Bidirectional deep neural networks to integrate RNA and DNA data for predicting outcome for patients with hepatocellular carcinoma

2021 ◽  
Author(s):  
Guojun Huang ◽  
Cheng Wang ◽  
Xi Fu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
Support Vector ◽  
Machine Model ◽  
Mrna Expression Data ◽  
Machine Learning Approach ◽  
Patient Profiling ◽  
Predicting Outcome ◽  
Subgroup Classification

Aims: Individualized patient profiling is instrumental for personalized management in hepatocellular carcinoma (HCC). This study built a model based on bidirectional deep neural networks (BiDNNs), an unsupervised machine-learning approach, to integrate multi-omics data and predict survival in HCC. Methods: DNA methylation and mRNA expression data for HCC samples from the TCGA database were integrated using BiDNNs. With optimal clusters as labels, a support vector machine model was developed to predict survival. Results: Using the BiDNN-based model, samples were clustered into two survival subgroups. The survival subgroup classification was an independent prognostic factor. BiDNNs were superior to multimodal autoencoders. Conclusion: This study constructed and validated a BiDNN-based model for predicting prognosis in HCC, with implications for individualized therapies in HCC.

414 Deep Neural Networks: A Survey Tool for Obstructive Sleep Apnea Prediction

SLEEP ◽  
2021 ◽  
Vol 44 (Supplement_2) ◽  
pp. A164-A164
Author(s):  
Pahnwat Taweesedt ◽  
JungYoon Kim ◽  
Jaehyun Park ◽  
Jangwoon Park ◽  
Munish Sharma ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Deep Neural Networks ◽  
Support Vector ◽  
Learning Models ◽  
Obstructive Sleep ◽  
Screening Questionnaires ◽  
Machine Learning Models

Abstract Introduction Obstructive sleep apnea (OSA) is a common sleep-related breathing disorder with an estimation of one billion people. Full-night polysomnography is considered the gold standard for OSA diagnosis. However, it is time-consuming, expensive and is not readily available in many parts of the world. Many screening questionnaires and scores have been proposed for OSA prediction with high sensitivity and low specificity. The present study is intended to develop models with various machine learning techniques to predict the severity of OSA by incorporating features from multiple questionnaires. Methods Subjects who underwent full-night polysomnography in Torr sleep center, Texas and completed 5 OSA screening questionnaires/scores were included. OSA was diagnosed by using Apnea-Hypopnea Index ≥ 5. We trained five different machine learning models including Deep Neural Networks with the scaled principal component analysis (DNN-PCA), Random Forest (RF), Adaptive Boosting classifier (ABC), and K-Nearest Neighbors classifier (KNC) and Support Vector Machine Classifier (SVMC). Training:Testing subject ratio of 65:35 was used. All features including demographic data, body measurement, snoring and sleepiness history were obtained from 5 OSA screening questionnaires/scores (STOP-BANG questionnaires, Berlin questionnaires, NoSAS score, NAMES score and No-Apnea score). Performance parametrics were used to compare between machine learning models. Results Of 180 subjects, 51.5 % of subjects were male with mean (SD) age of 53.6 (15.1). One hundred and nineteen subjects were diagnosed with OSA. Area Under the Receiver Operating Characteristic Curve (AUROC) of DNN-PCA, RF, ABC, KNC, SVMC, STOP-BANG questionnaire, Berlin questionnaire, NoSAS score, NAMES score, and No-Apnea score were 0.85, 0.68, 0.52, 0.74, 0.75, 0.61, 0.63, 0,61, 0.58 and 0,58 respectively. DNN-PCA showed the highest AUROC with sensitivity of 0.79, specificity of 0.67, positive-predictivity of 0.93, F1 score of 0.86, and accuracy of 0.77. Conclusion Our result showed that DNN-PCA outperforms OSA screening questionnaires, scores and other machine learning models. Support (if any):

scholarly journals Ship-Iceberg Classification in SAR and Multispectral Satellite Images with Neural Networks

2020 ◽  
Vol 12 (15) ◽  
pp. 2353
Author(s):  
Henning Heiselberg
Keyword(s):  
Neural Networks ◽  
Satellite Images ◽  
Deep Neural Networks ◽  
Data Augmentation ◽  
Neural Nets ◽  
The Arctic ◽  
Support Vector ◽  
Sar Images ◽  
Multispectral Satellite Images ◽  
The Cost

Classification of ships and icebergs in the Arctic in satellite images is an important problem. We study how to train deep neural networks for improving the discrimination of ships and icebergs in multispectral satellite images. We also analyze synthetic-aperture radar (SAR) images for comparison. The annotated datasets of ships and icebergs are collected from multispectral Sentinel-2 data and taken from the C-CORE dataset of Sentinel-1 SAR images. Convolutional Neural Networks with a range of hyperparameters are tested and optimized. Classification accuracies are considerably better for deep neural networks than for support vector machines. Deeper neural nets improve the accuracy per epoch but at the cost of longer processing time. Extending the datasets with semi-supervised data from Greenland improves the accuracy considerably whereas data augmentation by rotating and flipping the images has little effect. The resulting classification accuracies for ships and icebergs are 86% for the SAR data and 96% for the MSI data due to the better resolution and more multispectral bands. The size and quality of the datasets are essential for training the deep neural networks, and methods to improve them are discussed. The reduced false alarm rates and exploitation of multisensory data are important for Arctic search and rescue services.

scholarly journals Five weeks of intermittent transcutaneous vagus nerve stimulation shape neural networks: a machine learning approach

2021 ◽  
Author(s):  
Martina. A. Obst ◽  
Arkan Al-Zubaidi ◽  
Marcus Heldmann ◽  
Janis Marc Nolde ◽  
Nick Blümel ◽  
...  
Keyword(s):  
Neural Networks ◽  
Body Weight ◽  
Vagus Nerve ◽  
Nerve Stimulation ◽  
Vagus Nerve Stimulation ◽  
Low Frequency ◽  
Support Vector ◽  
Transcutaneous Vagus Nerve Stimulation ◽  
Machine Learning Approach ◽  
Stimulation Period

AbstractInvasive and transcutaneous vagus nerve stimulation [(t)-VNS] have been used to treat epilepsy, depression and migraine and has also shown effects on metabolism and body weight. To what extent this treatment shapes neural networks and how such network changes might be related to treatment effects is currently unclear. Using a pre-post mixed study design, we applied either a tVNS or sham stimulation (5 h/week) in 34 overweight male participants in the context of a study designed to assess effects of tVNS on body weight and metabolic and cognitive parameters resting state (rs) fMRI was measured about 12 h after the last stimulation period. Support vector machine (SVM) classification was applied to fractional amplitude low-frequency fluctuations (fALFF) on established rs-networks. All classification results were controlled for random effects and overfitting. Finally, we calculated multiple regressions between the classification results and reported food craving. We found a classification accuracy (CA) of 79 % in a subset of four brainstem regions suggesting that tVNS leads to lasting changes in brain networks. Five of eight salience network regions yielded 76,5 % CA. Our study shows tVNS’ post-stimulation effects on fALFF in the salience rs-network. More detailed investigations of this effect and their relationship with food intake seem reasonable for future studies.

scholarly journals Semi-Natural and Spontaneous Speech Recognition Using Deep Neural Networks with Hybrid Features Unification

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2286
Author(s):  
Ammar Amjad ◽  
Lal Khan ◽  
Hsien-Tsung Chang
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Feature Fusion ◽  
Spontaneous Speech ◽  
Identification Accuracy ◽  
Independent Experiment ◽  
Support Vector ◽  
Acoustic Feature ◽  
Hybrid Features ◽  
Feature Sets

Recently, identifying speech emotions in a spontaneous database has been a complex and demanding study area. This research presents an entirely new approach for recognizing semi-natural and spontaneous speech emotions with multiple feature fusion and deep neural networks (DNN). A proposed framework extracts the most discriminative features from hybrid acoustic feature sets. However, these feature sets may contain duplicate and irrelevant information, leading to inadequate emotional identification. Therefore, an support vector machine (SVM) algorithm is utilized to identify the most discriminative audio feature map after obtaining the relevant features learned by the fusion approach. We investigated our approach utilizing the eNTERFACE05 and BAUM-1s benchmark databases and observed a significant identification accuracy of 76% for a speaker-independent experiment with SVM and 59% accuracy with, respectively. Furthermore, experiments on the eNTERFACE05 and BAUM-1s dataset indicate that the suggested framework outperformed current state-of-the-art techniques on the semi-natural and spontaneous datasets.

scholarly journals Deep Neural Networks and Transfer Learning on a Multivariate Physiological Signal Dataset

2021 ◽  
Vol 8 (3) ◽  
pp. 35
Author(s):  
Andrea Bizzego ◽  
Giulio Gabrieli ◽  
Gianluca Esposito
Keyword(s):  
Neural Networks ◽  
Transfer Learning ◽  
Deep Neural Networks ◽  
Electrodermal Activity ◽  
Physiological Signals ◽  
Support Vector ◽  
Specific Measure ◽  
Physiological Signal ◽  
Different Types ◽  
Acceleration Signals

While Deep Neural Networks (DNNs) and Transfer Learning (TL) have greatly contributed to several medical and clinical disciplines, the application to multivariate physiological datasets is still limited. Current examples mainly focus on one physiological signal and can only utilise applications that are customised for that specific measure, thus it limits the possibility of transferring the trained DNN to other domains. In this study, we composed a dataset (n=813) of six different types of physiological signals (Electrocardiogram, Electrodermal activity, Electromyogram, Photoplethysmogram, Respiration and Acceleration). Signals were collected from 232 subjects using four different acquisition devices. We used a DNN to classify the type of physiological signal and to demonstrate how the TL approach allows the exploitation of the efficiency of DNNs in other domains. After the DNN was trained to optimally classify the type of signal, the features that were automatically extracted by the DNN were used to classify the type of device used for the acquisition using a Support Vector Machine. The dataset, the code and the trained parameters of the DNN are made publicly available to encourage the adoption of DNN and TL in applications with multivariate physiological signals.

scholarly journals Sentiment Analysis using Multiple Word Embedding for Words

2020 ◽  
Vol 9 (1) ◽  
pp. 1689-1693
Keyword(s):  
Deep Neural Networks ◽  
Word Embedding ◽  
Support Vector ◽  
Main Task ◽  
Word Embeddings ◽  
Special Review ◽  
Proposed Model ◽  
Machine Learning Approach ◽  
Result Analysis ◽  
The Given

Nowadays users express their opinions on different websites like e-commerce and special review websites. Analyzing customers' opinions and their responses is important for decision making. So the researchers worked on analyzing these reviews automatically using a classical machine learning approach like Support Vector Machine (SVM) and various modern deep neural networks. For these networks, words are represented by using vectors called word embeddings. The required word embeddings are taken from pre-trained Word2Vec or learned from a corpus of the given main task. But, each method has its demerits. In the case of pre-trained word embeddings, embeddings are learned from large general corpus so these embeddings are not task specific. While in the case of learning words from the corpus of the main task, it does not reflect the true semantics. To deal with these problems, we have proposed an embedding developer model. This model develops task specific word embedding which also reflects true semantics. Task specific word embeddings are generated from the given corpus using the embedding layer in Keras. It builds the embeddings by considering relationships between words in the window. While true semantics are taken from Word2Vec embeddings. The proposed model combines these two embeddings to generate true semantics and task specific word embeddings. Result analysis shows that the proposed system works better on many benchmark dataset

scholarly journals Assessment of bilateral knee pain from MR imaging using deep neural networks

2018 ◽  
Author(s):  
Gary H. Chang ◽  
David T. Felson ◽  
Shangran Qiu ◽  
Terence D. Capellini ◽  
Vijaya B. Kolachalama
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Neural Networks ◽  
Deep Learning ◽  
Knee Pain ◽  
Deep Neural Networks ◽  
Learning Approach ◽  
Mr Images ◽  
Bilateral Knee ◽  
Machine Learning Approach

ABSTRACTBackground and objectiveIt remains difficult to characterize pain in knee joints with osteoarthritis solely by radiographic findings. We sought to understand how advanced machine learning methods such as deep neural networks can be used to analyze raw MRI scans and predict bilateral knee pain, independent of other risk factors.MethodsWe developed a deep learning framework to associate information from MRI slices taken from the left and right knees of subjects from the Osteoarthritis Initiative with bilateral knee pain. Model training was performed by first extracting features from two-dimensional (2D) sagittal intermediate-weighted turbo spin echo slices. The extracted features from all the 2D slices were subsequently combined to directly associate using a fused deep neural network with the output of interest as a binary classification problem.ResultsThe deep learning model resulted in predicting bilateral knee pain on test data with 70.1% mean accuracy, 51.3% mean sensitivity, and 81.6% mean specificity. Systematic analysis of the predictions on the test data revealed that the model performance was consistent across subjects of different Kellgren-Lawrence grades.ConclusionThe study demonstrates a proof of principle that a machine learning approach can be applied to associate MR images with bilateral knee pain.SIGNIFICANCE AND INNOVATIONKnee pain is typically considered as an early indicator of osteoarthritis (OA) risk. Emerging evidence suggests that MRI changes are linked to pre-clinical OA, thus underscoring the need for building image-based models to predict knee pain. We leveraged a state-of-the-art machine learning approach to associate raw MR images with bilateral knee pain, independent of other risk factors.

scholarly journals Support vector machine for the prediction of heating energy use

2018 ◽  
Vol 22 (Suppl. 4) ◽  
pp. 1171-1181 ◽  
Author(s):  
Aleksandra Sretenovic ◽  
Radisa Jovanovic ◽  
Vojislav Novakovic ◽  
Natasa Nord ◽  
Branislav Zivkovic
Keyword(s):  
Neural Networks ◽  
Support Vector Machine ◽  
Energy Use ◽  
Support Vector Machine Model ◽  
District Heating ◽  
Support Vector ◽  
University Campus ◽  
Machine Model ◽  
Proposed Model ◽  
The Individual

Prediction of a building energy use for heating is very important for adequate energy planning. In this paper the daily district heating use of one university campus was predicted using the support vector machine model. Support vector machine is the artificial intelligence method that has recently proved that it can achieve comparable, or even better prediction results than the much more used artificial neural networks. The proposed model was trained and tested on the real, measured data. The model accuracy was compared with the results of the previously published models (various neural networks and their ensembles) on the same database. The results showed that the support vector machine model can achieve better results than the individual neural networks, but also better than the conventional and multistage ensembles. It is expected that this theoretically well-known methodology finds wider application, especially in prediction tasks.

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