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1. Optimizing Near-Data Processing for Spark

   Rachuri, Sri Pramodh ; Gantasala, Arun ; Emanuel, Prajeeth ; Gandhi, Anshul ; Foley, Robert ; Puhov, Peter ; Gkountouvas, Theodoros ; Lei, Hui ( January 2022 , Proceedings of the 42nd IEEE International Conference on Distributed Computing Systems (ICDCS '22))

   Resource disaggregation (RD) is an emerging paradigm for data center computing whereby resource-optimized servers are employed to minimize resource fragmentation and improve resource utilization. Apache Spark deployed under the RD paradigm employs a cluster of compute-optimized servers to run executors and a cluster of storage-optimized servers to host the data on HDFS. However, the network transfer from storage to compute cluster becomes a severe bottleneck for big data processing. Near-data processing (NDP) is a concept that aims to alleviate network load in such cases by offloading (or “pushing down”) some of the compute tasks to the storage cluster. Employing NDP for Spark under the RD paradigm is challenging because storage-optimized servers have limited computational resources and cannot host the entire Spark processing stack. Further, even if such a lightweight stack could be developed and deployed on the storage cluster, it is not entirely obvious which Spark queries would benefit from pushdown, and which tasks of a given query should be pushed down to storage. This paper presents the design and implementation of a near-data processing system for Spark, SparkNDP, that aims to address the aforementioned challenges. SparkNDP works by implementing novel NDP Spark capabilities on the storage cluster using a lightweight library of SQL operators and then developing an analytical model to help determine which Spark tasks should be pushed down to storage based on the current network and system state. Simulation and prototype implementation results show that SparkNDP can help reduce Spark query execution times when compared to both the default approach of not pushing down any tasks to storage and the outright NDP approach of pushing all tasks to storage. 

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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. Geometric deep optical sensing

   https://doi.org/10.1126/science.ade1220  

   Yuan, Shaofan ; Ma, Chao ; Fetaya, Ethan ; Mueller, Thomas ; Naveh, Doron ; Zhang, Fan ; Xia, Fengnian ( March 2023 , Science)

   BACKGROUND Optical sensing devices measure the rich physical properties of an incident light beam, such as its power, polarization state, spectrum, and intensity distribution. Most conventional sensors, such as power meters, polarimeters, spectrometers, and cameras, are monofunctional and bulky. For example, classical Fourier-transform infrared spectrometers and polarimeters, which characterize the optical spectrum in the infrared and the polarization state of light, respectively, can occupy a considerable portion of an optical table. Over the past decade, the development of integrated sensing solutions by using miniaturized devices together with advanced machine-learning algorithms has accelerated rapidly, and optical sensing research has evolved into a highly interdisciplinary field that encompasses devices and materials engineering, condensed matter physics, and machine learning. To this end, future optical sensing technologies will benefit from innovations in device architecture, discoveries of new quantum materials, demonstrations of previously uncharacterized optical and optoelectronic phenomena, and rapid advances in the development of tailored machine-learning algorithms. ADVANCES Recently, a number of sensing and imaging demonstrations have emerged that differ substantially from conventional sensing schemes in the way that optical information is detected. A typical example is computational spectroscopy. In this new paradigm, a compact spectrometer first collectively captures the comprehensive spectral information of an incident light beam using multiple elements or a single element under different operational states and generates a high-dimensional photoresponse vector. An advanced algorithm then interprets the vector to achieve reconstruction of the spectrum. This scheme shifts the physical complexity of conventional grating- or interference-based spectrometers to computation. Moreover, many of the recent developments go well beyond optical spectroscopy, and we discuss them within a common framework, dubbed “geometric deep optical sensing.” The term “geometric” is intended to emphasize that in this sensing scheme, the physical properties of an unknown light beam and the corresponding photoresponses can be regarded as points in two respective high-dimensional vector spaces and that the sensing process can be considered to be a mapping from one vector space to the other. The mapping can be linear, nonlinear, or highly entangled; for the latter two cases, deep artificial neural networks represent a natural choice for the encoding and/or decoding processes, from which the term “deep” is derived. In addition to this classical geometric view, the quantum geometry of Bloch electrons in Hilbert space, such as Berry curvature and quantum metrics, is essential for the determination of the polarization-dependent photoresponses in some optical sensors. In this Review, we first present a general perspective of this sensing scheme from the viewpoint of information theory, in which the photoresponse measurement and the extraction of light properties are deemed as information-encoding and -decoding processes, respectively. We then discuss demonstrations in which a reconfigurable sensor (or an array thereof), enabled by device reconfigurability and the implementation of neural networks, can detect the power, polarization state, wavelength, and spatial features of an incident light beam. OUTLOOK As increasingly more computing resources become available, optical sensing is becoming more computational, with device reconfigurability playing a key role. On the one hand, advanced algorithms, including deep neural networks, will enable effective decoding of high-dimensional photoresponse vectors, which reduces the physical complexity of sensors. Therefore, it will be important to integrate memory cells near or within sensors to enable efficient processing and interpretation of a large amount of photoresponse data. On the other hand, analog computation based on neural networks can be performed with an array of reconfigurable devices, which enables direct multiplexing of sensing and computing functions. We anticipate that these two directions will become the engineering frontier of future deep sensing research. On the scientific frontier, exploring quantum geometric and topological properties of new quantum materials in both linear and nonlinear light-matter interactions will enrich the information-encoding pathways for deep optical sensing. In addition, deep sensing schemes will continue to benefit from the latest developments in machine learning. Future highly compact, multifunctional, reconfigurable, and intelligent sensors and imagers will find applications in medical imaging, environmental monitoring, infrared astronomy, and many other areas of our daily lives, especially in the mobile domain and the internet of things. Schematic of deep optical sensing. The n -dimensional unknown information ( w ) is encoded into an m -dimensional photoresponse vector ( x ) by a reconfigurable sensor (or an array thereof), from which w′ is reconstructed by a trained neural network ( n ′ = n and w′   ≈   w ). Alternatively, x may be directly deciphered to capture certain properties of w . Here, w , x , and w′ can be regarded as points in their respective high-dimensional vector spaces ℛ n , ℛ m , and ℛ n ′ . 

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4. Protean: An Energy-Efficient and Heterogeneous Platform for Adaptive and Hardware-Accelerated Battery-Free Computing

   https://doi.org/10.1145/3560905.3568561  

   Bakar, Abu ; Goel, Rishabh ; de Winkel, Jasper ; Huang, Jason ; Ahmed, Saad ; Islam, Bashima ; Pawełczak, Przemysław ; Yıldırım, Kasım Sinan ; Hester, Josiah ( November 2022 , Proceedings of the 20th ACM Conference on Embedded Networked Sensor Systems (SenSys'22))

   Battery-free and intermittently powered devices offer long lifetimes and enable deployment in new applications and environments. Unfortunately, developing sophisticated inference-capable applications is still challenging due to the lack of platform support for more advanced (32-bit) microprocessors and specialized accelerators---which can execute data-intensive machine learning tasks, but add complexity across the stack when dealing with intermittent power. We present Protean to bridge the platform gap for inference-capable battery-free sensors. Designed for runtime scalability, meeting the dynamic range of energy harvesters with matching heterogeneous processing elements like neural network accelerators. We develop a modular "plug-and-play" hardware platform, SuperSensor, with a reconfigurable energy storage circuit that powers a 32-bit ARM-based microcontroller with a convolutional neural network accelerator. An adaptive task-based runtime system, Chameleon, provides intermittency-proof execution of machine learning tasks across heterogeneous processing elements. The runtime automatically scales and dispatches these tasks based on incoming energy, current state, and programmer annotations. A code generator, Metamorph, automates conversion of ML models to intermittent safe execution across heterogeneous compute elements. We evaluate Protean with audio and image workloads and demonstrate up to 666x improvement in inference energy efficiency by enabling usage of modern computational elements within intermittent computing. Further, Protean provides up to 166% higher throughput compared to non-adaptive baselines. 

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5. Research Opportunities in Heterogeneous Computing for Machine Learning

   https://doi.org/10.1109/HPCS.2018.00094  

   Lam, Herman ; Ojika, David ( July 2018 , International Workshop on High Performance and Dynamic Reconfigurable Systems and Networks (DRSN))

   In recent times, AI and deep learning have witnessed explosive growth in almost every subject involving data. Complex data analyses problems that took prolonged periods, or required laborious manual effort, are now being tackled through AI and deep-learning techniques with unprecedented accuracy. Machine learning (ML) using Convolutional Neural Networks (CNNs) has shown great promise for such applications. However, traditional CPU-based sequential computing no longer can meet the requirements of mission-critical applications which are compute-intensive and require low latency. Heterogeneous computing (HGC), with CPUs integrated with accelerators such as GPUs and FPGAs, offers unique capabilities to accelerate CNNs. In this presentation, we will focus on using FPGA-based reconfigurable computing to accelerate various aspects of CNN. We will begin with the current state of the art in using FPGAs for CNN acceleration, followed by the related R&D activities (outlined below) in the SHREC* Center at the University of Florida, based on which we will discuss the opportunities in heterogeneous computing for machine learning. 

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