOD-62254, C-index = 0.706). Conclusion: We propose and validate a robust and stable BiDNN-based survival stratification model in gastric cancer.

scholarly journals Towards computer-aided severity assessment via deep neural networks for geographic and opacity extent scoring of SARS-CoV-2 chest X-rays

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. Wong ◽  
Z. Q. Lin ◽  
L. Wang ◽  
A. G. Chung ◽  
B. Shen ◽  
...  
Keyword(s):  
Neural Networks ◽  
Monte Carlo ◽  
Lung Disease ◽  
Disease Severity ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
X Rays ◽  
Computer Aided ◽  
Monte Carlo Cross Validation ◽  
Validation Experiments

AbstractA critical step in effective care and treatment planning for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause for the coronavirus disease 2019 (COVID-19) pandemic, is the assessment of the severity of disease progression. Chest x-rays (CXRs) are often used to assess SARS-CoV-2 severity, with two important assessment metrics being extent of lung involvement and degree of opacity. In this proof-of-concept study, we assess the feasibility of computer-aided scoring of CXRs of SARS-CoV-2 lung disease severity using a deep learning system. Data consisted of 396 CXRs from SARS-CoV-2 positive patient cases. Geographic extent and opacity extent were scored by two board-certified expert chest radiologists (with 20+ years of experience) and a 2nd-year radiology resident. The deep neural networks used in this study, which we name COVID-Net S, are based on a COVID-Net network architecture. 100 versions of the network were independently learned (50 to perform geographic extent scoring and 50 to perform opacity extent scoring) using random subsets of CXRs from the study, and we evaluated the networks using stratified Monte Carlo cross-validation experiments. The COVID-Net S deep neural networks yielded R$$^2$$ 2 of $$0.664 \pm 0.032$$ 0.664 ± 0.032 and $$0.635 \pm 0.044$$ 0.635 ± 0.044 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively, in stratified Monte Carlo cross-validation experiments. The best performing COVID-Net S networks achieved R$$^2$$ 2 of 0.739 and 0.741 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively. The results are promising and suggest that the use of deep neural networks on CXRs could be an effective tool for computer-aided assessment of SARS-CoV-2 lung disease severity, although additional studies are needed before adoption for routine clinical use.

scholarly journals Forecasting Reservoir Water Levels Using Deep Neural Networks: A Case Study of Angat Dam in the Philippines

Water ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 34
Author(s):  
Sebastian C. Ibañez ◽  
Carlo Vincienzo G. Dajac ◽  
Marissa P. Liponhay ◽  
Erika Fille T. Legara ◽  
Jon Michael H. Esteban ◽  
...  
Keyword(s):  
Neural Networks ◽  
Time Series ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
The Philippines ◽  
Water Levels ◽  
Short Term ◽  
Exogenous Variables ◽  
Reservoir Water ◽  
Forecasting Performance

Forecasting reservoir water levels is essential in water supply management, impacting both operations and intervention strategies. This paper examines the short-term and long-term forecasting performance of several statistical and machine learning-based methods for predicting the water levels of the Angat Dam in the Philippines. A total of six forecasting methods are compared: naïve/persistence; seasonal mean; autoregressive integrated moving average (ARIMA); gradient boosting machines (GBM); and two deep neural networks (DNN) using a long short-term memory-based (LSTM) encoder-decoder architecture: a univariate model (DNN-U) and a multivariate model (DNN-M). Daily historical water levels from 2001 to 2021 are used in predicting future water levels. In addition, we include meteorological data (rainfall and the Oceanic Niño Index) and irrigation data as exogenous variables. To evaluate the forecast accuracy of our methods, we use a time series cross-validation approach to establish a more robust estimate of the error statistics. Our results show that our DNN-U model has the best accuracy in the 1-day-ahead scenario with a mean absolute error (MAE) and root mean square error (RMSE) of 0.2 m. In the 30-day-, 90-day-, and 180-day-ahead scenarios, the DNN-M shows the best performance with MAE (RMSE) scores of 2.9 (3.3), 5.1 (6.0), and 6.7 (8.1) meters, respectively. Additionally, we demonstrate that further improvements in performance are possible by scanning over all possible combinations of the exogenous variables and only using a subset of them as features. In summary, we provide a comprehensive framework for evaluating water level forecasting by defining a baseline accuracy, analyzing performance across multiple prediction horizons, using time series cross-validation to assess accuracy and uncertainty, and examining the effects of exogenous variables on forecasting performance. In the process, our work addresses several notable gaps in the methodologies of previous works.

scholarly journals Classifying Breast Cancer Subtypes Using Deep Neural Networks Based on Multi-Omics Data

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 888
Author(s):  
Yuqi Lin ◽  
Wen Zhang ◽  
Huanshen Cao ◽  
Gaoyang Li ◽  
Wei Du
Keyword(s):  
Breast Cancer ◽  
Neural Networks ◽  
Feature Selection ◽  
Deep Neural Networks ◽  
Selection Process ◽  
Breast Cancer Subtype ◽  
The Cancer Genome Atlas ◽  
Breast Cancer Subtypes ◽  
Omics Data ◽  
Cancer Subtypes

With the high prevalence of breast cancer, it is urgent to find out the intrinsic difference between various subtypes, so as to infer the underlying mechanisms. Given the available multi-omics data, their proper integration can improve the accuracy of breast cancer subtype recognition. In this study, DeepMO, a model using deep neural networks based on multi-omics data, was employed for classifying breast cancer subtypes. Three types of omics data including mRNA data, DNA methylation data, and copy number variation (CNV) data were collected from The Cancer Genome Atlas (TCGA). After data preprocessing and feature selection, each type of omics data was input into the deep neural network, which consists of an encoding subnetwork and a classification subnetwork. The results of DeepMO based on multi-omics on binary classification are better than other methods in terms of accuracy and area under the curve (AUC). Moreover, compared with other methods using single omics data and multi-omics data, DeepMO also had a higher prediction accuracy on multi-classification. We also validated the effect of feature selection on DeepMO. Finally, we analyzed the enrichment gene ontology (GO) terms and biological pathways of these significant genes, which were discovered during the feature selection process. We believe that the proposed model is useful for multi-omics data analysis.

scholarly journals CoCoNet: Boosting RNA contact prediction by convolutional neural networks

2020 ◽  
Author(s):  
Mehari B Zerihun ◽  
Fabrizio Pucci ◽  
Alexander Schug
Keyword(s):  
Neural Networks ◽  
Structure Prediction ◽  
Prediction Accuracy ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
Rna Structures ◽  
Contact Prediction ◽  
Contact Maps ◽  
Direct Coupling Analysis ◽  
Protein Contact Maps

Physics-based co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict protein contact maps with astonishing accuracy. Such contacts can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins but not for RNAs. Here, we demonstrate how the small amount of data available for RNA can be used to significantly improve prediction of RNA contact maps. We introduce an algorithm called CoCoNet that is based on a combination of a Coevolutionary model and a shallow Convolutional Neural Network. Despite its simplicity and the small number of trained parameters, the method boosts the contact prediction accuracy by about 70% with respect to straightforward DCA as tested by cross-validation on a dataset of about sixty RNA structures. Both our extensive robustness tests and the limited number of parameters allow the generalization properties of our model. Finally, applications to other RNAs highlight the power of our approach. CoCoNet is freely available and can be found at https://github.com/KIT-MBS/coconet.

scholarly journals Deep Neural Networks with Transfer Learning Model for Brain Tumors Classification

2020 ◽  
Vol 37 (4) ◽  
pp. 593-601
Author(s):  
Premamayudu Bulla ◽  
Lakshmipathi Anantha ◽  
Subbarao Peram
Keyword(s):  
Neural Networks ◽  
Brain Tumors ◽  
Mr Imaging ◽  
Transfer Learning ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
Mr Images ◽  
Patient Level ◽  
Group 10 ◽  
Fold Cross Validation

To investigate the effect of deep neural networks with transfer learning on MR images for tumor classification and improve the classification metrics by building image-level, stratified image-level, and patient-level models. Three thousand sixty-four T1-weighted magnetic resonance (MR) imaging from two hundred thirty-three patient cases of three brain tumors types (meningioma, glioma, and pituitary) were collected and it includes coronal, sagittal and axial views. The average number of brain images of each patient in three views is fourteen in the collected dataset. The classification is performed in a model of cross-trained with a pre-trained InceptionV3 model. Three image-level and one patient-level models are built on the MR imaging dataset. The models are evaluated in classification metrics such as accuracy, loss, precision, recall, kappa, and AUC. The proposed models are validated using four approaches: holdout validation, 10-fold cross-validation, stratified 10-fold cross-validation, and group 10-fold cross-validation. The generalization capability and improvement of the network are tested by using cropped and uncropped images of the dataset. The best results for group 10-fold cross-validation (patient-level) are obtained on the used dataset (ACC=99.82). A deep neural network with transfer learning can be used to classify brain tumors from MR images. Our patient-level network model noted the best results in classification to improve accuracy.

scholarly journals A three-stage learning algorithm for deep multilayer perceptron with effective weight initialisation based on sparse auto-encoder

2019 ◽  
Vol 8 (1) ◽  
pp. 41
Author(s):  
Maysa Ibrahem Almulla Khalaf ◽  
John Q Gan
Keyword(s):  
Neural Networks ◽  
Feature Extraction ◽  
Multilayer Perceptron ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
Learning Algorithm ◽  
Back Propagation ◽  
Error Back Propagation ◽  
Second Stage ◽  
Propagation Network

A three-stage learning algorithm for deep multilayer perceptron (DMLP) with effective weight initialisation based on sparse auto-encoder is proposed in this paper, which aims to overcome difficulties in training deep neural networks with limited training data in high-dimensional feature space. At the first stage, unsupervised learning is adopted using sparse auto-encoder to obtain the initial weights of the feature extraction layers of the DMLP. At the second stage, error back-propagation is used to train the DMLP by fixing the weights obtained at the first stage for its feature extraction layers. At the third stage, all the weights of the DMLP obtained at the second stage are refined by error back-propagation. Network structures and values of learning parameters are determined through cross-validation, and test datasets unseen in the cross-validation are used to evaluate the performance of the DMLP trained using the three-stage learning algorithm. Experimental results show that the proposed method is effective in combating overfitting in training deep neural networks.

Deep neural networks trained with heavier data augmentation learn features closer to representations in hIT

2018 ◽  
Author(s):  
Alex Hernández-García ◽  
Johannes Mehrer ◽  
Nikolaus Kriegeskorte ◽  
Peter König ◽  
Tim C. Kietzmann
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Data Augmentation

Representation of adversarial images in deep neural networks and the human brain

2018 ◽  
Author(s):  
Chi Zhang ◽  
Xiaohan Duan ◽  
Ruyuan Zhang ◽  
Li Tong
Keyword(s):  
Neural Networks ◽  
Human Brain ◽  
Deep Neural Networks
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