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1. CS 5604 2020: Information Storage and Retrieval TWT - Tweet Collection Management Team

   Baadkar, Hitesh ; Chimote, Pranav ; Hicks, Megan ; Juneja, Ikjot ; Kusuma, Manisha ; Mehta, Ujjval ; Patil, Akash ; Sharma, Irith ; Wang, Xinyue ; Fox, Edward A. ( December 2020 , Information storage and retrieval)

   null (Ed.)

   The Tweet Collection Management (TWT) Team aims to ingest 5 billion tweets, clean this data, analyze the metadata present, extract key information, classify tweets into categories, and finally, index these tweets into Elasticsearch to browse and query. The main deliverable of this project is a running software application for searching tweets and for viewing Twitter collections from Digital Library Research Laboratory (DLRL) event archive projects. As a starting point, we focused on two development goals: (1) hashtag-based and (2) username-based search for tweets. For IR1, we completed extraction of two fields within our sample collection: hashtags and username. Sample code for TwiRole, a user-classification program, was investigated for use in our project. We were able to sample from multiple collections of tweets, spanning topics like COVID-19 and hurricanes. Initial work encompassed using a sample collection, provided via Google Drive. An NFS-based persistent storage was later involved to allow access to larger collections. In total, we have developed 9 services to extract key information like username, hashtags, geo-location, and keywords from tweets. We have also developed services to allow for parsing and cleaning of raw API data, and backup of data in an Apache Parquet filestore. All services are Dockerized and added to the GitLab Container Registry. The services are deployed in the CS cloud cluster to integrate services into the full search engine workflow. A service is created to convert WARC files to JSON for reading archive files into the application. Unit testing of services is complete and end-to-end tests have been conducted to improve system robustness and avoid failure during deployment. The TWT team has indexed 3,200 tweets into the Elasticsearch index. Future work could involve parallelization of the extraction of metadata, an alternative feature-flag approach, advanced geo-location inference, and adoption of the DMI-TCAT format. Key deliverables include a data body that allows for search, sort, filter, and visualization of raw tweet collections and metadata analysis; a running software application for searching tweets and for viewing Twitter collections from Digital Library Research Laboratory (DLRL) event archive projects; and a user guide to assist those using the system. 

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2. Mapping Spatiotemporal Tourist Behaviors and Hotspots Through Location-Based Photo-Sharing Service (Flickr) Data.

   https://doi.org/10.1007/978-3-319-71470-7_16  

   Lee, Joey Ying ; Tsou, Ming-Hsiang ( December 2017 , Progress in Location Based Services 2018. LBS 2018. Lecture Notes in Geoinformation and Cartography. Springer, Cham)

   Social media services and location-based photo-sharing applications, such as Flickr, Twitter, and Instagram, provide a promising opportunity for studying tourist behaviors and activities. Researchers can use public accessible geo-tagged photos to map and analyze hotspots and tourist activities in various tourist attractions. This research studies geo-tagged Flickr photos collected from the Grand Canyon area within 12 months (2014/12/01–2015/11/30) using kernel density estimate (KDE) mapping, Exif (Exchangeable image file format) data, and dynamic time warping (DTW) methods. Different spatiotemporal movement patterns of tourists and popular points of interests (POIs) in the Grand Canyon area are identified and visualized in GIS maps. The frequency of Flickr’s monthly photos is similar (but not identical) to the actual tourist total numbers in the Grand Canyon. We found that winter tourists in the Grand Canyon explore fewer POIs comparing to summer tourists based on their Flickr data. Tourists using high-end cameras are more active and explore more POIs than tourists using smart phones photos. Weekend tourists are more likely to stay around the lodge area comparing to weekday tourists who have visited more remote areas in the park, such as the north of Pima Point. These tourist activities and spatiotemporal patterns can be used for the improvement of national park facility management, regional tourism, and local transportation plans. 

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3. Jupyter Notebooks, the PmagPy Software Package and the Magnetics Information Consortium (MagIC) Database

   https://doi.org/10.1002/essoar.10504416.1  

   Tauxe, L. ( June 2020 , Earthcube2020)

   PmagPy Online: Jupyter Notebooks, the PmagPy Software Package and the Magnetics Information Consortium (MagIC) Database Lisa Tauxe$^1$, Rupert Minnett$^2$, Nick Jarboe$^1$, Catherine Constable$^1$, Anthony Koppers$^2$, Lori Jonestrask$^1$, Nick Swanson-Hysell$^3$ $^1$Scripps Institution of Oceanography, United States of America; $^2$ Oregon State University; $^3$ University of California, Berkely; ltauxe@ucsd.edu The Magnetics Information Consortium (MagIC), hosted at http://earthref.org/MagIC is a database that serves as a Findable, Accessible, Interoperable, Reusable (FAIR) archive for paleomagnetic and rock magnetic data. It has a flexible, comprehensive data model that can accomodate most kinds of paleomagnetic data. The PmagPy software package is a cross-platform and open-source set of tools written in Python for the analysis of paleomagnetic data that serves as one interface to MagIC, accommodating various levels of user expertise. It is available through github.com/PmagPy. Because PmagPy requires installation of Python, several non-standard Python modules, and the PmagPy software package, there is a speed bump for many practitioners on beginning to use the software. In order to make the software and MagIC more accessible to the broad spectrum of scientists interested in paleo and rock magnetism, we have prepared a set of Jupyter notebooks, hosted on jupyterhub.earthref.org which serve a set of purposes. 1) There is a complete course in Python for Earth Scientists, 2) a set of notebooks that introduce PmagPy (pulling the software package from the github repository) and illustrate how it can be used to create data products and figures for typical papers, and 3) show how to prepare data from the laboratory to upload into the MagIC database. The latter will satisfy expectations from NSF for data archiving and for example the AGU publication data archiving requirements. Getting started To use the PmagPy notebooks online, go to website at https://jupyterhub.earthref.org/. Create an Earthref account using your ORCID and log on. [This allows you to keep files in a private work space.] Open the PmagPy Online - Setup notebook and execute the two cells. Then click on File = > Open and click on the PmagPy_Online folder. Open the PmagPy_online notebook and work through the examples. There are other notebooks that are useful for the working paleomagnetist. Alternatively, you can install Python and the PmagPy software package on your computer (see https://earthref.org/PmagPy/cookbook for instructions). Follow the instructions for "Full PmagPy install and update" through section 1.4 (Quickstart with PmagPy notebooks). This notebook is in the collection of PmagPy notebooks. Overview of MagIC The Magnetics Information Consortium (MagIC), hosted at http://earthref.org/MagIC is a database that serves as a Findable, Accessible, Interoperable, Reusable (FAIR) archive for paleomagnetic and rock magnetic data. Its datamodel is fully described here: https://www2.earthref.org/MagIC/data-models/3.0. Each contribution is associated with a publication via the DOI. There are nine data tables: contribution: metadata of the associated publication. locations: metadata for locations, which are groups of sites (e.g., stratigraphic section, region, etc.) sites: metadata and derived data at the site level (units with a common expectation) samples: metadata and derived data at the sample level. specimens: metadata and derived data at the specimen level. criteria: criteria by which data are deemed acceptable ages: ages and metadata for sites/samples/specimens images: associated images and plots. Overview of PmagPy The functionality of PmagPy is demonstrated within notebooks in the PmagPy repository: PmagPy_online.ipynb: serves as an introdution to PmagPy and MagIC (this conference). It highlights the link between PmagPy and the Findable Accessible Interoperable Reusabe (FAIR) database maintained by the Magnetics Information Consortium (MagIC) at https://earthref.org/MagIC. Other notebooks of interest are: PmagPy_calculations.ipynb: demonstrates many of the PmagPy calculation functions such as those that rotate directions, return statistical parameters, and simulate data from specified distributions. PmagPy_plots_analysis.ipynb: demonstrates PmagPy functions that can be used to visual data as well as those that conduct statistical tests that have associated visualizations. PmagPy_MagIC.ipynb: demonstrates how PmagPy can be used to read and write data to and from the MagIC database format including conversion from many individual lab measurement file formats. Please see also our YouTube channel with more presentations from the 2020 MagIC workshop here: https://www.youtube.com/playlist?list=PLirL2unikKCgUkHQ3m8nT29tMCJNBj4kj 

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4. Integration and Implementation (INT) CS 5604 F2020

   Hicks, Alexander ; Thazhath, Mohit ; Gupta, Suraj ; Long, Xingyu ; Poland, Cherie ; Hsieh, Hsinhan ; Mahajan, Yash ; Chandrasekar, Prashant ; Fox, Edward A. ( December 2020 , Information storage and retrieval)

   null (Ed.)

   The first major goal of this project is to build a state-of-the-art information storage, retrieval, and analysis system that utilizes the latest technology and industry methods. This system is leveraged to accomplish another major goal, supporting modern search and browse capabilities for a large collection of tweets from the Twitter social media platform, web pages, and electronic theses and dissertations (ETDs). The backbone of the information system is a Docker container cluster running with Rancher and Kubernetes. Information retrieval and visualization is accomplished with containers in a pipelined fashion, whether in the cluster or on virtual machines, for Elasticsearch and Kibana, respectively. In addition to traditional searching and browsing, the system supports full-text and metadata searching. Search results include facets as a modern means of browsing among related documents. The system supports text analysis and machine learning to reveal new properties of collection data. These new properties assist in the generation of available facets. Recommendations are also presented with search results based on associations among documents and with logged user activity. The information system is co-designed by five teams of Virginia Tech graduate students, all members of the same computer science class, CS 5604. Although the project is an academic exercise, it is the practice of the teams to work and interact as though they are groups within a company developing a product. The teams on this project include three collection management groups -- Electronic Theses and Dissertations (ETD), Tweets (TWT), and Web-Pages (WP) -- as well as the Front-end (FE) group and the Integration (INT) group to help provide the overarching structure for the application. This submission focuses on the work of the Integration (INT) team, which creates and administers Docker containers for each team in addition to administering the cluster infrastructure. Each container is a customized application environment that is specific to the needs of the corresponding team. Each team will have several of these containers set up in a pipeline formation to allow scaling and extension of the current system. The INT team also contributes to a cross-team effort for exploring the use of Elasticsearch and its internally associated database. The INT team administers the integration of the Ceph data storage system into the CS Department Cloud and provides support for interactions between containers and the Ceph filesystem. During formative stages of development, the INT team also has a role in guiding team evaluations of prospective container components and workflows. The INT team is responsible for the overall project architecture and facilitating the tools and tutorials that assist the other teams in deploying containers in a development environment according to mutual specifications agreed upon with each team. The INT team maintains the status of the Kubernetes cluster, deploying new containers and pods as needed by the collection management teams as they expand their workflows. This team is responsible for utilizing a continuous integration process to update existing containers. During the development stage the INT team collaborates specifically with the collection management teams to create the pipeline for the ingestion and processing of new collection documents, crossing services between those teams as needed. The INT team develops a reasoner engine to construct workflows with information goal as input, which are then programmatically authored, scheduled, and monitored using Apache Airflow. The INT team is responsible for the flow, management, and logging of system performance data and making any adjustments necessary based on the analysis of testing results. The INT team has established a Gitlab repository for archival code related to the entire project and has provided the other groups with the documentation to deposit their code in the repository. This repository will be expanded using Gitlab CI in order to provide continuous integration and testing once it is available. Finally, the INT team will provide a production distribution that includes all embedded Docker containers and sub-embedded Git source code repositories. The INT team will archive this distribution on the Virginia Tech Docker Container Registry and deploy it on the Virginia Tech CS Cloud. The INT-2020 team owes a sincere debt of gratitude to the work of the INT-2019 team. This is a very large undertaking and the wrangling of all of the products and processes would not have been possible without their guidance in both direct and written form. We have relied heavily on the foundation they and their predecessors have provided for us. We continue their work with systematic improvements, but also want to acknowledge their efforts Ibid. Without them, our progress to date would not have been possible. 

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5. 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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