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1. Parallel Strong Connectivity Based on Faster Reachability

   https://doi.org/10.1145/3589259  

   Wang, Letong ; Dong, Xiaojun ; Gu, Yan ; Sun, Yihan ( June 2023 , Proceedings of the ACM on Management of Data)

   Computing strongly connected components (SCC) is among the most fundamental problems in graph analytics. Given the large size of today's real-world graphs, parallel SCC implementation is increasingly important. SCC is challenging in the parallel setting and is particularly hard on large-diameter graphs. Many existing parallel SCC implementations can be even slower than Tarjan's sequential algorithm on large-diameter graphs.

   To tackle this challenge, we propose an efficient parallel SCC implementation using a new parallel reachability approach. Our solution is based on a novel idea referred to as vertical granularity control (VGC). It breaks the synchronization barriers to increase parallelism and hide scheduling overhead. To use VGC in our SCC algorithm, we also design an efficient data structure called the parallel hash bag. It uses parallel dynamic resizing to avoid redundant work in maintaining frontiers (vertices processed in a round).

   We implement the parallel SCC algorithm by Blelloch et al. (J. ACM, 2020) using our new parallel reachability approach. We compare our implementation to the state-of-the-art systems, including GBBS, iSpan, Multi-step, and our highly optimized Tarjan's (sequential) algorithm, on 18 graphs, including social, web, k-NN, and lattice graphs. On a machine with 96 cores, our implementation is the fastest on 16 out of 18 graphs. On average (geometric means) over all graphs, our SCC is 6.0× faster than the best previous parallel code (GBBS), 12.8× faster than Tarjan's sequential algorithms, and 2.7× faster than the best existing implementation on each graph.

   We believe that our techniques are of independent interest. We also apply our parallel hash bag and VGC scheme to other graph problems, including connectivity and least-element lists (LE-lists). Our implementations improve the performance of the state-of-the-art parallel implementations for these two problems.

    

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2. Fast and Space-Efficient Parallel Algorithms for Influence Maximization

   https://doi.org/10.14778/3632093.3632104  

   Wang, Letong ; Ding, Xiangyun ; Gu, Yan ; Sun, Yihan ( November 2023 , Proceedings of the VLDB Endowment)

   Influence Maximization (IM) is a crucial problem in data science. The goal is to find a fixed-size set of highly influentialseedvertices on a network to maximize the influence spread along the edges. While IM is NP-hard on commonly used diffusion models, a greedy algorithm can achieve (1 - 1/e)-approximation by repeatedly selecting the vertex with the highestmarginal gainin influence as the seed. However, we observe two performance issues in the existing work that prevent them from scaling to today's large-scale graphs: space-inefficient memorization to estimate marginal gain, and time-inefficient seed selection process due to a lack of parallelism.

   This paper significantly improves the scalability of IM using two key techniques. The first is asketch-compressiontechnique for the independent cascading model on undirected graphs. It allows combining the simulation and sketching approaches to achieve a time-space tradeoff. The second technique includes new data structures for parallel seed selection. Using our new approaches, we implementedPaC-IM: Parallel and Compressed IM.

   We comparePaC-IMwith state-of-the-art parallel IM systems on a 96-core machine with 1.5TB memory.PaC-IMcan process the ClueWeb graph with 978M vertices and 75B edges in about 2 hours. On average, across all tested graphs, our uncompressed version is 5--18x faster and about 1.4x more space-efficient than existing parallel IM systems. Using compression further saves 3.8x space with only 70% overhead in time on average.

    

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3. 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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4. Sustained Space and Cumulative Complexity Trade-Offs for Data-Dependent Memory-Hard Functions

   Blocki, Jeremiah ; Holman, Blake ( October 2022 , Dodis, Y., Shrimpton, T. (eds) Advances in Cryptology – CRYPTO 2022)

   Dodis, Y. (Ed.)

   Memory-hard functions (MHFs) are a useful cryptographic primitive which can be used to design egalitarian proof of work puzzles and to protect low entropy secrets like passwords against brute-force attackers. Intuitively, a memory-hard function is a function whose evaluation costs are dominated by memory costs even if the attacker uses specialized hardware (FPGAs/ASICs), and several cost metrics have been proposed to quantify this intuition. For example, space-time cost looks at the product of running time and the maximum space usage over the entire execution of an algorithm. Alwen and Serbinenko (STOC 2015) observed that the space-time cost of evaluating a function multiple times may not scale linearly in the number of instances being evaluated and introduced the stricter requirement that a memory-hard function has high cumulative memory complexity (CMC) to ensure that an attacker’s amortized space-time costs remain large even if the attacker evaluates the function on multiple different inputs in parallel. Alwen et al. (EUROCRYPT 2018) observed that the notion of CMC still gives the attacker undesirable flexibility in selecting space-time tradeoffs e.g., while the MHF Scrypt has maximal CMC Ω(N^2), an attacker could evaluate the function with constant O(1) memory in time O(N^2). Alwen et al. introduced an even stricter notion of Sustained Space complexity and designed an MHF which has s=Ω(N/logN) sustained complexity t=Ω(N) i.e., any algorithm evaluating the function in the parallel random oracle model must have at least t=Ω(N) steps where the memory usage is at least Ω(N/logN). In this work, we use dynamic pebbling games and dynamic graphs to explore tradeoffs between sustained space complexity and cumulative memory complexity for data-dependent memory-hard functions such as Argon2id and Scrypt. We design our own dynamic graph (dMHF) with the property that any dynamic pebbling strategy either (1) has Ω(N) rounds with Ω(N) space, or (2) has CMC Ω(N^{3−ϵ})—substantially larger than N^2. For Argon2id we show that any dynamic pebbling strategy either(1) has Ω(N) rounds with Ω(N^{1−ϵ}) space, or (2) has CMC ω(N^2). We also present a dynamic version of DRSample (Alwen et al. 2017) for which any dynamic pebbling strategy either (1) has Ω(N) rounds with Ω(N/log N) space, or (2) has CMC Ω(N^3/log N). 

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5. Local Access to Huge Random Objects Through Partial Sampling

   Biswas, Amartya Shankha ; Rubinfeld, Ronitt ; Yodpinyanee, Anak ( January 2020 , 11th Innovations in Theoretical Computer Science Conference, ITCS 2020)

   null (Ed.)

   Consider an algorithm performing a computation on a huge random object (for example a random graph or a "long" random walk). Is it necessary to generate the entire object prior to the computation, or is it possible to provide query access to the object and sample it incrementally "on-the-fly" (as requested by the algorithm)? Such an implementation should emulate the random object by answering queries in a manner consistent with an instance of the random object sampled from the true distribution (or close to it). This paradigm is useful when the algorithm is sub-linear and thus, sampling the entire object up front would ruin its efficiency. Our first set of results focus on undirected graphs with independent edge probabilities, i.e. each edge is chosen as an independent Bernoulli random variable. We provide a general implementation for this model under certain assumptions. Then, we use this to obtain the first efficient local implementations for the Erdös-Rényi G(n,p) model for all values of p, and the Stochastic Block model. As in previous local-access implementations for random graphs, we support Vertex-Pair and Next-Neighbor queries. In addition, we introduce a new Random-Neighbor query. Next, we give the first local-access implementation for All-Neighbors queries in the (sparse and directed) Kleinberg’s Small-World model. Our implementations require no pre-processing time, and answer each query using O(poly(log n)) time, random bits, and additional space. Next, we show how to implement random Catalan objects, specifically focusing on Dyck paths (balanced random walks on the integer line that are always non-negative). Here, we support Height queries to find the location of the walk, and First-Return queries to find the time when the walk returns to a specified location. This in turn can be used to implement Next-Neighbor queries on random rooted ordered trees, and Matching-Bracket queries on random well bracketed expressions (the Dyck language). Finally, we introduce two features to define a new model that: (1) allows multiple independent (and even simultaneous) instantiations of the same implementation, to be consistent with each other without the need for communication, (2) allows us to generate a richer class of random objects that do not have a succinct description. Specifically, we study uniformly random valid q-colorings of an input graph G with maximum degree Δ. This is in contrast to prior work in the area, where the relevant random objects are defined as a distribution with O(1) parameters (for example, n and p in the G(n,p) model). The distribution over valid colorings is instead specified via a "huge" input (the underlying graph G), that is far too large to be read by a sub-linear time algorithm. Instead, our implementation accesses G through local neighborhood probes, and is able to answer queries to the color of any given vertex in sub-linear time for q ≥ 9Δ, in a manner that is consistent with a specific random valid coloring of G. Furthermore, the implementation is memory-less, and can maintain consistency with non-communicating copies of itself. 

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