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Title: Allan Variance-based Granulation Technique for Large Temporal Databases
decrease query response time with limited main memory and storage space, data reduction techniques that preserve data quality are needed. Existing data reduction techniques, however, are often computationally expensive and rely on heuristics for deciding how to split or reduce the original dataset. In this paper, we propose an effective granular data reduction technique for temporal databases, based on Allan Variance (AVAR). AVAR is used to systematically determine the temporal window length over which data remains relevant. The entire dataset to be reduced is then separated into granules with size equal to the AVAR-determined window length. Data reduction is achieved by generating aggregated information for each such granule. The proposed method is tested using a large database that contains temporal information for vehicular data. Then comparison experiments are conducted and the outstanding runtime performance is illustrated by comparing with three clustering-based data reduction methods. The performance results demonstrate that the proposed Allan Variance-based technique can efficiently generate reduced representation of the original data without losing data quality, while significantly reducing computation time.  more » « less
Award ID(s):
1932138
NSF-PAR ID:
10299310
Author(s) / Creator(s):
; ; ; ; ; ; ;
Date Published:
Journal Name:
13th International Conference on Knowledge Management and Information Systems
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    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. 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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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In this study we build on the author identifier approach by considering commonalities in fielded data between authors containing the same surname and first initial of their first name. We illustrate our approach using three case studies. Design/methodology/approach The approach we advance in this study is based on commonalities among fielded data in search results. We cast a broad initial net—i.e., a Web of Science (WOS) search for a given author’s last name, followed by a comma, followed by the first initial of his or her first name (e.g., a search for ‘John Doe’ would assume the form: ‘Doe, J’). Results for this search typically contain all of the scholarship legitimately belonging to this author in the given database (i.e., all of his or her true positives), along with a large amount of noise, or scholarship not belonging to this author (i.e., a large number of false positives). From this corpus we proceed to iteratively weed out false positives and retain true positives. Author identifiers provide a good starting point—e.g., if ‘Doe, J’ and ‘Doe, John’ share the same author identifier, this would be sufficient for us to conclude these are one and the same individual. We find email addresses similarly adequate—e.g., if two author names which share the same surname and same first initial have an email address in common, we conclude these authors are the same person. Author identifier and email address data is not always available, however. When this occurs, other fields are used to address the author uncertainty problem. Commonalities among author data other than unique identifiers and email addresses is less conclusive for name consolidation purposes. For example, if ‘Doe, John’ and ‘Doe, J’ have an affiliation in common, do we conclude that these names belong the same person? They may or may not; affiliations have employed two or more faculty members sharing the same last and first initial. Similarly, it’s conceivable that two individuals with the same last name and first initial publish in the same journal, publish with the same co-authors, and/or cite the same references. Should we then ignore commonalities among these fields and conclude they’re too imprecise for name consolidation purposes? It is our position that such commonalities are indeed valuable for addressing the author uncertainty problem, but more so when used in combination. Our approach makes use of automation as well as manual inspection, relying initially on author identifiers, then commonalities among fielded data other than author identifiers, and finally manual verification. To achieve name consolidation independent of author identifier matches, we have developed a procedure that is used with bibliometric software called VantagePoint (see www.thevantagepoint.com) While the application of our technique does not exclusively depend on VantagePoint, it is the software we find most efficient in this study. The script we developed to implement this procedure is designed to implement our name disambiguation procedure in a way that significantly reduces manual effort on the user’s part. Those who seek to replicate our procedure independent of VantagePoint can do so by manually following the method we outline, but we note that the manual application of our procedure takes a significant amount of time and effort, especially when working with larger datasets. Our script begins by prompting the user for a surname and a first initial (for any author of interest). It then prompts the user to select a WOS field on which to consolidate author names. After this the user is prompted to point to the name of the authors field, and finally asked to identify a specific author name (referred to by the script as the primary author) within this field whom the user knows to be a true positive (a suggested approach is to point to an author name associated with one of the records that has the author’s ORCID iD or email address attached to it). The script proceeds to identify and combine all author names sharing the primary author’s surname and first initial of his or her first name who share commonalities in the WOS field on which the user was prompted to consolidate author names. This typically results in significant reduction in the initial dataset size. After the procedure completes the user is usually left with a much smaller (and more manageable) dataset to manually inspect (and/or apply additional name disambiguation techniques to). Research limitations Match field coverage can be an issue. When field coverage is paltry dataset reduction is not as significant, which results in more manual inspection on the user’s part. Our procedure doesn’t lend itself to scholars who have had a legal family name change (after marriage, for example). Moreover, the technique we advance is (sometimes, but not always) likely to have a difficult time dealing with scholars who have changed careers or fields dramatically, as well as scholars whose work is highly interdisciplinary. Practical implications The procedure we advance has the ability to save a significant amount of time and effort for individuals engaged in name disambiguation research, especially when the name under consideration is a more common family name. It is more effective when match field coverage is high and a number of match fields exist. Originality/value Once again, the procedure we advance has the ability to save a significant amount of time and effort for individuals engaged in name disambiguation research. It combines preexisting with more recent approaches, harnessing the benefits of both. Findings Our study applies the name disambiguation procedure we advance to three case studies. Ideal match fields are not the same for each of our case studies. We find that match field effectiveness is in large part a function of field coverage. Comparing original dataset size, the timeframe analyzed for each case study is not the same, nor are the subject areas in which they publish. Our procedure is more effective when applied to our third case study, both in terms of list reduction and 100% retention of true positives. We attribute this to excellent match field coverage, and especially in more specific match fields, as well as having a more modest/manageable number of publications. While machine learning is considered authoritative by many, we do not see it as practical or replicable. The procedure advanced herein is both practical, replicable and relatively user friendly. It might be categorized into a space between ORCID and machine learning. Machine learning approaches typically look for commonalities among citation data, which is not always available, structured or easy to work with. The procedure we advance is intended to be applied across numerous fields in a dataset of interest (e.g. emails, coauthors, affiliations, etc.), resulting in multiple rounds of reduction. Results indicate that effective match fields include author identifiers, emails, source titles, co-authors and ISSNs. While the script we present is not likely to result in a dataset consisting solely of true positives (at least for more common surnames), it does significantly reduce manual effort on the user’s part. Dataset reduction (after our procedure is applied) is in large part a function of (a) field availability and (b) field coverage. 
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