Deep artificial neural network based on environmental sound data for the generation of a children activity classification model.
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ABSTRACT:
SUBMITTER: Garcia-Dominguez A
PROVIDER: S-EPMC7924663 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundDeep learning has made tremendous successes in numerous artificial intelligence applications and is unsurprisingly penetrating into various biomedical domains. High-throughput omics data in the form of molecular profile matrices, such as transcriptomes and metabolomes, have long existed as a valuable resource for facilitating diagnosis of patient statuses/stages. It is timely imperative to compare deep learning neural networks against classical machine learning methods in the setting of matrix-formed omics data in terms of classification accuracy and robustness.ResultsUsing 37 high throughput omics datasets, covering transcriptomes and metabolomes, we evaluated the classification power of deep learning compared to traditional machine learning methods. Representative deep learning methods, Multi-Layer Perceptrons (MLP) and Convolutional Neural Networks (CNN), were deployed and explored in seeking optimal architectures for the best classification performance. Together with five classical supervised classification methods (Linear Discriminant Analysis, Multinomial Logistic Regression, Naïve Bayes, Random Forest, Support Vector Machine), MLP and CNN were comparatively tested on the 37 datasets to predict disease stages or to discriminate diseased samples from normal samples. MLPs achieved the highest overall accuracy among all methods tested. More thorough analyses revealed that single hidden layer MLPs with ample hidden units outperformed deeper MLPs. Furthermore, MLP was one of the most robust methods against imbalanced class composition and inaccurate class labels.ConclusionOur results concluded that shallow MLPs (of one or two hidden layers) with ample hidden neurons are sufficient to achieve superior and robust classification performance in exploiting numerical matrix-formed omics data for diagnosis purpose. Specific observations regarding optimal network width, class imbalance tolerance, and inaccurate labeling tolerance will inform future improvement of neural network applications on functional genomics data.
| S-EPMC6399893 | biostudies-literature
Project description:This data manuscript presents a set of signals collected from the Llaima volcano located at the western edge of the Andes in Araucania Region, Chile. The signals were recorded from the LAV station between 2010 and 2016. After individually processing and analyzing every signal, specialists from the Observatorio Vulcanológico de los Andes Sur (OVDAS) classified them into four class according to their event source: i) Volcano-Tectonic (VT); ii) Long Period (LP); iii) Tremor (TR), and iv) Tectonic (TC). The dataset is composed of 3592 signals separated by class and filtered to select the segment that contains the most representative part of the seismic event. This dataset is important to support researchers interested in studying seismic signals from active volcanoes and developing new methods to model time-dependent data. In this sense, we have published the manuscript "In-Depth Comparison of Deep Artificial Neural Network Architectures on Seismic Events Classification" [1] analyzing such signals with different Deep Neural Networks (DNN). The main contribution of such manuscript is a new DNN architecture called SeismicNet, which provided classification results among the best in the literature without demanding explicit signal pre-processing steps. Therefore, the reader is referred to such manuscript for the interpretation of the data.
| S-EPMC7206203 | biostudies-literature
Project description:STUDY OBJECTIVES:Portable devices for home sleep apnea testing are often limited by their inability to discriminate sleep/wake status, possibly resulting in underestimations. Tracheal sound (TS), which can be visualized as a spectrogram, carries information about apnea/hypopnea and sleep/wake status. We hypothesized that image analysis of all-night TS recordings by a deep neural network (DNN) would be capable of detecting breathing events and classifying sleep/wake status. The aim of this study is to develop a DNN-based system for sleep apnea testing and validate it using a large sampling of polysomnography (PSG) data. METHODS:PSG examinations for the evaluation of sleep-disordered breathing (SDB) were performed for 1,852 patients: 1,548 PSG records were used to develop the system, and the remaining 304 records were used for validation. TS spectrogram images were obtained every 60 seconds and labeled with the PSG scoring results (breathing event and sleep/wake status), then introduced to DNN learning. Two different DNNs were trained for breathing status and sleep/wake status, respectively. RESULTS:A DNN with convolutional layers showed the best performance for discriminating breathing status. The same DNN structure was trained for sleep/wake discrimination. In the validation study, the DNN analysis was capable of discriminating the sleep/wake status with reasonable accuracy. The diagnostic sensitivity, specificity, and area under the receiver operating characteristic curves for diagnosis of SDB with apnea-hypopnea index of > 5, 15, and 30 were 0.98, 0.76, and 0.99; 0.97, 0.90, and 0.99; and 0.92, 0.94, and 0.98, respectively. CONCLUSIONS:The developed system using the TS DNN analysis has a good performance for SDB testing. CITATION:Nakano H, Furukawa T, Tanigawa T. Tracheal sound analysis using a deep neural network to detect sleep apnea. J Clin Sleep Med. 2019;15(8): 1125-1133.
| S-EPMC6707047 | biostudies-literature
Project description:An efficient code for classifying environmental sounds is described that exploits a recent significant advance in signal processing known as compressed sensing (CS) [cf.Donoho, D. (2006). IEEE Trans. Inf. Theory 52, 1289-1306]. CS involves a novel approach to sampling in which the salient information in signals is recovered from the projection onto a small set of random basis functions. The advantage of the random basis over traditional Fourier or wavelet representations is that it allows accurate classification at low target-to-interference ratios based on few samples and little or no prior information about signals.
| S-EPMC2723904 | biostudies-other
Project description:Accurate behavioral state classification is critical for many research applications. Researchers typically rely upon manual identification of behavioral state through visual inspection of electrophysiological signals, but this approach is time intensive and subject to low inter-rater reliability. To overcome these limitations, a diverse set of algorithmic approaches have been put forth to automate the classification process. Recently, novel machine learning approaches have been detailed that produce rapid and highly accurate classifications. These approaches however, are often computationally expensive, require significant expertise to implement, and/or require proprietary software that limits broader adoption. Here we detail a novel artificial neural network that uses electrophysiological features to automatically classify behavioral state in rats with high accuracy, sensitivity, and specificity. Common parameters of interest to sleep scientists, including state-dependent power spectra and homeostatic non-REM slow wave activity, did not significantly differ when using this automated classifier as compared to manual scoring. Flexible options enable researchers to further increase classification accuracy through manual rescoring of a small subset of time intervals with low model prediction certainty or further decrease researcher time by generalizing trained networks across multiple recording days. The algorithm is fully open-source and coded within a popular, and freely available, software platform to increase access to this research tool and provide additional flexibility for future researchers. In sum, we have developed a readily implementable, efficient, and effective approach for automated behavioral state classification in rats.
| S-EPMC8435206 | biostudies-literature
Project description:The established model-free methods for the processing of two-electron dipolar spectroscopy data [DEER (double electron-electron resonance), PELDOR (pulsed electron double resonance), DQ-EPR (double-quantum electron paramagnetic resonance), RIDME (relaxation-induced dipolar modulation enhancement), etc.] use regularized fitting. In this communication, we describe an attempt to process DEER data using artificial neural networks trained on large databases of simulated data. Accuracy and reliability of neural network outputs from real experimental data were found to be unexpectedly high. The networks are also able to reject exchange interactions and to return a measure of uncertainty in the resulting distance distributions. This paper describes the design of the training databases, discusses the training process, and rationalizes the observed performance. Neural networks produced in this work are incorporated as options into Spinach and DeerAnalysis packages.
| S-EPMC6108566 | biostudies-literature
Project description:Cardiotocography records fetal heart rates and their temporal relationship to uterine contractions. To identify high risk fetuses, obstetricians inspect cardiotocograms (CTGs) by eye. Therefore, CTG traces are often interpreted differently among obstetricians, resulting in inappropriate interventions. However, few studies have focused on quantitative and nonbiased algorithms for CTG evaluation. In this study, we propose a newly constructed deep neural network model (CTG-net) to detect compromised fetal status. CTG-net consists of three convolutional layers that extract temporal patterns and interrelationships between fetal heart rate and uterine contraction signals. We aimed to classify the abnormal group (umbilical artery pH < 7.20 or Apgar score at 1 min < 7) and the normal group from CTG data. We evaluated the performance of the CTG-net with the F1 score and compared it with conventional algorithms, namely, support vector machine and k-means clustering, and another deep neural network model, long short-term memory. CTG-net showed the area under the receiver operating characteristic curve of 0.73 ± 0.04, which was significantly higher than that of long short-term memory. CTG-net, a quantitative and automated diagnostic aid system, enables early intervention for putatively abnormal fetuses, resulting in a reduction in the number of cases of hypoxic injury.
| S-EPMC8238938 | biostudies-literature
Project description:Conjunctival hyperaemia is a common clinical ophthalmological finding and can be a symptom of various ocular disorders. Although several severity classification criteria have been proposed, none include objective severity criteria. Neural networks and deep learning have been utilised in ophthalmology, but not for the purpose of classifying the severity of conjunctival hyperaemia objectively. To develop a conjunctival hyperaemia grading software, we used 3700 images as the training data and 923 images as the validation test data. We trained the nine neural network models and validated the performance of these networks. We finally chose the best combination of these networks. The DenseNet201 model was the best individual model. The combination of the DenseNet201, DenseNet121, VGG19, and ResNet50 were the best model. The correlation between the multimodel responses, and the vessel-area occupied was 0.737 (p < 0.01). This system could be as accurate and comprehensive as specialists but would be significantly faster and consistent with objective values.
| S-EPMC6589312 | biostudies-literature
Project description:BackgroundTranscriptome sequencing has been broadly available in clinical studies. However, it remains a challenge to utilize these data effectively for clinical applications due to the high dimension of the data and the highly correlated expression between individual genes.MethodsWe proposed a method to transform RNA sequencing data into artificial image objects (AIOs) and applied convolutional neural network (CNN) algorithms to classify these AIOs. With the AIO technique, we considered each gene as a pixel in an image and its expression level as pixel intensity. Using the GSE96058 (n = 2976), GSE81538 (n = 405), and GSE163882 (n = 222) datasets, we created AIOs for the subjects and designed CNN models to classify biomarker Ki67 and Nottingham histologic grade (NHG).ResultsWith fivefold cross-validation, we accomplished a classification accuracy and AUC of 0.821 ± 0.023 and 0.891 ± 0.021 for Ki67 status. For NHG, the weighted average of categorical accuracy was 0.820 ± 0.012, and the weighted average of AUC was 0.931 ± 0.006. With GSE96058 as training data and GSE81538 as testing data, the accuracy and AUC for Ki67 were 0.826 ± 0.037 and 0.883 ± 0.016, and that for NHG were 0.764 ± 0.052 and 0.882 ± 0.012, respectively. These results were 10% better than the results reported in the original studies. For Ki67, the calls generated from our models had a better power for prediction of survival as compared to the calls from trained pathologists in survival analyses.ConclusionsWe demonstrated that RNA sequencing data could be transformed into AIOs and be used to classify Ki67 status and NHG with CNN algorithms. The AIO method could handle high-dimensional data with highly correlated variables, and there was no need for variable selection. With the AIO technique, a data-driven, consistent, and automation-ready model could be developed to classify biomarkers with RNA sequencing data and provide more efficient care for cancer patients.
| S-EPMC8504079 | biostudies-literature
Project description:Identifying localization of proteins and their specific subpopulations associated with certain cellular compartments is crucial for understanding protein function and interactions with other macromolecules. Fluorescence microscopy is a powerful method to assess protein localizations, with increasing demand of automated high throughput analysis methods to supplement the technical advancements in high throughput imaging. Here, we study the applicability of deep neural network-based artificial intelligence in classification of protein localization in 13 cellular subcompartments. We use deep learning-based on convolutional neural network and fully convolutional network with similar architectures for the classification task, aiming at achieving accurate classification, but importantly, also comparison of the networks. Our results show that both types of convolutional neural networks perform well in protein localization classification tasks for major cellular organelles. Yet, in this study, the fully convolutional network outperforms the convolutional neural network in classification of images with multiple simultaneous protein localizations. We find that the fully convolutional network, using output visualizing the identified localizations, is a very useful tool for systematic protein localization assessment.
| S-EPMC7916854 | biostudies-literature