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1. Tailwind: Fast and Atomic RDMA-based Replication

   Taleb, Y ; Stutsman, R ; Antoniu, G ; Cortes, T ( July 2018 , USENIX Annual Technical Conference)

   Replication is essential for fault-tolerance. However, in in-memory systems, it is a source of high overhead. Remote direct memory access (RDMA) is attractive to create redundant copies of data, since it is low-latency and has no CPU overhead at the target. However, existing approaches still result in redundant data copying and active receivers. To ensure atomic data transfers, receivers check and apply only fully received messages. Tailwind is a zero-copy recovery-log replication protocol for scale-out in-memory databases. Tailwind is the first replication protocol that eliminates all CPU-driven data copying and fully bypasses target server CPUs, thus leaving backups idle. Tailwind ensures all writes are atomic by leveraging a protocol that detects incomplete RDMA transfers. Tailwind substantially improves replication throughput and response latency compared with conventional RPC-based replication. In symmetric systems where servers both serve requests and act as replicas, Tailwind also improves normal-case throughput by freeing server CPU resources for request processing. We implemented and evaluated Tailwind on RAMCloud, a low-latency in-memory storage system. Experiments show Tailwind improves RAMCloud's normal-case request processing throughput by 1.7x. It also cuts down writes median and 99th percentile latencies by 2x and 3x respectively. 

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2. Exploring the Potential of Next Generation Software-Defined In-Memory Frameworks

   https://doi.org/10.1109/SBAC-PAD.2018.00042  

   Chen, Shouwei ; Rodero, Ivan ( January 2018 , 2018 30th International Symposium on Computer Architecture and High Performance Computing)

   As in-memory data analytics become increasingly important in a wide range of domains, the ability to develop large-scale and sustainable platforms faces significant challenges related to storage latency and memory size constraints. These challenges can be resolved by adopting new and effective formulations and novel architectures such as software-defined infrastructure. This paper investigates the key issue of data persistency for in-memory processing systems by evaluating persistence methods using different storage and memory devices for Apache Spark and the use of Alluxio. It also proposes and evaluates via simulation a Spark execution model for using disaggregated off- rack memory and non-volatile memory targeting next-generation software-defined infrastructure. Experimental results provide better understanding of behaviors and requirements for improving data persistence in current in-memory systems and provide data points to better understand requirements and design choices for next-generation software-defined infrastructure. The findings indicate that in-memory processing systems can benefit from ongoing software-defined infrastructure implementations; however current frameworks need to be enhanced appropriately to run efficiently at scale. 

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3. OpenMSIStream: A Python package for facilitatingintegration of streaming data in diverse laboratory environments

   https://doi.org/10.21105/joss.04896  

   Eminizer, Margaret ; Tabrisky, Sam ; Sharifzadeh, Amir ; DiMarco, Christopher ; Diamond, Jacob M. ; Ramesh, K. T. ; Hufnagel, Todd C. ; McQueen, Tyrel M. ; Elbert, David ( March 2023 , Journal of Open Source Software)

   OpenMSIStream provides seamless connection of scientific data stores with streaming infrastructure to allow researchers to leverage the power of decoupled, real-time data streaming architectures. Data streaming is the process of transmitting, ingesting, and processing data continuously rather than in batches. Access to streaming data has revolutionized many industries in the past decade and created entirely new standards of practice and types of analytics. While not yet commonly used in scientific research, data streaming has the potential to become a key technology to drive rapid advances in scientific data collection (e.g., Brookhaven National Lab (2022)). This paucity of streaming infrastructures linking complex scientific systems is due to a lack of tools that facilitate streaming in the diverse and distributed systems common in modern research. OpenMSIStream closes this gap between underlying streaming systems and common scientific infrastructure. Closing this gap empowers novel streaming applications for scientific data including automation of data curation, reduction, and analysis; real-time experiment monitoring and control; and flexible deployment of AI/ML to guide autonomous research. Streaming data generally refers to data continuously generated from multiple sources and passed in small packets (termed messages). Streaming data messages are typically organized in groups called topics and persist for periods of time conducive to processing for multiple uses either sequentially or in small groups. The resulting flows of raw data, metadata, and processing results form “ecosystems” that automate varied data-driven tasks. A strength of data streaming ecosystems is the use of publish-subscribe (“pub/sub”) messaging backbones that decouple data senders (publishers) and recipients (subscribers). Popular message-focused middleware solutions such as RabbitMQ (VMware, 2022), Apache Pulsar (Apache Software Foundation, 2022b), and Apache Kafka (Apache Software Foundation, 2022a) all provide differing capabilities as backbones. OpenMSIStream provides robust and efficient, yet easy, access to the rich data streaming systems of Apache Kafka. 

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4. 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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5. Data-trace types for distributed stream processing systems

   https://doi.org/10.1145/3314221.3314580  

   Mamouras, Konstantinos ; Stanford, Caleb ; Alur, Rajeev ; Ives, Zachary G. ; Tannen, Val ( January 2019 , 40th ACM SIGPLAN Conference on Programming Language Design and Implementation)

   Distributed architectures for efficient processing of streaming data are increasingly critical to modern information processing systems. The goal of this paper is to develop type-based programming abstractions that facilitate correct and efficient deployment of a logical specification of the desired computation on such architectures. In the proposed model, each communication link has an associated type specifying tagged data items along with a dependency relation over tags that captures the logical partial ordering constraints over data items. The semantics of a (distributed) stream processing system is then a function from input data traces to output data traces, where a data trace is an equivalence class of sequences of data items induced by the dependency relation. This data-trace transduction model generalizes both acyclic synchronous data-flow and relational query processors, and can specify computations over data streams with a rich variety of partial ordering and synchronization characteristics. We then describe a set of programming templates for data-trace transductions: abstractions corresponding to common stream processing tasks. Our system automatically maps these high-level programs to a given topology on the distributed implementation platform Apache Storm while preserving the semantics. Our experimental evaluation shows that (1) while automatic parallelization deployed by existing systems may not preserve semantics, particularly when the computation is sensitive to the ordering of data items, our programming abstractions allow a natural specification of the query that contains a mix of ordering constraints while guaranteeing correct deployment, and (2) the throughput of the automatically compiled distributed code is comparable to that of hand-crafted distributed implementations. 

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