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1. A Deep Learning-Based Real-time Seizure Detection System

   https://doi.org/10.1109/SPMB50085.2020.9353623  

   Shawki, N. ; Elseify, T. ; Cap, T. ; Shah, V. ; Obeid, I. ; Picone, J. ( December 2020 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad Selesnick (Ed.)

   Electroencephalography (EEG) is a popular clinical monitoring tool used for diagnosing brain-related disorders such as epilepsy [1]. As monitoring EEGs in a critical-care setting is an expensive and tedious task, there is a great interest in developing real-time EEG monitoring tools to improve patient care quality and efficiency [2]. However, clinicians require automatic seizure detection tools that provide decisions with at least 75% sensitivity and less than 1 false alarm (FA) per 24 hours [3]. Some commercial tools recently claim to reach such performance levels, including the Olympic Brainz Monitor [4] and Persyst 14 [5]. In this abstract, we describe our efforts to transform a high-performance offline seizure detection system [3] into a low latency real-time or online seizure detection system. An overview of the system is shown in Figure 1. The main difference between an online versus offline system is that an online system should always be causal and has minimum latency which is often defined by domain experts. The offline system, shown in Figure 2, uses two phases of deep learning models with postprocessing [3]. The channel-based long short term memory (LSTM) model (Phase 1 or P1) processes linear frequency cepstral coefficients (LFCC) [6] features from each EEG channel separately. We use the hypotheses generated by the P1 model and create additional features that carry information about the detected events and their confidence. The P2 model uses these additional features and the LFCC features to learn the temporal and spatial aspects of the EEG signals using a hybrid convolutional neural network (CNN) and LSTM model. Finally, Phase 3 aggregates the results from both P1 and P2 before applying a final postprocessing step. The online system implements Phase 1 by taking advantage of the Linux piping mechanism, multithreading techniques, and multi-core processors. To convert Phase 1 into an online system, we divide the system into five major modules: signal preprocessor, feature extractor, event decoder, postprocessor, and visualizer. The system reads 0.1-second frames from each EEG channel and sends them to the feature extractor and the visualizer. The feature extractor generates LFCC features in real time from the streaming EEG signal. Next, the system computes seizure and background probabilities using a channel-based LSTM model and applies a postprocessor to aggregate the detected events across channels. The system then displays the EEG signal and the decisions simultaneously using a visualization module. The online system uses C++, Python, TensorFlow, and PyQtGraph in its implementation. The online system accepts streamed EEG data sampled at 250 Hz as input. The system begins processing the EEG signal by applying a TCP montage [8]. Depending on the type of the montage, the EEG signal can have either 22 or 20 channels. To enable the online operation, we send 0.1-second (25 samples) length frames from each channel of the streamed EEG signal to the feature extractor and the visualizer. Feature extraction is performed sequentially on each channel. The signal preprocessor writes the sample frames into two streams to facilitate these modules. In the first stream, the feature extractor receives the signals using stdin. In parallel, as a second stream, the visualizer shares a user-defined file with the signal preprocessor. This user-defined file holds raw signal information as a buffer for the visualizer. The signal preprocessor writes into the file while the visualizer reads from it. Reading and writing into the same file poses a challenge. The visualizer can start reading while the signal preprocessor is writing into it. To resolve this issue, we utilize a file locking mechanism in the signal preprocessor and visualizer. Each of the processes temporarily locks the file, performs its operation, releases the lock, and tries to obtain the lock after a waiting period. The file locking mechanism ensures that only one process can access the file by prohibiting other processes from reading or writing while one process is modifying the file [9]. The feature extractor uses circular buffers to save 0.3 seconds or 75 samples from each channel for extracting 0.2-second or 50-sample long center-aligned windows. The module generates 8 absolute LFCC features where the zeroth cepstral coefficient is replaced by a temporal domain energy term. For extracting the rest of the features, three pipelines are used. The differential energy feature is calculated in a 0.9-second absolute feature window with a frame size of 0.1 seconds. The difference between the maximum and minimum temporal energy terms is calculated in this range. Then, the first derivative or the delta features are calculated using another 0.9-second window. Finally, the second derivative or delta-delta features are calculated using a 0.3-second window [6]. The differential energy for the delta-delta features is not included. In total, we extract 26 features from the raw sample windows which add 1.1 seconds of delay to the system. We used the Temple University Hospital Seizure Database (TUSZ) v1.2.1 for developing the online system [10]. The statistics for this dataset are shown in Table 1. A channel-based LSTM model was trained using the features derived from the train set using the online feature extractor module. A window-based normalization technique was applied to those features. In the offline model, we scale features by normalizing using the maximum absolute value of a channel [11] before applying a sliding window approach. Since the online system has access to a limited amount of data, we normalize based on the observed window. The model uses the feature vectors with a frame size of 1 second and a window size of 7 seconds. We evaluated the model using the offline P1 postprocessor to determine the efficacy of the delayed features and the window-based normalization technique. As shown by the results of experiments 1 and 4 in Table 2, these changes give us a comparable performance to the offline model. The online event decoder module utilizes this trained model for computing probabilities for the seizure and background classes. These posteriors are then postprocessed to remove spurious detections. The online postprocessor receives and saves 8 seconds of class posteriors in a buffer for further processing. It applies multiple heuristic filters (e.g., probability threshold) to make an overall decision by combining events across the channels. These filters evaluate the average confidence, the duration of a seizure, and the channels where the seizures were observed. The postprocessor delivers the label and confidence to the visualizer. The visualizer starts to display the signal as soon as it gets access to the signal file, as shown in Figure 1 using the “Signal File” and “Visualizer” blocks. Once the visualizer receives the label and confidence for the latest epoch from the postprocessor, it overlays the decision and color codes that epoch. The visualizer uses red for seizure with the label SEIZ and green for the background class with the label BCKG. Once the streaming finishes, the system saves three files: a signal file in which the sample frames are saved in the order they were streamed, a time segmented event (TSE) file with the overall decisions and confidences, and a hypotheses (HYP) file that saves the label and confidence for each epoch. The user can plot the signal and decisions using the signal and HYP files with only the visualizer by enabling appropriate options. For comparing the performance of different stages of development, we used the test set of TUSZ v1.2.1 database. It contains 1015 EEG records of varying duration. The any-overlap performance [12] of the overall system shown in Figure 2 is 40.29% sensitivity with 5.77 FAs per 24 hours. For comparison, the previous state-of-the-art model developed on this database performed at 30.71% sensitivity with 6.77 FAs per 24 hours [3]. The individual performances of the deep learning phases are as follows: Phase 1’s (P1) performance is 39.46% sensitivity and 11.62 FAs per 24 hours, and Phase 2 detects seizures with 41.16% sensitivity and 11.69 FAs per 24 hours. We trained an LSTM model with the delayed features and the window-based normalization technique for developing the online system. Using the offline decoder and postprocessor, the model performed at 36.23% sensitivity with 9.52 FAs per 24 hours. The trained model was then evaluated with the online modules. The current performance of the overall online system is 45.80% sensitivity with 28.14 FAs per 24 hours. Table 2 summarizes the performances of these systems. The performance of the online system deviates from the offline P1 model because the online postprocessor fails to combine the events as the seizure probability fluctuates during an event. The modules in the online system add a total of 11.1 seconds of delay for processing each second of the data, as shown in Figure 3. In practice, we also count the time for loading the model and starting the visualizer block. When we consider these facts, the system consumes 15 seconds to display the first hypothesis. The system detects seizure onsets with an average latency of 15 seconds. Implementing an automatic seizure detection model in real time is not trivial. We used a variety of techniques such as the file locking mechanism, multithreading, circular buffers, real-time event decoding, and signal-decision plotting to realize the system. A video demonstrating the system is available at: https://www.isip.piconepress.com/projects/nsf_pfi_tt/resources/videos/realtime_eeg_analysis/v2.5.1/video_2.5.1.mp4. The final conference submission will include a more detailed analysis of the online performance of each module. ACKNOWLEDGMENTS Research reported in this publication was most recently supported by the National Science Foundation Partnership for Innovation award number IIP-1827565 and the Pennsylvania Commonwealth Universal Research Enhancement Program (PA CURE). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the official views of any of these organizations. REFERENCES [1] A. Craik, Y. He, and J. L. Contreras-Vidal, “Deep learning for electroencephalogram (EEG) classification tasks: a review,” J. Neural Eng., vol. 16, no. 3, p. 031001, 2019. https://doi.org/10.1088/1741-2552/ab0ab5. [2] A. C. Bridi, T. Q. Louro, and R. C. L. Da Silva, “Clinical Alarms in intensive care: implications of alarm fatigue for the safety of patients,” Rev. Lat. Am. Enfermagem, vol. 22, no. 6, p. 1034, 2014. https://doi.org/10.1590/0104-1169.3488.2513. [3] M. Golmohammadi, V. Shah, I. Obeid, and J. Picone, “Deep Learning Approaches for Automatic Seizure Detection from Scalp Electroencephalograms,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York, New York, USA: Springer, 2020, pp. 233–274. https://doi.org/10.1007/978-3-030-36844-9_8. [4] “CFM Olympic Brainz Monitor.” [Online]. Available: https://newborncare.natus.com/products-services/newborn-care-products/newborn-brain-injury/cfm-olympic-brainz-monitor. [Accessed: 17-Jul-2020]. [5] M. L. Scheuer, S. B. Wilson, A. Antony, G. Ghearing, A. Urban, and A. I. Bagic, “Seizure Detection: Interreader Agreement and Detection Algorithm Assessments Using a Large Dataset,” J. Clin. Neurophysiol., 2020. https://doi.org/10.1097/WNP.0000000000000709. [6] A. Harati, M. Golmohammadi, S. Lopez, I. Obeid, and J. Picone, “Improved EEG Event Classification Using Differential Energy,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium, 2015, pp. 1–4. https://doi.org/10.1109/SPMB.2015.7405421. [7] V. Shah, C. Campbell, I. Obeid, and J. Picone, “Improved Spatio-Temporal Modeling in Automated Seizure Detection using Channel-Dependent Posteriors,” Neurocomputing, 2021. [8] W. Tatum, A. Husain, S. Benbadis, and P. Kaplan, Handbook of EEG Interpretation. New York City, New York, USA: Demos Medical Publishing, 2007. [9] D. P. Bovet and C. Marco, Understanding the Linux Kernel, 3rd ed. O’Reilly Media, Inc., 2005. https://www.oreilly.com/library/view/understanding-the-linux/0596005652/. [10] V. Shah et al., “The Temple University Hospital Seizure Detection Corpus,” Front. Neuroinform., vol. 12, pp. 1–6, 2018. https://doi.org/10.3389/fninf.2018.00083. [11] F. Pedregosa et al., “Scikit-learn: Machine Learning in Python,” J. Mach. Learn. Res., vol. 12, pp. 2825–2830, 2011. https://dl.acm.org/doi/10.5555/1953048.2078195. [12] J. Gotman, D. Flanagan, J. Zhang, and B. Rosenblatt, “Automatic seizure detection in the newborn: Methods and initial evaluation,” Electroencephalogr. Clin. Neurophysiol., vol. 103, no. 3, pp. 356–362, 1997. https://doi.org/10.1016/S0013-4694(97)00003-9. 

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2. Semiparametric Estimation of the Accelerated Mean Model with Panel Count Data Under Informative Examination Times

   https://doi.org/10.1111/biom.12840  

   Chiou, Sy Han ; Xu, Gongjun ; Yan, Jun ; Huang, Chiung-Yu ( December 2017 , Biometrics)

   Panel count data arise when the number of recurrent events experienced by each subject is observed intermittently at discrete examination times. The examination time process can be informative about the underlying recurrent event process even after conditioning on covariates. We consider a semiparametric accelerated mean model for the recurrent event process and allow the two processes to be correlated through a shared frailty. The regression parameters have a simple marginal interpretation of modifying the time scale of the cumulative mean function of the event process. A novel estimation procedure for the regression parameters and the baseline rate function is proposed based on a conditioning technique. In contrast to existing methods, the proposed method is robust in the sense that it requires neither the strong Poisson-type assumption for the underlying recurrent event process nor a parametric assumption on the distribution of the unobserved frailty. Moreover, the distribution of the examination time process is left unspecified, allowing for arbitrary dependence between the two processes. Asymptotic consistency of the estimator is established, and the variance of the estimator is estimated by a model-based smoothed bootstrap procedure. Numerical studies demonstrated that the proposed point estimator and variance estimator perform well with practical sample sizes. The methods are applied to data from a skin cancer chemoprevention trial.

    

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3. A spatial–temporal graph deep learning model for urban flood nowcasting leveraging heterogeneous community features

   https://doi.org/10.1038/s41598-023-32548-x  

   Farahmand, Hamed ; Xu, Yuanchang ; Mostafavi, Ali ( December 2023 , Scientific Reports)

   Flood nowcasting refers to near-future prediction of flood status as an extreme weather event unfolds to enhance situational awareness. The objective of this study was to adopt and test a novel structured deep-learning model for urban flood nowcasting by integrating physics-based and human-sensed features. We present a new computational modeling framework including an attention-based spatial–temporal graph convolution network (ASTGCN) model and different streams of data that are collected in real-time, preprocessed, and fed into the model to consider spatial and temporal information and dependencies that improve flood nowcasting. The novelty of the computational modeling framework is threefold: first, the model is capable of considering spatial and temporal dependencies in inundation propagation thanks to the spatial and temporal graph convolutional modules; second, it enables capturing the influence of heterogeneous temporal data streams that can signal flooding status, including physics-based features (e.g., rainfall intensity and water elevation) and human-sensed data (e.g., residents’ flood reports and fluctuations of human activity) on flood nowcasting. Third, its attention mechanism enables the model to direct its focus to the most influential features that vary dynamically and influence the flood nowcasting. We show the application of the modeling framework in the context of Harris County, Texas, as the study area and 2017 Hurricane Harvey as the flood event. Three categories of features are used for nowcasting the extent of flood inundation in different census tracts: (i) static features that capture spatial characteristics of various locations and influence their flood status similarity, (ii) physics-based dynamic features that capture changes in hydrodynamic variables, and (iii) heterogeneous human-sensed dynamic features that capture various aspects of residents’ activities that can provide information regarding flood status. Results indicate that the ASTGCN model provides superior performance for nowcasting of urban flood inundation at the census-tract level, with precision 0.808 and recall 0.891, which shows the model performs better compared with other state-of-the-art models. Moreover, ASTGCN model performance improves when heterogeneous dynamic features are added into the model that solely relies on physics-based features, which demonstrates the promise of using heterogenous human-sensed data for flood nowcasting. Given the results of the comparisons of the models, the proposed modeling framework has the potential to be more investigated when more data of historical events are available in order to develop a predictive tool to provide community responders with an enhanced prediction of the flood inundation during urban flood.

    

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4. High Spatial Order Energy Stable FDTD Methods for Maxwell’s Equations in Nonlinear Optical Media in One Dimension

   Bokil, Vrushali A ; Cheng, Yingda ; Jiang, Yan ; Li, Fengyan ( April 2018 , Journal of scientific computing)

   In this paper, we consider electromagnetic (EM) wave propagation in nonlinear optical media in one spatial dimension. We model the EM wave propagation by the time- dependent Maxwell’s equations coupled with a system of nonlinear ordinary differential equations (ODEs) for the response of the medium to the EM waves. The nonlinearity in the ODEs describes the instantaneous electronic Kerr response and the residual Raman molecular vibrational response. The ODEs also include the single resonance linear Lorentz dispersion. For such model, we will design and analyze fully discrete finite difference time domain (FDTD) methods that have arbitrary (even) order in space and second order in time. It is challenging to achieve provable stability for fully discrete methods, and this depends on the choices of temporal discretizations of the nonlinear terms. In Bokil et al. (J Comput Phys 350:420–452, 2017), we proposed novel modifications of second-order leap-frog and trapezoidal temporal schemes in the context of discontinuous Galerkin methods to discretize the nonlinear terms in this Maxwell model. Here, we continue this work by developing similar time discretizations within the framework of FDTD methods. More specifically, we design fully discrete modified leap-frog FDTD methods which are proved to be stable under appropriate CFL conditions. These method can be viewed as an extension of the Yee-FDTD scheme to this nonlinear Maxwell model. We also design fully discrete trapezoidal FDTD methods which are proved to be unconditionally stable. The performance of the fully discrete FDTD methods are demonstrated through numerical experiments involving kink, antikink waves and third harmonic generation in soliton propagation. 

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5. Strain Localization Patterns and Thrust Propagation in 3‐D Discrete Element Method (DEM) Models of Accretionary Wedges

   https://doi.org/10.1029/2022TC007707  

   del Castillo, Enrique M. ; Ferdowsi, Behrooz ; Rubin, Allan M. ; Schoene, Blair ( August 2023 , Tectonics)

   High‐resolution three‐dimensional discrete element method (DEM) simulations of sandbox‐scale models of accretionary wedges suggest thrusts follow a variety of propagation processes and orientations depending on a number of factors. These include the stage of development of the wedge (precritical vs. critical), basal friction, and type of thrust (forward vs. backward‐vergent). In terms of propagation processes, two clear mechanisms are identified. The first involves propagation from the décollement to the wedge top, similar to the standard model of thrust propagation seen in many kinematic models, and in the second, thrusts grow downward from an initial nucleation point just below the top surface of the wedge as well as upward from the décollement joining in the middle. In terms of orientation, forward‐vergent thrusts initially form at Roscoe (θ_R = 45° − Ψ/2) or Arthur orientations (θ_A = 45° − (ϕ + Ψ)/4), and over greater shortening, rotate into Coulomb orientations (θ_C = 45° − ϕ/2). To arrive at these results, a wide array of continuum parameters and fields were extracted from the DEM simulations, including stress, strain, strain rate, kinetic energy, Mohr‐Coulomb parameters, and proximity to yielding using the Drucker‐Prager criterion to visualize thrust nucleation and propagation. Lastly, the advantages and disadvantages of these continuum proxies for discerning failure in the granular assembly are considered, and the spatial and temporal relationship between proximity to yielding and strain localization (both pre‐peak and subsequent persistent shear banding) in the granular model of an accretionary wedge is explored.

    

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