Automated sleep stage scoring employing a reasoning mechanism and evaluation of its explainability.
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ABSTRACT:
SUBMITTER: Horie K
PROVIDER: S-EPMC9329306 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:PurposeTo develop an automated framework for sleep stage scoring from PSG via a deep neural network.MethodsAn automated deep neural network was proposed by using a multi-model integration strategy with multiple signal channels as input. All of the data were collected from one single medical center from July 2017 to April 2019. Model performance was evaluated by overall classification accuracy, precision, recall, weighted F1 score, and Cohen's Kappa.ResultsTwo hundred ninety-four sleep studies were included in this study; 122 composed the training dataset, 20 composed the validation dataset, and 152 were used in the testing dataset. The network achieved human-level annotation performance with an average accuracy of 0.8181, weighted F1 score of 0.8150, and Cohen's Kappa of 0.7276. Top-2 accuracy (the proportion of test samples for which the true label is among the two most probable labels given by the model) was significantly improved compared to the overall classification accuracy, with the average being 0.9602. The number of arousals affected the model's performance.ConclusionThis research provides a robust and reliable model with the inter-rater agreement nearing that of human experts. Determining the most appropriate evaluation parameters for sleep staging is a direction for future research.
| S-EPMC7289784 | biostudies-literature
Project description:The classification of sleep stages is the first and an important step in the quantitative analysis of polysomnographic recordings. Sleep stage scoring relies heavily on visual pattern recognition by a human expert and is time consuming and subjective. Thus, there is a need for automatic classification. In this work we developed machine learning algorithms for sleep classification: random forest (RF) classification based on features and artificial neural networks (ANNs) working both with features and raw data. We tested our methods in healthy subjects and in patients. Most algorithms yielded good results comparable to human interrater agreement. Our study revealed that deep neural networks (DNNs) working with raw data performed better than feature-based methods. We also demonstrated that taking the local temporal structure of sleep into account a priori is important. Our results demonstrate the utility of neural network architectures for the classification of sleep.
| S-EPMC6232272 | biostudies-literature
Project description:PurposeTo determine the agreement between the manual scoring of home sleep apnea tests (HSATs) by international sleep technologists and automated scoring systems.MethodsFifteen HSATs, previously recorded using a type 3 monitor, were saved in European Data Format. The studies were scored by nine experienced technologists from the sleep centers of the Sleep Apnea Global Interdisciplinary Consortium (SAGIC) using the locally available software. Each study was scored separately by human scorers using the nasal pressure (NP), flow derived from the NP signal (transformed NP), or respiratory inductive plethysmography (RIP) flow. The same procedure was followed using two automated scoring systems: Remlogic (RLG) and Noxturnal (NOX).ResultsThe intra-class correlation coefficients (ICCs) of the apnea-hypopnea index (AHI) scoring using the NP, transformed NP, and RIP flow were 0.96 [95% CI 0.93-0.99], 0.98 [0.96-0.99], and 0.97 [0.95-0.99], respectively. Using the NP signal, the mean differences in AHI between the average of the manual scoring and the automated systems were - 0.9 ± 3.1/h (AHIRLG vs AHIMANUAL) and - 1.3 ± 2.6/h (AHINOX vs AHIMANUAL). Using the transformed NP, the mean differences in AHI were - 1.9 ± 3.3/h (AHIRLG vs AHIMANUAL) and 1.6 ± 3.0/h (AHINOX vs AHIMANUAL). Using the RIP flow, the mean differences in AHI were - 2.7 ± 4.5/h (AHIRLG vs AHIMANUAL) and 2.3 ± 3.4/h (AHINOX vs AHIMANUAL).ConclusionsThere is very strong agreement in the scoring of the AHI for HSATs between the automated systems and experienced international technologists. Automated scoring of HSATs using commercially available software may be useful to standardize scoring in future endeavors involving international sleep centers.
| S-EPMC6615031 | biostudies-literature
Project description:Study objectivesInter-scorer variability in scoring polysomnograms is a well-known problem. Most of the existing automated sleep scoring systems are trained using labels annotated by a single-scorer, whose subjective evaluation is transferred to the model. When annotations from two or more scorers are available, the scoring models are usually trained on the scorer consensus. The averaged scorer's subjectivity is transferred into the model, losing information about the internal variability among different scorers. In this study, we aim to insert the multiple-knowledge of the different physicians into the training procedure. The goal is to optimize a model training, exploiting the full information that can be extracted from the consensus of a group of scorers.MethodsWe train two lightweight deep learning-based models on three different multi-scored databases. We exploit the label smoothing technique together with a soft-consensus (LSSC) distribution to insert the multiple-knowledge in the training procedure of the model. We introduce the averaged cosine similarity metric (ACS) to quantify the similarity between the hypnodensity-graph generated by the models with-LSSC and the hypnodensity-graph generated by the scorer consensus.ResultsThe performance of the models improves on all the databases when we train the models with our LSSC. We found an increase in ACS (up to 6.4%) between the hypnodensity-graph generated by the models trained with-LSSC and the hypnodensity-graph generated by the consensus.ConclusionOur approach definitely enables a model to better adapt to the consensus of the group of scorers. Future work will focus on further investigations on different scoring architectures and hopefully large-scale-heterogeneous multi-scored datasets.
| S-EPMC10171642 | biostudies-literature
Project description:BackgroundThe advent of home sleep testing has allowed for the development of an ambulatory care model for OSA that most health-care providers can easily deploy. Although automated algorithms that accompany home sleep monitors can identify and classify disordered breathing events, it is unclear whether manual scoring followed by expert review of home sleep recordings is of any value. Thus, this study examined the agreement between automated and manual scoring of home sleep recordings.MethodsTwo type 3 monitors (ApneaLink Plus [ResMed] and Embletta [Embla Systems]) were examined in distinct study samples. Data from manual and automated scoring were available for 200 subjects. Two thresholds for oxygen desaturation (≥ 3% and ≥ 4%) were used to define disordered breathing events. Agreement between manual and automated scoring was examined using Pearson correlation coefficients and Bland-Altman analyses.ResultsAutomated scoring consistently underscored disordered breathing events compared with manual scoring for both sleep monitors irrespective of whether a ≥ 3% or ≥ 4% oxygen desaturation threshold was used to define the apnea-hypopnea index (AHI). For the ApneaLink Plus monitor, Bland-Altman analyses revealed an average AHI difference between manual and automated scoring of 6.1 (95% CI, 4.9-7.3) and 4.6 (95% CI, 3.5-5.6) events/h for the ≥ 3% and ≥ 4% oxygen desaturation thresholds, respectively. Similarly for the Embletta monitor, the average difference between manual and automated scoring was 5.3 (95% CI, 3.2-7.3) and 8.4 (95% CI, 7.2-9.6) events/h, respectively.ConclusionsAlthough agreement between automated and manual scoring of home sleep recordings varies based on the device used, modest agreement was observed between the two approaches. However, manual review of home sleep test recordings can decrease the misclassification of OSA severity, particularly for those with mild disease.Trial registryClinicalTrials.gov; No.: NCT01503164; www.clinicaltrials.gov.
| S-EPMC4347534 | biostudies-literature
Project description:Studying the biology of sleep requires the accurate assessment of the state of experimental subjects, and manual analysis of relevant data is a major bottleneck. Recently, deep learning applied to electroencephalogram and electromyogram data has shown great promise as a sleep scoring method, approaching the limits of inter-rater reliability. As with any machine learning algorithm, the inputs to a sleep scoring classifier are typically standardized in order to remove distributional shift caused by variability in the signal collection process. However, in scientific data, experimental manipulations introduce variability that should not be removed. For example, in sleep scoring, the fraction of time spent in each arousal state can vary between control and experimental subjects. We introduce a standardization method, mixture z-scoring, that preserves this crucial form of distributional shift. Using both a simulated experiment and mouse in vivo data, we demonstrate that a common standardization method used by state-of-the-art sleep scoring algorithms introduces systematic bias, but that mixture z-scoring does not. We present a free, open-source user interface that uses a compact neural network and mixture z-scoring to allow for rapid sleep scoring with accuracy that compares well to contemporary methods. This work provides a set of computational tools for the robust automation of sleep scoring.
| S-EPMC6910668 | biostudies-literature
Project description:Machine learning has been applied in recent years to categorize sleep stages (NREM, REM, and wake) using electroencephalogram (EEG) recordings; however, a well-validated sleep scoring automatic pipeline in rodent research is still not publicly available. Here, we present IntelliSleepScorer, a software package with a graphic user interface to score sleep stages automatically in mice. IntelliSleepScorer uses the light gradient boosting machine (LightGBM) to score sleep stages for each epoch of recordings. We developed LightGBM models using a large cohort of data, which consisted of 5776 h of sleep EEG and electromyogram (EMG) signals across 519 unique recordings from 124 mice. The LightGBM model achieved an overall accuracy of 95.2% and a Cohen's kappa of 0.91, which outperforms the baseline models such as the logistic regression model (accuracy = 93.3%, kappa = 0.88) and the random forest model (accuracy = 94.3%, kappa = 0.89). The overall performance of the LightGBM model as well as the performance across different sleep stages are on par with that of the human experts. Most importantly, we validated the generalizability of the LightGBM models: (1) The LightGBM model performed well on two publicly available, independent datasets (kappa > = 0.80), which have different sampling frequency and epoch lengths; (2) The LightGBM model performed well on data recorded at a lower sampling frequency (kappa = 0.90); (3) The performance of the LightGBM model is not affected by the light/dark cycle; and (4) A modified LightGBM model performed well on data containing only one EEG and one EMG electrode (kappa > = 0.89). Taken together, the LightGBM models offer state-of-the-art performance for automatic sleep stage scoring in mice. Last, we implemented the IntelliSleepScorer software package based on the validated model to provide an out-of-box solution to sleep researchers (available for download at https://sites.broadinstitute.org/pan-lab/resources ).
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Project description:Unobservable mechanisms that tie causes to their effects generate observable events. How can one make inferences about hidden causal structures? This paper introduces the domain-matching heuristic to explain how humans perform causal reasoning when lacking mechanistic knowledge. We posit that people reduce the otherwise vast space of possible causal relations by focusing only on the likeliest ones. When thinking about a cause, people tend to think about possible effects that participate in the same domain, and vice versa. To explore the specific domains that people use, we asked people to cluster artifacts. The analyses revealed three commonly employed mechanism domains: the mechanical, chemical, and electromagnetic. Using these domains, we tested the domain-matching heuristic by testing adults’ and children’s causal attribution, prediction, judgment, and subjective understanding. We found that people’s responses conform with domain-matching. These results provide evidence for a heuristic that explains how people engage in causal reasoning without directly appealing to mechanistic or probabilistic knowledge.
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Project description:BackgroundWith the large amount of pharmacological and biological knowledge available in literature, finding novel drug indications for existing drugs using in silico approaches has become increasingly feasible. Typical literature-based approaches generate new hypotheses in the form of protein-protein interactions networks by means of linking concepts based on their cooccurrences within abstracts. However, this kind of approaches tends to generate too many hypotheses, and identifying new drug indications from large networks can be a time-consuming process.MethodologyIn this work, we developed a method that acquires the necessary facts from literature and knowledge bases, and identifies new drug indications through automated reasoning. This is achieved by encoding the molecular effects caused by drug-target interactions and links to various diseases and drug mechanism as domain knowledge in AnsProlog, a declarative language that is useful for automated reasoning, including reasoning with incomplete information. Unlike other literature-based approaches, our approach is more fine-grained, especially in identifying indirect relationships for drug indications.Conclusion/significanceTo evaluate the capability of our approach in inferring novel drug indications, we applied our method to 943 drugs from DrugBank and asked if any of these drugs have potential anti-cancer activities based on information on their targets and molecular interaction types alone. A total of 507 drugs were found to have the potential to be used for cancer treatments. Among the potential anti-cancer drugs, 67 out of 81 drugs (a recall of 82.7%) are indeed known cancer drugs. In addition, 144 out of 289 drugs (a recall of 49.8%) are non-cancer drugs that are currently tested in clinical trials for cancer treatments. These results suggest that our method is able to infer drug indications (original or alternative) based on their molecular targets and interactions alone and has the potential to discover novel drug indications for existing drugs.
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Project description:In this paper we propose a novel approach to the design and implementation of knowledge-based decision support systems for translational research, specifically tailored to the analysis and interpretation of data from high-throughput experiments. Our approach is based on a general epistemological model of the scientific discovery process that provides a well-founded framework for integrating experimental data with preexisting knowledge and with automated inference tools. In order to demonstrate the usefulness and power of the proposed framework, we present its application to Genome-Wide Association Studies, and we use it to reproduce a portion of the initial analysis performed on the well-known WTCCC dataset. Finally, we describe a computational system we are developing, aimed at assisting translational research. The system, based on the proposed model, will be able to automatically plan and perform knowledge discovery steps, to keep track of the inferences performed, and to explain the obtained results.
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