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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. EquiTensors: Learning Fair Integrations of Heterogeneous Urban Data

   https://doi.org/10.1145/3448016.3452777  

   Yan, An ; Howe, Bill ( June 2021 , SIGMOD/PODS '21: Proceedings of the 2021 International Conference on Management of Data)

   null (Ed.)

   Neural methods are state-of-the-art for urban prediction problems such as transportation resource demand, accident risk, crowd mobility, and public safety. Model performance can be improved by integrating exogenous features from open data repositories (e.g., weather, housing prices, traffic, etc.), but these uncurated sources are often too noisy, incomplete, and biased to use directly. We propose to learn integrated representations, called EquiTensors, from heterogeneous datasets that can be reused across a variety of tasks. We align datasets to a consistent spatio-temporal domain, then describe an unsupervised model based on convolutional denoising autoencoders to learn shared representations. We extend this core integrative model with adaptive weighting to prevent certain datasets from dominating the signal. To combat discriminatory bias, we use adversarial learning to remove correlations with a sensitive attribute (e.g., race or income). Experiments with 23 input datasets and 4 real applications show that EquiTensors could help mitigate the effects of the sensitive information embodied in the biased data. Meanwhile, applications using EquiTensors outperform models that ignore exogenous features and are competitive with "oracle" models that use hand-selected datasets. 

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3. HOPE: High-order Graph ODE For Modeling Interacting Dynamics

   Luo, Xiao ; Yuan, Jingyang ; Huang, Zijie ; Jiang, Huiyu ; Qin, Yifang ; Ju, Wei ; Zhang, Ming ; Sun, Yizhou ( July 2023 , Proceedings of the 40th International Conference on Machine Learning)

   Leading graph ordinary differential equation (ODE) models have offered generalized strategies to model interacting multi-agent dynamical systems in a data-driven approach. They typically consist of a temporal graph encoder to get the initial states and a neural ODE-based generative model to model the evolution of dynamical systems. However, existing methods have severe deficiencies in capacity and efficiency due to the failure to model high-order correlations in long-term temporal trends. To tackle this, in this paper, we propose a novel model named High-Order graPh ODE (HOPE) for learning from dynamic interaction data, which can be naturally represented as a graph. It first adopts a twin graph encoder to initialize the latent state representations of nodes and edges, which consists of two branches to capture spatio-temporal correlations in complementary manners. More importantly, our HOPE utilizes a second-order graph ODE function which models the dynamics for both nodes and edges in the latent space respectively, which enables efficient learning of long-term dependencies from complex dynamical systems. Experiment results on a variety of datasets demonstrate both the effectiveness and efficiency of our proposed method. 

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4. Mining Shape Expressions from Positive Examples

   https://doi.org/10.1109/TCAD.2020.3012240  

   Bartocci, Ezio ; Deshmukh, Jyotirmoy ; Gigler, Felix ; Mateis, Cristinel ; Nickovic, Dejan ; Qin, Xin ( October 2020 , IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems)

   null (Ed.)

   Shape expressions (SEs) is a novel specification language that was recently introduced to express behavioral patterns over real-valued signals observed during the execution of cyber-physical systems. An SE is a regular expression composed of arbitrary parameterized shapes, such as lines, exponential curves, and sinusoids as atomic symbols with symbolic constraints on the shape parameters. SEs enable a natural and intuitive specification of complex temporal patterns over possibly noisy data. In this article, we propose a novel method for mining a broad and interesting fragment of SEs from time-series data using a combination of techniques from linear regression, unsupervised clustering, and learning finite automata from positive examples. The learned SE for a given dataset provides an explainable and intuitive model of the observed system behavior. We demonstrate the applicability of our approach on two case studies from different application domains and experimentally evaluate the implemented specification mining procedure. 

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5. Automatic Detection of Volcanic Surface Deformation Using Deep Learning

   https://doi.org/10.1029/2020JB019840  

   Sun, Jian ; Wauthier, Christelle ; Stephens, Kirsten ; Gervais, Melissa ; Cervone, Guido ; La Femina, Peter ; Higgins, Machel ( September 2020 , Journal of Geophysical Research: Solid Earth)

   Interferometric Synthetic Aperture Radar (InSAR) provides subcentimetric measurements of surface displacements, which are key for characterizing and monitoring magmatic processes in volcanic regions. The abundant measurements of surface displacements in multitemporal InSAR data routinely acquired by SAR satellites can facilitate near real‐time volcano monitoring on a global basis. However, the presence of atmospheric signals in interferograms complicates the interpretation of those InSAR measurements, which can even lead to a misinterpretation of InSAR signals and volcanic unrest. Given the vast quantities of SAR data available, an automatic InSAR data processing and denoising approach is required to separate volcanic signals that are cause of concern from atmospheric signals and noise. In this study, we employ a deep learning strategy that directly removes atmospheric and other noise signals from time‐consecutive unwrapped surface displacements obtained through an InSAR time series approach using an end‐to‐end convolutional neural network (CNN) with an encoder‐decoder architecture, modified U‐net. The CNN is trained with simulated synthetic unwrapped surface displacement maps and is then applied to real InSAR data. Our proposed architecture is capable of detecting dynamic spatio‐temporal patterns of volcanic surface displacements. We find that an ensemble‐average strategy is recommended to stabilize detected results for varying deformation rates and signal‐to‐noise ratios (SNRs). A case study is also presented where this method is applied to InSAR data covering Masaya volcano, Nicaragua and the results are validated using continuous GPS data. The results confirm that our network can indeed efficiently suppress atmospheric and other noise to reveal the noise‐free surface deformation.

    

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