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1. Combining Filtering and Cross-Correlation Efficiently for Streaming Time Series

   https://doi.org/10.1145/3502738  

   Zhong, Sheng ; Souza, Vinicius M. ; Mueen, Abdullah ( October 2022 , ACM Transactions on Knowledge Discovery from Data)

   Monitoring systems have hundreds or thousands of distributed sensors gathering and transmitting real-time streaming data. The early detection of events in these systems, such as an earthquake in a seismic monitoring system, is the base for essential tasks as warning generations. To detect such events is usual to compute pairwise correlation across the disparate signals generated by the sensors. Since the data sources (e.g., sensors) are spatially separated, it is essential to consider the lagged correlation between the signals. Besides, many applications require to process a specific band of frequencies depending on the event’s type, demanding a pre-processing step of filtering before computing correlations. Due to the high speed of data generation and a large number of sensors in these systems, the operations of filtering and lagged cross-correlation need to be efficient to provide real-time responses without data losses. This article proposes a technique named FilCorr that efficiently computes both operations in one single step. We achieve an order of magnitude speedup by maintaining frequency transforms over sliding windows. Our method is exact, devoid of sensitive parameters, and easily parallelizable. Besides our algorithm, we also provide a publicly available real-time system named Seisviz that employs FilCorr in its core mechanism for monitoring a seismometer network. We demonstrate that our technique is suitable for several monitoring applications as seismic signal monitoring, motion monitoring, and neural activity monitoring. 

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2. 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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3. COMAP Early Science. III. CO Data Processing

   https://doi.org/10.3847/1538-4357/ac63ca  

   Foss, Marie K. ; Ihle, Håvard T. ; Borowska, Jowita ; Cleary, Kieran A. ; Eriksen, Hans Kristian ; Harper, Stuart E. ; Kim, Junhan ; Lamb, James W. ; Lunde, Jonas G. S. ; Philip, Liju ; et al ( July 2022 , The Astrophysical Journal)

   We describe the first-season CO Mapping Array Project (COMAP) analysis pipeline that converts raw detector readouts to calibrated sky maps. This pipeline implements four main steps: gain calibration, filtering, data selection, and mapmaking. Absolute gain calibration relies on a combination of instrumental and astrophysical sources, while relative gain calibration exploits real-time total-power variations. High-efficiency filtering is achieved through spectroscopic common-mode rejection within and across receivers, resulting in nearly uncorrelated white noise within single-frequency channels. Consequently, near-optimal but biased maps are produced by binning the filtered time stream into pixelized maps; the corresponding signal bias transfer function is estimated through simulations. Data selection is performed automatically through a series of goodness-of-fit statistics, includingχ²and multiscale correlation tests. Applying this pipeline to the first-season COMAP data, we produce a data set with very low levels of correlated noise. We find that one of our two scanning strategies (the Lissajous type) is sensitive to residual instrumental systematics. As a result, we no longer use this type of scan and exclude data taken this way from our Season 1 power spectrum estimates. We perform a careful analysis of our data processing and observing efficiencies and take account of planned improvements to estimate our future performance. Power spectrum results derived from the first-season COMAP maps are presented and discussed in companion papers.

    

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4. Optimal stacking of noise cross-correlation functions

   https://doi.org/10.1093/gji/ggac410  

   Yang, Xiaotao ; Bryan, Jared ; Okubo, Kurama ; Jiang, Chengxin ; Clements, Timothy ; Denolle, Marine A. ( October 2022 , Geophysical Journal International)

   Cross-correlations of ambient seismic noise are widely used for seismic velocity imaging, monitoring and ground motion analyses. A typical step in analysing noise cross-correlation functions (NCFs) is stacking short-term NCFs over longer time periods to increase the signal quality. Spurious NCFs could contaminate the stack, degrade its quality and limit its use. Many methods have been developed to improve the stacking of coherent waveforms, including earthquake waveforms, receiver functions and NCFs. This study systematically evaluates and compares the performance of eight stacking methods, including arithmetic mean or linear stacking, robust stacking, selective stacking, cluster stacking, phase-weighted stacking, time–frequency phase-weighted stacking, Nth-root stacking and averaging after applying an adaptive covariance filter. Our results demonstrate that, in most cases, all methods can retrieve clear ballistic or first arrivals. However, they yield significant differences in preserving the phase and amplitude information. This study provides a practical guide for choosing the optimal stacking method for specific research applications in ambient noise seismology. We evaluate the performance using multiple onshore and offshore seismic arrays in the Pacific Northwest region. We compare these stacking methods for NCFs calculated from raw ambient noise (referred to as Raw NCFs) and from ambient noise normalized using a one-bit clipping time normalization method (referred to as One-bit NCFs). We evaluate six metrics, including signal-to-noise ratios, phase dispersion images, convergence rate, temporal changes in the ballistic and coda waves, relative amplitude decays with distance and computational time. We show that robust stacking is the best choice for all applications (velocity tomography, monitoring and attenuation studies) using Raw NCFs. For applications using One-bit NCFs, all methods but phase-weighted and Nth-root stacking are good choices for seismic velocity tomography. Linear, robust and selective stacking methods are all equally appropriate choices when using One-bit NCFs for monitoring applications. For applications relying on accurate relative amplitudes, the linear, robust, selective and cluster stacking methods all perform well with One-bit NCFs. The evaluations in this study can be generalized to a broad range of time-series analysis that utilizes data coherence to perform ensemble stacking. Another contribution of this study is the accompanying open-source software package, StackMaster, which can be used for general purposes of time-series stacking.

    

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5. PROS: an efficient pattern-driven compressive sensing framework for low-power biopotential-based wearables with on-chip intelligence

   https://doi.org/10.1145/3495243.3560533  

   Pham, Nhat ; Jia, Hong ; Tran, Minh ; Dinh, Tuan ; Bui, Nam ; Kwon, Young ; Ma, Dong ; Nguyen, Phuc ; Mascolo, Cecilia ; Vu, Tam ( October 2022 , Proceedings of the 28th Annual International Conference on Mobile Computing And Networking)

   While the global healthcare market of wearable devices has been growing significantly in recent years and is predicted to reach $60 billion by 2028, many important healthcare applications such as seizure monitoring, drowsiness detection, etc. have not been deployed due to the limited battery lifetime, slow response rate, and inadequate biosignal quality.This study proposes PROS, an efficient pattern-driven compressive sensing framework for low-power biopotential-based wearables. PROS eliminates the conventional trade-off between signal quality, response time, and power consumption by introducing tiny pattern recognition primitives and a pattern-driven compressive sensing technique that exploits the sparsity of biosignals. Specifically, we (i) develop tiny machine learning models to eliminate irrelevant biosignal patterns, (ii) efficiently perform compressive sampling of relevant biosignals with appropriate sparse wavelet domains, and (iii) optimize hardware and OS operations to push processing efficiency. PROS also provides an abstraction layer, so the application only needs to care about detected relevant biosignal patterns without knowing the optimizations underneath.We have implemented and evaluated PROS on two open biosignal datasets with 120 subjects and six biosignal patterns. The experimental results on unknown subjects of a practical use case such as epileptic seizure monitoring are very encouraging. PROS can reduce the streaming data rate by 24X while maintaining high fidelity signal. It boosts the power efficiency of the wearable device by more than 1200\% and enables the ability to react to critical events immediately on the device. The memory and runtime overheads of PROS are minimal, with a few KBs and 10s of milliseconds for each biosignal pattern, respectively. PROS is currently adopted in research projects in multiple universities and hospitals. 

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