An ensemble of neural networks provides expert-level prenatal detection of complex congenital heart disease.
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ABSTRACT:
SUBMITTER: Arnaout R
PROVIDER: S-EPMC8380434 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Objectives:Scoring laboratory polysomnography (PSG) data remains a manual task of visually annotating 3 primary categories: sleep stages, sleep disordered breathing, and limb movements. Attempts to automate this process have been hampered by the complexity of PSG signals and physiological heterogeneity between patients. Deep neural networks, which have recently achieved expert-level performance for other complex medical tasks, are ideally suited to PSG scoring, given sufficient training data. Methods:We used a combination of deep recurrent and convolutional neural networks (RCNN) for supervised learning of clinical labels designating sleep stages, sleep apnea events, and limb movements. The data for testing and training were derived from 10 000 clinical PSGs and 5804 research PSGs. Results:When trained on the clinical dataset, the RCNN reproduces PSG diagnostic scoring for sleep staging, sleep apnea, and limb movements with accuracies of 87.6%, 88.2% and 84.7% on held-out test data, a level of performance comparable to human experts. The RCNN model performs equally well when tested on the independent research PSG database. Only small reductions in accuracy were noted when training on limited channels to mimic at-home monitoring devices: frontal leads only for sleep staging, and thoracic belt signals only for the apnea-hypopnea index. Conclusions:By creating accurate deep learning models for sleep scoring, our work opens the path toward broader and more timely access to sleep diagnostics. Accurate scoring automation can improve the utility and efficiency of in-lab and at-home approaches to sleep diagnostics, potentially extending the reach of sleep expertise beyond specialty clinics.
| S-EPMC6289549 | biostudies-literature
Project description:ImportanceConvolutional neural networks (CNNs) achieve expert-level accuracy in the diagnosis of pigmented melanocytic lesions. However, the most common types of skin cancer are nonpigmented and nonmelanocytic, and are more difficult to diagnose.ObjectiveTo compare the accuracy of a CNN-based classifier with that of physicians with different levels of experience.Design, setting, and participantsA CNN-based classification model was trained on 7895 dermoscopic and 5829 close-up images of lesions excised at a primary skin cancer clinic between January 1, 2008, and July 13, 2017, for a combined evaluation of both imaging methods. The combined CNN (cCNN) was tested on a set of 2072 unknown cases and compared with results from 95 human raters who were medical personnel, including 62 board-certified dermatologists, with different experience in dermoscopy.Main outcomes and measuresThe proportions of correct specific diagnoses and the accuracy to differentiate between benign and malignant lesions measured as an area under the receiver operating characteristic curve served as main outcome measures.ResultsAmong 95 human raters (51.6% female; mean age, 43.4 years; 95% CI, 41.0-45.7 years), the participants were divided into 3 groups (according to years of experience with dermoscopy): beginner raters (<3 years), intermediate raters (3-10 years), or expert raters (>10 years). The area under the receiver operating characteristic curve of the trained cCNN was higher than human ratings (0.742; 95% CI, 0.729-0.755 vs 0.695; 95% CI, 0.676-0.713; P < .001). The specificity was fixed at the mean level of human raters (51.3%), and therefore the sensitivity of the cCNN (80.5%; 95% CI, 79.0%-82.1%) was higher than that of human raters (77.6%; 95% CI, 74.7%-80.5%). The cCNN achieved a higher percentage of correct specific diagnoses compared with human raters (37.6%; 95% CI, 36.6%-38.4% vs 33.5%; 95% CI, 31.5%-35.6%; P = .001) but not compared with experts (37.3%; 95% CI, 35.7%-38.8% vs 40.0%; 95% CI, 37.0%-43.0%; P = .18).Conclusions and relevanceNeural networks are able to classify dermoscopic and close-up images of nonpigmented lesions as accurately as human experts in an experimental setting.
| S-EPMC6439580 | biostudies-literature
Project description:We propose a novel, scalable, and accurate method for detecting neuronal ensembles from a population of spiking neurons. Our approach offers a simple yet powerful tool to study ensemble activity. It relies on clustering synchronous population activity (population vectors), allows the participation of neurons in different ensembles, has few parameters to tune and is computationally efficient. To validate the performance and generality of our method, we generated synthetic data, where we found that our method accurately detects neuronal ensembles for a wide range of simulation parameters. We found that our method outperforms current alternative methodologies. We used spike trains of retinal ganglion cells obtained from multi-electrode array recordings under a simple ON-OFF light stimulus to test our method. We found a consistent stimuli-evoked ensemble activity intermingled with spontaneously active ensembles and irregular activity. Our results suggest that the early visual system activity could be organized in distinguishable functional ensembles. We provide a Graphic User Interface, which facilitates the use of our method by the scientific community.
| S-EPMC8323916 | biostudies-literature
Project description:Background: Decision-making in epilepsy surgery is strongly connected to the interpretation of the intracranial EEG (iEEG). Although deep learning approaches have demonstrated efficiency in processing extracranial EEG, few studies have addressed iEEG seizure detection, in part due to the small number of seizures per patient typically available from intracranial investigations. This study aims to evaluate the efficiency of deep learning methodology in detecting iEEG seizures using a large dataset of ictal patterns collected from epilepsy patients implanted with a responsive neurostimulation system (RNS). Methods: Five thousand two hundred and twenty-six ictal events were collected from 22 patients implanted with RNS. A convolutional neural network (CNN) architecture was created to provide personalized seizure annotations for each patient. Accuracy of seizure identification was tested in two scenarios: patients with seizures occurring following a period of chronic recording (scenario 1) and patients with seizures occurring immediately following implantation (scenario 2). The accuracy of the CNN in identifying RNS-recorded iEEG ictal patterns was evaluated against human neurophysiology expertise. Statistical performance was assessed via the area-under-precision-recall curve (AUPRC). Results: In scenario 1, the CNN achieved a maximum mean binary classification AUPRC of 0.84 ± 0.19 (95%CI, 0.72-0.93) and mean regression accuracy of 6.3 ± 1.0 s (95%CI, 4.3-8.5 s) at 30 seed samples. In scenario 2, maximum mean AUPRC was 0.80 ± 0.19 (95%CI, 0.68-0.91) and mean regression accuracy was 6.3 ± 0.9 s (95%CI, 4.8-8.3 s) at 20 seed samples. We obtained near-maximum accuracies at seed size of 10 in both scenarios. CNN classification failures can be explained by ictal electro-decrements, brief seizures, single-channel ictal patterns, highly concentrated interictal activity, changes in the sleep-wake cycle, and progressive modulation of electrographic ictal features. Conclusions: We developed a deep learning neural network that performs personalized detection of RNS-derived ictal patterns with expert-level accuracy. These results suggest the potential for automated techniques to significantly improve the management of closed-loop brain stimulation, including during the initial period of recording when the device is otherwise naïve to a given patient's seizures.
| S-EPMC8126697 | biostudies-literature
Project description:The cardiac neural crest arises in the hindbrain, then migrates to the heart and contributes to critical structures, including the outflow tract septum. Chick cardiac crest ablation results in failure of this septation, phenocopying the human heart defect persistent truncus arteriosus (PTA), which trunk neural crest fails to rescue. Here, we probe the molecular mechanisms underlying the cardiac crest's unique potential. Transcriptional profiling identified cardiac-crest-specific transcription factors, with single-cell RNA sequencing revealing surprising heterogeneity, including an ectomesenchymal subpopulation within the early migrating population. Loss-of-function analyses uncovered a transcriptional subcircuit, comprised of Tgif1, Ets1, and Sox8, critical for cardiac neural crest and heart development. Importantly, ectopic expression of this subcircuit was sufficient to imbue trunk crest with the ability to rescue PTA after cardiac crest ablation. Together, our results reveal a transcriptional program sufficient to confer cardiac potential onto trunk neural crest cells, thus implicating new genes in cardiovascular birth defects.
| S-EPMC7255058 | biostudies-literature
Project description:BackgroundThis report evaluates results of a screening program on prenatal detection of congenital heart defects in a geographical cohort of western Sweden between January 1st, 2013 and June 31st, 2017. During the study period 88,230 children were born in VGR.MethodsRetrospective data on pregnant women from the Västra Götaland region that were referred to fetal cardiologists in Gothenburg were retrieved. To determine prenatal detection rate, all neonates who underwent surgery or catheter intervention for a critical congenital heart defect born between January 1st, 2014 and December 31st, 2016 were included. The four-chamber view was implemented into the routine scan in 2009 and implementation of the ISUOG guidelines, including the outflow tracts, started in the region in 2015.Results113 fetuses received a prenatal diagnosis of a major congenital heart defect. 89% of these were referred because of a suspected cardiac malformation and 88% were diagnosed before 22 completed weeks. 59% of the patients diagnosed before 22 completed weeks opted for termination of pregnancy. During 2014-2016, 61 fetuses had a prenatal diagnosis of a critical congenital heart defect and a further 47 were diagnosed after birth, hence 56% were diagnosed prenatally, 82% for those which had a combination with an extracardiac abnormality and/or chromosomal aberration compared to 50% if an isolated critical congenital heart defect was diagnosed. For single ventricle cardiac defects such as hypoplastic left heart syndrome, double inlet left ventricle and tricuspid atresia, the detection rate was 100%. The detection rate for transposition of the great arteries and coarctation of the aorta was 9 and 18% respectively.Conclusions56% of all fetuses with a critical congenital heart defect were diagnosed prenatally during 2014-2016 and approximately 53% of all major congenital heart defects 2013-2017 as compared to 13.8% in 2009 in the same region. An increased focus towards the fetal heart in the routine scan improved the prenatal detection rate of major congenital heart defects. The detection of congenital heart defects affecting the four-chamber view seems sufficient, but more training is needed to improve the quality of the examination of the outflow tracts.
| S-EPMC8380393 | biostudies-literature
Project description:With over 3500 mosquito species described, accurate species identification of the few implicated in disease transmission is critical to mosquito borne disease mitigation. Yet this task is hindered by limited global taxonomic expertise and specimen damage consistent across common capture methods. Convolutional neural networks (CNNs) are promising with limited sets of species, but image database requirements restrict practical implementation. Using an image database of 2696 specimens from 67 mosquito species, we address the practical open-set problem with a detection algorithm for novel species. Closed-set classification of 16 known species achieved 97.04 ± 0.87% accuracy independently, and 89.07 ± 5.58% when cascaded with novelty detection. Closed-set classification of 39 species produces a macro F1-score of 86.07 ± 1.81%. This demonstrates an accurate, scalable, and practical computer vision solution to identify wild-caught mosquitoes for implementation in biosurveillance and targeted vector control programs, without the need for extensive image database development for each new target region.
| S-EPMC8249627 | biostudies-literature
Project description:BackgroundDeep learning-based head and neck lymph node level (HN_LNL) autodelineation is of high relevance to radiotherapy research and clinical treatment planning but still underinvestigated in academic literature. In particular, there is no publicly available open-source solution for large-scale autosegmentation of HN_LNL in the research setting.MethodsAn expert-delineated cohort of 35 planning CTs was used for training of an nnU-net 3D-fullres/2D-ensemble model for autosegmentation of 20 different HN_LNL. A second cohort acquired at the same institution later in time served as the test set (n = 20). In a completely blinded evaluation, 3 clinical experts rated the quality of deep learning autosegmentations in a head-to-head comparison with expert-created contours. For a subgroup of 10 cases, intraobserver variability was compared to the average deep learning autosegmentation accuracy on the original and recontoured set of expert segmentations. A postprocessing step to adjust craniocaudal boundaries of level autosegmentations to the CT slice plane was introduced and the effect of autocontour consistency with CT slice plane orientation on geometric accuracy and expert rating was investigated.ResultsBlinded expert ratings for deep learning segmentations and expert-created contours were not significantly different. Deep learning segmentations with slice plane adjustment were rated numerically higher (mean, 81.0 vs. 79.6, p = 0.185) and deep learning segmentations without slice plane adjustment were rated numerically lower (77.2 vs. 79.6, p = 0.167) than manually drawn contours. In a head-to-head comparison, deep learning segmentations with CT slice plane adjustment were rated significantly better than deep learning contours without slice plane adjustment (81.0 vs. 77.2, p = 0.004). Geometric accuracy of deep learning segmentations was not different from intraobserver variability (mean Dice per level, 0.76 vs. 0.77, p = 0.307). Clinical significance of contour consistency with CT slice plane orientation was not represented by geometric accuracy metrics (volumetric Dice, 0.78 vs. 0.78, p = 0.703).ConclusionsWe show that a nnU-net 3D-fullres/2D-ensemble model can be used for highly accurate autodelineation of HN_LNL using only a limited training dataset that is ideally suited for large-scale standardized autodelineation of HN_LNL in the research setting. Geometric accuracy metrics are only an imperfect surrogate for blinded expert rating.
| S-EPMC9978473 | biostudies-literature
Project description:Sensor devices in wireless sensor networks are vulnerable to faults during their operation in unmonitored and hazardous environments. Though various methods have been proposed by researchers to detect sensor faults, only very few research studies have reported on capturing the dynamics of the inherent states in sensor data during fault occurrence. The continuous density hidden Markov model (CDHMM) is proposed in this research to determine the dynamics of the state transitions due to fault occurrence, while neural networks are utilized to classify the faults based on the state transition probability density generated by the CDHMM. Therefore, this paper focuses on the fault detection and classification using the hybridization of CDHMM and various neural networks (NNs), namely the learning vector quantization, probabilistic neural network, adaptive probabilistic neural network, and radial basis function. The hybrid models of each NN are used for the classification of sensor faults, namely bias, drift, random, and spike. The proposed methods are evaluated using four performance metrics which includes detection accuracy, false positive rate, F1-score, and the Matthews correlation coefficient. The simulation results show that the learning vector quantization NN classifier outperforms the detection accuracy rate when compared to the other classifiers. In addition, an ensemble NN framework based on the hybrid CDHMM classifier is built with majority voting scheme for decision making and classification. The results of the hybrid CDHMM ensemble classifiers clearly indicates the efficacy of the proposed scheme in capturing the dynamics of change of statesm which is the vital aspect in determining rapidly-evolving instant faults that occur in wireless sensor networks.
| S-EPMC7038388 | biostudies-literature
Project description:White matter hyperintensities (WMHs) represent the most common neuroimaging marker of cerebral small vessel disease (CSVD). The volume and location of WMHs are important clinical measures. We present a pipeline using deep fully convolutional network and ensemble models, combining U-Net, SE-Net, and multi-scale features, to automatically segment WMHs and estimate their volumes and locations. We evaluated our method in two datasets: a clinical routine dataset comprising 60 patients (selected from Chinese National Stroke Registry, CNSR) and a research dataset composed of 60 patients (selected from MICCAI WMH Challenge, MWC). The performance of our pipeline was compared with four freely available methods: LGA, LPA, UBO detector, and U-Net, in terms of a variety of metrics. Additionally, to access the model generalization ability, another research dataset comprising 40 patients (from Older Australian Twins Study and Sydney Memory and Aging Study, OSM), was selected and tested. The pipeline achieved the best performance in both research dataset and the clinical routine dataset with DSC being significantly higher than other methods (p < .001), reaching .833 and .783, respectively. The results of model generalization ability showed that the model trained on the research dataset (DSC = 0.736) performed higher than that trained on the clinical dataset (DSC = 0.622). Our method outperformed widely used pipelines in WMHs segmentation. This system could generate both image and text outputs for whole brain, lobar and anatomical automatic labeling WMHs. Additionally, software and models of our method are made publicly available at https://www.nitrc.org/projects/what_v1.
| S-EPMC8764480 | biostudies-literature