Clinical Validation of the Champagne Algorithm for Epilepsy Spike Localization.
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ABSTRACT:
SUBMITTER: Cai C
PROVIDER: S-EPMC8172809 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In this paper, we present an extensive performance evaluation of a novel source localization algorithm, Champagne. It is derived in an empirical Bayesian framework that yields sparse solutions to the inverse problem. It is robust to correlated sources and learns the statistics of non-stimulus-evoked activity to suppress the effect of noise and interfering brain activity. We tested Champagne on both simulated and real M/EEG data. The source locations used for the simulated data were chosen to test the performance on challenging source configurations. In simulations, we found that Champagne outperforms the benchmark algorithms in terms of both the accuracy of the source localizations and the correct estimation of source time courses. We also demonstrate that Champagne is more robust to correlated brain activity present in real MEG data and is able to resolve many distinct and functionally relevant brain areas with real MEG and EEG data.
| S-EPMC4096349 | biostudies-literature
Project description: Not available
| S-BSST208 | biostudies-other
Project description:ObjectiveTo provide a multi-atlas framework for automated hippocampus segmentation in temporal lobe epilepsy (TLE) and clinically validate the results with respect to surgical lateralization and post-surgical outcome.MethodsWe retrospectively identified 47 TLE patients who underwent surgical resection and 12 healthy controls. T1-weighted 3?T MRI scans were acquired for all subjects, and patients were identified by a neuroradiologist with regards to lateralization and degree of hippocampal sclerosis (HS). Automated segmentation was implemented through the Joint Label Fusion/Corrective Learning (JLF/CL) method. Gold standard lateralization was determined from the surgically resected side in Engel I (seizure-free) patients at the two-year timepoint. ROC curves were used to identify appropriate thresholds for hippocampal asymmetry ratios, which were then used to analyze JLF/CL lateralization.ResultsThe optimal template atlas based on subject images with varying appearances, from normal-appearing to severe HS, was demonstrated to be composed entirely of normal-appearing subjects, with good agreement between automated and manual segmentations. In applying this atlas to 26 surgically resected seizure-free patients at a two-year timepoint, JLF/CL lateralized seizure onset 92% of the time. In comparison, neuroradiology reads lateralized 65% of patients, but correctly lateralized seizure onset in these patients 100% of the time. When compared to lateralized neuroradiology reads, JLF/CL was in agreement and correctly lateralized all 17 patients. When compared to nonlateralized radiology reads, JLF/CL correctly lateralized 78% of the nine patients.SignificanceWhile a neuroradiologist's interpretation of MR imaging is a key, albeit imperfect, diagnostic tool for seizure localization in medically-refractory TLE patients, automated hippocampal segmentation may provide more efficient and accurate epileptic foci localization. These promising findings demonstrate the clinical utility of automated segmentation in the TLE MR imaging pipeline prior to surgical resection, and suggest that further investigation into JLF/CL-assisted MRI reading could improve clinical outcomes. Our JLF/CL software is publicly available at https://www.nitrc.org/projects/ashs/.
| S-EPMC6205355 | biostudies-literature
Project description:The aim of this prospective blinded study was to evaluate an automated algorithm for spike-and-wave discharge (SWD) detection applied to EEGs from genetic absence epilepsy rats from Strasbourg (GAERS). Five GAERS underwent four sessions of 20-min EEG recording. Each EEG was manually analyzed for SWDs longer than one second by two investigators and automatically using an algorithm developed in MATLAB®. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for the manual (reference) versus the automatic (test) methods. The results showed that the algorithm had specificity, sensitivity, PPV and NPV >94%, comparable to published methods that are based on analyzing EEG changes in the frequency domain. This provides a good alternative as a method designed to mimic human manual marking in the time domain.
| S-EPMC5563679 | biostudies-other
Project description:ObjectiveManual detection of spike-wave discharges (SWDs) from electroencephalography (EEG) records is time intensive, costly, and subject to inconsistencies/biases. In addition, manual scoring often omits information on SWD confidence/intensity, which may be important for the investigation of mechanistic-based research questions. Our objective is to develop an automated method for the detection of SWDs in a mouse model of absence epilepsy that is focused on the characteristics of human scoring of preselected events to establish a confidence-based, continuous-valued scoring.MethodsWe develop a support vector machine (SVM)-based algorithm for the automated detection of SWDs in the ?2R43Q mouse model of absence epilepsy. The algorithm first identifies putative SWD events using frequency- and amplitude-based peak detection. Four humans scored a set of 2500 putative events identified by the algorithm. Then, using predictors calculated from the wavelet transform of each event and the labels from human scoring, we trained an SVM to classify (SWD/nonSWD) and assign confidence scores to each event identified from 60, 24-hour EEG records. We provide a detailed assessment of intra- and interrater scoring that demonstrates advantages of automated scoring.ResultsThe algorithm scored SWDs along a continuum that is highly correlated with human confidence and that allows us to more effectively characterize ambiguous events. We demonstrate that events along our scoring continuum are temporally and proportionately correlated with abrupt changes in spectral power bands relevant to normal behavioral states including sleep.SignificanceAlthough there are automated and semi-automated methods for the detection of SWDs in humans and rats, we contribute to the need for continued development of SWD detection in mice. Our results demonstrate the value of viewing detection of SWDs as a continuous classification problem to better understand "ground truth" in SWD detection (ie, the most reliable features agreed upon by humans that also correlate with objective physiologic measures).
| S-EPMC6398153 | biostudies-literature
Project description:BackgroundStep counts are increasingly used in public health and clinical research to assess wellbeing, lifestyle, and health status. However, estimating step counts using commercial activity trackers has several limitations, including a lack of reproducibility, generalizability, and scalability. Smartphones are a potentially promising alternative, but their step-counting algorithms require robust validation that accounts for temporal sensor body location, individual gait characteristics, and heterogeneous health states.ObjectiveOur goal was to evaluate an open-source step-counting method for smartphones under various measurement conditions against step counts estimated from data collected simultaneously from different body locations ("internal" validation), manually ascertained ground truth ("manual" validation), and step counts from a commercial activity tracker (Fitbit Charge 2) in patients with advanced cancer ("wearable" validation).MethodsWe used eight independent datasets collected in controlled, semi-controlled, and free-living environments with different devices (primarily Android smartphones and wearable accelerometers) carried at typical body locations. Five datasets (N=103) were used for internal validation, two datasets (N=107) for manual validation, and one dataset (N=45) used for wearable validation. In each scenario, step counts were estimated using a previously published step-counting method for smartphones that uses raw sub-second level accelerometer data. We calculated mean bias and limits of agreement (LoA) between step count estimates and validation criteria using Bland-Altman analysis.ResultsIn the internal validation datasets, participants performed 751.7±581.2 (mean±SD) steps, and the mean bias was -7.2 steps (LoA -47.6, 33.3) or -0.5%. In the manual validation datasets, the ground truth step count was 367.4±359.4 steps while the mean bias was -0.4 steps (LoA -75.2, 74.3) or 0.1 %. In the wearable validation dataset, Fitbit devices indicated mean step counts of 1931.2±2338.4, while the calculated bias was equal to -67.1 steps (LoA -603.8, 469.7) or a difference of 0.3 %.ConclusionsThis study demonstrates that our open-source step counting method for smartphone data provides reliable step counts across sensor locations, measurement scenarios, and populations, including healthy adults and patients with cancer.
| S-EPMC10081434 | biostudies-literature
Project description:Mean systemic filling pressure (Pms) is a promising parameter in determining intravascular fluid status. Pms derived from venous return curves during inspiratory holds with incremental airway pressures (Pms-Insp) estimates Pms reliably but is labor-intensive. A computerized algorithm to calculate Pms (Pmsa) at the bedside has been proposed. In previous studies Pmsa and Pms-Insp correlated well but with considerable bias. This observational study was performed to validate Pmsa with Pms-Insp in cardiac surgery patients. Cardiac output, right atrial pressure and mean arterial pressure were prospectively recorded to calculate Pmsa using a bedside monitor. Pms-Insp was calculated offline after performing inspiratory holds. Intraclass-correlation coefficient (ICC) and assessment of agreement were used to compare Pmsa with Pms-Insp. Bias, coefficient of variance (COV), precision and limits of agreement (LOA) were calculated. Proportional bias was assessed with linear regression. A high degree of inter-method reliability was found between Pmsa and Pms-Insp (ICC 0.89; 95%CI 0.72-0.96, p = 0.01) in 18 patients. Pmsa and Pms-Insp differed not significantly (11.9 mmHg, IQR 9.8-13.4 vs. 12.7 mmHg, IQR 10.5-14.4, p = 0.38). Bias was -0.502 ± 1.90 mmHg (p = 0.277). COV was 4% with LOA -4.22 - 3.22 mmHg without proportional bias. Conversion coefficient Pmsa ➔ Pms-Insp was 0.94. This assessment of agreement demonstrates that the measures Pms-Insp and the computerized Pmsa-algorithm are interchangeable (bias -0.502 ± 1.90 mmHg with conversion coefficient 0.94). The choice of Pmsa is straightforward, it is non-interventional and available continuously at the bedside in contrast to Pms-Insp which is interventional and calculated off-line. Further studies should be performed to determine the place of Pmsa in the circulatory management of critically ill patients. ( www.clinicaltrials.gov ; TRN NCT04202432, release date 16-12-2019; retrospectively registered).Clinical Trial Registration www.ClinicalTrials.gov , TRN: NCT04202432, initial release date 16-12-2019 (retrospectively registered).
| S-EPMC8011774 | biostudies-literature
Project description:Spike timing is precise in the auditory system and it has been argued that it conveys information about auditory stimuli, in particular about the location of a sound source. However, beyond simple time differences, the way in which neurons might extract this information is unclear and the potential computational advantages are unknown. The computational difficulty of this task for an animal is to locate the source of an unexpected sound from two monaural signals that are highly dependent on the unknown source signal. In neuron models consisting of spectro-temporal filtering and spiking nonlinearity, we found that the binaural structure induced by spatialized sounds is mapped to synchrony patterns that depend on source location rather than on source signal. Location-specific synchrony patterns would then result in the activation of location-specific assemblies of postsynaptic neurons. We designed a spiking neuron model which exploited this principle to locate a variety of sound sources in a virtual acoustic environment using measured human head-related transfer functions. The model was able to accurately estimate the location of previously unknown sounds in both azimuth and elevation (including front/back discrimination) in a known acoustic environment. We found that multiple representations of different acoustic environments could coexist as sets of overlapping neural assemblies which could be associated with spatial locations by Hebbian learning. The model demonstrates the computational relevance of relative spike timing to extract spatial information about sources independently of the source signal.
| S-EPMC2978676 | biostudies-literature
Project description:Neural decoding and its applications to brain computer interfaces (BCI) are essential for understanding the association between neural activity and behavior. A prerequisite for many decoding approaches is spike sorting, the assignment of action potentials (spikes) to individual neurons. Current spike sorting algorithms, however, can be inaccurate and do not properly model uncertainty of spike assignments, therefore discarding information that could potentially improve decoding performance. Recent advances in high-density probes (e.g., Neuropixels) and computational methods now allow for extracting a rich set of spike features from unsorted data; these features can in turn be used to directly decode behavioral correlates. To this end, we propose a spike sorting-free decoding method that directly models the distribution of extracted spike features using a mixture of Gaussians (MoG) encoding the uncertainty of spike assignments, without aiming to solve the spike clustering problem explicitly. We allow the mixing proportion of the MoG to change over time in response to the behavior and develop variational inference methods to fit the resulting model and to perform decoding. We benchmark our method with an extensive suite of recordings from different animals and probe geometries, demonstrating that our proposed decoder can consistently outperform current methods based on thresholding (i.e. multi-unit activity) and spike sorting. Open source code is available at https://github.com/yzhang511/density_decoding.
| S-EPMC10542538 | biostudies-literature
Project description:BackgroundOver the past decade, the emergence of several large federated clinical data networks has enabled researchers to access data on millions of patients at dozens of health care organizations. Typically, queries are broadcast to each of the sites in the network, which then return aggregate counts of the number of matching patients. However, because patients can receive care from multiple sites in the network, simply adding the numbers frequently double counts patients. Various methods such as the use of trusted third parties or secure multiparty computation have been proposed to link patient records across sites. However, they either have large trade-offs in accuracy and privacy or are not scalable to large networks.ObjectiveThis study aims to enable accurate estimates of the number of patients matching a federated query while providing strong guarantees on the amount of protected medical information revealed.MethodsWe introduce a novel probabilistic approach to running federated network queries. It combines an algorithm called HyperLogLog with obfuscation in the form of hashing, masking, and homomorphic encryption. It is tunable, in that it allows networks to balance accuracy versus privacy, and it is computationally efficient even for large networks. We built a user-friendly free open-source benchmarking platform to simulate federated queries in large hospital networks. Using this platform, we compare the accuracy, k-anonymity privacy risk (with k=10), and computational runtime of our algorithm with several existing techniques.ResultsIn simulated queries matching 1 to 100 million patients in a 100-hospital network, our method was significantly more accurate than adding aggregate counts while maintaining k-anonymity. On average, it required a total of 12 kilobytes of data to be sent to the network hub and added only 5 milliseconds to the overall federated query runtime. This was orders of magnitude better than other approaches, which guaranteed the exact answer.ConclusionsUsing our method, it is possible to run highly accurate federated queries of clinical data repositories that both protect patient privacy and scale to large networks.
| S-EPMC7671849 | biostudies-literature