Biomedical Engineering - Research Publications
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ItemNo Preview AvailableModel Parameter Estimation As Features to Predict the Duration of Epileptic Seizures From Onset(Institute of Electrical and Electronics Engineers, 2023)The durations of epileptic seizures are linked to severity and risk for patients. It is unclear if the spatiotemporal evolution of a seizure has any relationship with its duration. Understanding such mechanisms may help reveal treatments for reducing the duration of a seizure. Here, we present a novel method to predict whether a seizure is going to be short or long at its onset using features that can be interpreted in the parameter space of a brain model. The parameters of a Jansen-Rit neural mass model were tracked given intracranial electroencephalography (iEEG) signals, and were processed as time series features using MINIROCKET. By analysing 2954 seizures from 10 patients, patient-specific classifiers were built to predict if a seizure would be short or long given 7 s of iEEG at seizure onset. The method achieved an area under the receiver operating characteristic curve (AUC) greater than 0.6 for five of 10 patients. The behaviour in the parameter space has shown different mechanisms are associated with short/long seizures.Clinical relevance—This shows that it is possible to classify whether a seizure will be short or long based on its early characteristics. Timely interventions and treatments can be applied if the duration of the seizures can be predicted.
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ItemNo Preview AvailableBrain model state space reconstruction using an LSTM neural network(IOP Publishing Ltd, 2023-06-01)Objective. Kalman filtering has previously been applied to track neural model states and parameters, particularly at the scale relevant to electroencephalography (EEG). However, this approach lacks a reliable method to determine the initial filter conditions and assumes that the distribution of states remains Gaussian. This study presents an alternative, data-driven method to track the states and parameters of neural mass models (NMMs) from EEG recordings using deep learning techniques, specifically a long short-term memory (LSTM) neural network.Approach. An LSTM filter was trained on simulated EEG data generated by a NMM using a wide range of parameters. With an appropriately customised loss function, the LSTM filter can learn the behaviour of NMMs. As a result, it can output the state vector and parameters of NMMs given observation data as the input.Main results. Test results using simulated data yielded correlations withRsquared of around 0.99 and verified that the method is robust to noise and can be more accurate than a nonlinear Kalman filter when the initial conditions of the Kalman filter are not accurate. As an example of real-world application, the LSTM filter was also applied to real EEG data that included epileptic seizures, and revealed changes in connectivity strength parameters at the beginnings of seizures.Significance. Tracking the state vector and parameters of mathematical brain models is of great importance in the area of brain modelling, monitoring, imaging and control. This approach has no need to specify the initial state vector and parameters, which is very difficult to do in practice because many of the variables being estimated cannot be measured directly in physiological experiments. This method may be applied using any NMM and, therefore, provides a general, novel, efficient approach to estimate brain model variables that are often difficult to measure.
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ItemNo Preview AvailableSpace-time resolved inference-based neurophysiological process imaging: Application to resting-state alpha rhythm(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2022-11)Neural processes are complex and difficult to image. This paper presents a new space-time resolved brain imaging framework, called Neurophysiological Process Imaging (NPI), that identifies neurophysiological processes within cerebral cortex at the macroscopic scale. By fitting uncoupled neural mass models to each electromagnetic source time-series using a novel nonlinear inference method, population averaged membrane potentials and synaptic connection strengths are efficiently and accurately inferred and imaged across the whole cerebral cortex at a resolution afforded by source imaging. The efficiency of the framework enables return of the augmented source imaging results overnight using high performance computing. This suggests it can be used as a practical and novel imaging tool. To demonstrate the framework, it has been applied to resting-state magnetoencephalographic source estimates. The results suggest that endogenous inputs to cingulate, occipital, and inferior frontal cortex are essential modulators of resting-state alpha power. Moreover, endogenous input and inhibitory and excitatory neural populations play varied roles in mediating alpha power in different resting-state sub-networks. The framework can be applied to arbitrary neural mass models and has broad applicability to image neural processes of different brain states.
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ItemEnsembling crowdsourced seizure prediction algorithms using long-term human intracranial EEG(Wiley, 2020-02)Seizure prediction is feasible, but greater accuracy is needed to make seizure prediction clinically viable across a large group of patients. Recent work crowdsourced state‐of‐the‐art prediction algorithms in a worldwide competition, yielding improvements in seizure prediction performance for patients whose seizures were previously found hard to anticipate. The aim of the current analysis was to explore potential performance improvements using an ensemble of the top competition algorithms. The results suggest that minor increments in performance may be possible; however, the outcomes of statistical testing limit the confidence in these increments. Our results suggest that for the specific algorithms, evaluation framework, and data considered here, incremental improvements are achievable but there may be upper bounds on machine learning–based seizure prediction performance for some patients whose seizures are challenging to predict. Other more tailored approaches that, for example, take into account a deeper understanding of preictal mechanisms, patient‐specific sleep‐wake rhythms, or novel measurement approaches, may still offer further gains for these types of patients.
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ItemIdentifying seizure risk factors: A comparison of sleep, weather, and temporal features using a Bayesian forecast(WILEY, 2021-02)OBJECTIVE: Most seizure forecasting algorithms have relied on features specific to electroencephalographic recordings. Environmental and physiological factors, such as weather and sleep, have long been suspected to affect brain activity and seizure occurrence but have not been fully explored as prior information for seizure forecasts in a patient-specific analysis. The study aimed to quantify whether sleep, weather, and temporal factors (time of day, day of week, and lunar phase) can provide predictive prior probabilities that may be used to improve seizure forecasts. METHODS: This study performed post hoc analysis on data from eight patients with a total of 12.2 years of continuous intracranial electroencephalographic recordings (average = 1.5 years, range = 1.0-2.1 years), originally collected in a prospective trial. Patients also had sleep scoring and location-specific weather data. Histograms of future seizure likelihood were generated for each feature. The predictive utility of individual features was measured using a Bayesian approach to combine different features into an overall forecast of seizure likelihood. Performance of different feature combinations was compared using the area under the receiver operating curve. Performance evaluation was pseudoprospective. RESULTS: For the eight patients studied, seizures could be predicted above chance accuracy using sleep (five patients), weather (two patients), and temporal features (six patients). Forecasts using combined features performed significantly better than chance in six patients. For four of these patients, combined forecasts outperformed any individual feature. SIGNIFICANCE: Environmental and physiological data, including sleep, weather, and temporal features, provide significant predictive information on upcoming seizures. Although forecasts did not perform as well as algorithms that use invasive intracranial electroencephalography, the results were significantly above chance. Complementary signal features derived from an individual's historic seizure records may provide useful prior information to augment traditional seizure detection or forecasting algorithms. Importantly, many predictive features used in this study can be measured noninvasively.
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ItemForecasting cycles of seizure likelihood(Wiley, 2020-03-27)Objective Seizure unpredictability is rated as one of the most challenging aspects of living with epilepsy. Seizure likelihood can be influenced by a range of environmental and physiological factors that are difficult to measure and quantify. However, some generalizable patterns have been demonstrated in seizure onset. A majority of people with epilepsy exhibit circadian rhythms in their seizure times, and many also show slower, multiday patterns. Seizure cycles can be measured using a range of recording modalities, including self‐reported electronic seizure diaries. This study aimed to develop personalized forecasts from a mobile seizure diary app. Methods Forecasts based on circadian and multiday seizure cycles were tested pseudoprospectively using data from 50 app users (mean of 109 seizures per subject). Individuals' strongest cycles were estimated from their reported seizure times and used to derive the likelihood of future seizures. The forecasting approach was validated using self‐reported events and electrographic seizures from the Neurovista dataset, an existing database of long‐term electroencephalography that has been widely used to develop forecasting algorithms. Results The validation dataset showed that forecasts of seizure likelihood based on self‐reported cycles were predictive of electrographic seizures for approximately half the cohort. Forecasts using only mobile app diaries allowed users to spend an average of 67.1% of their time in a low‐risk state, with 14.8% of their time in a high‐risk warning state. On average, 69.1% of seizures occurred during high‐risk states and 10.5% of seizures occurred in low‐risk states. Significance Seizure diary apps can provide personalized forecasts of seizure likelihood that are accurate and clinically relevant for electrographic seizures. These results have immediate potential for translation to a prospective seizure forecasting trial using a mobile diary app. It is our hope that seizure forecasting apps will one day give people with epilepsy greater confidence in managing their daily activities.
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ItemA taxonomy of seizure dynamotypes(eLIFE SCIENCES PUBL LTD, 2020-07-21)Seizures are a disruption of normal brain activity present across a vast range of species and conditions. We introduce an organizing principle that leads to the first objective Taxonomy of Seizure Dynamics (TSD) based on bifurcation theory. The 'dynamotype' of a seizure is the dynamic composition that defines its observable characteristics, including how it starts, evolves and ends. Analyzing over 2000 focal-onset seizures from multiple centers, we find evidence of all 16 dynamotypes predicted in TSD. We demonstrate that patients' dynamotypes evolve during their lifetime and display complex but systematic variations including hierarchy (certain types are more common), non-bijectivity (a patient may display multiple types) and pairing preference (multiple types may occur during one seizure). TSD provides a way to stratify patients in complement to present clinical classifications, a language to describe the most critical features of seizure dynamics, and a framework to guide future research focused on dynamical properties.
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ItemCritical slowing down as a biomarker for seizure susceptibility.(Nature Research (part of Springer Nature), 2020-05-01)The human brain has the capacity to rapidly change state, and in epilepsy these state changes can be catastrophic, resulting in loss of consciousness, injury and even death. Theoretical interpretations considering the brain as a dynamical system suggest that prior to a seizure, recorded brain signals may exhibit critical slowing down, a warning signal preceding many critical transitions in dynamical systems. Using long-term intracranial electroencephalography (iEEG) recordings from fourteen patients with focal epilepsy, we monitored key signatures of critical slowing down prior to seizures. The metrics used to detect critical slowing down fluctuated over temporally long scales (hours to days), longer than would be detectable in standard clinical evaluation settings. Seizure risk was associated with a combination of these signals together with epileptiform discharges. These results provide strong validation of theoretical models and demonstrate that critical slowing down is a reliable indicator that could be used in seizure forecasting algorithms.