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Title: Batched Predecessor and Sorting with Size-Priced Information in External Memory
In the unit-cost comparison model, a black box takes an input two items and outputs the result of the comparison. Problems like sorting and searching have been studied in this model, and it has been general- ized to include the concept of priced information, where different pairs of items (say database records) have different comparison costs. These comparison costs can be arbitrary (in which case no algorithm can be close to optimal (Charikar et al. STOC 2000)), structured (for exam- ple, the comparison cost may depend on the length of the databases (Gupta et al. FOCS 2001)), or stochastic (Angelov et al. LATIN 2008). Motivated by the database setting where the cost depends on the sizes of the items, we consider the problems of sorting and batched predecessor where two non-uniform sets of items A and B are given as input.
(1) In the RAM setting, we consider the scenario where both sets have n keys each. The cost to compare two items in A is a, to compare an item of A to an item of B is b, and to compare two items in B is c. We give upper and lower bounds for the case a ≤ b more »
≤ c, the case that serves as a warmup for the generalization to the external-memory model. Notice that the case b = 1,a = c = ∞ is the famous “nuts and bolts” problem.
) In the Disk-Access Model (DAM), where transferring elements between disk and internal memory is the main bottleneck, we con- sider the scenario where elements in B are larger than elements in A. The larger items take more I/Os to be brought into memory, consume more space in internal memory, and are required in their entirety for comparisons.
A key observation is that the complexity of sorting depends heavily on the interleaving of the small and large items in the final sorted order. If all large elements come after all small elements in the final sorted order, sorting each type separately and concatenating is optimal. However, if the set of predecessors of B in A has size k ≪ n, one must solve an associated batched predecessor problem in order to achieve optimality.
We first give output-sensitive lower and upper bounds on the batched predecessor problem, and use these to derive bounds on the complexity of sorting in the two models. Our bounds are tight in most cases, and require novel generalizations of the classical lower bound techniques in external memory to accommodate the non-uniformity of keys. « less
Bender, Michael A; Goswami, Mayank; Medjedovic, Dzejla; Montes, Pablo; Tsichlas, Kostas(
, Latin American Symposium on Theoretical Informatics)
The fundamental problems of sorting and searching, traditionally studied in the unit-cost comparison model, have been generalized to include priced information, where different pairs of items have different comparison costs. These costs can be arbitrary (Charikar et al. STOC 2000), structured (Gupta et al. FOCS 2001), or stochastic (Angelov et al. LATIN 2008). Motivated by the database setting where the comparison cost depends on the sizes of the records, we consider the problems of sorting and batched predecessor where two non-uniform sets of items A and B are given as input. In the RAM model, pairwise comparisons (A-A, A-B andmore »B-B) have respective comparison costs a, b and c. We give upper and lower bounds for the case a<= b <= c, which serves as a warmup for the generalization to the external-memory model. In the Disk-Access Model (DAM), where transferring elements between disk and RAM is the main bottleneck, we consider the scenario where elements in B are larger than elements in A. All items are required in their entirety for comparisons in RAM. A key observation is that the complexity of sorting depends on the interleaving of the small and large items in the final sorted order, and with a high degree of interleaving, the lower bound is dominated by an associated batched predecessor problem. We give output-sensitive bounds on the batched predecessor and sorting; our bounds are tight in most cases. Our lower bounds require novel generalizations of lower bound techniques in external memory to accommodate non-uniform keys.« less
Afshani, Peyman; Bender, Michael; Farach-Colton, Martin; Fineman, Jeremy; Goswami, Mayank; Tsai, Meng-Tsung Tsai(
, Proceedings of the Twenty-Eighth Annual ACM-SIAM Symposium on Discrete Algorithms)
Dictionaries remain the most well studied class of data structures. A dictionary supports insertions, deletions, membership queries, and usually successor, predecessor, and extract-min. In a RAM, all such operations take O(log n) time on n elements. Dictionaries are often cross-referenced as follows. Consider a set of tuples {〈ai,bi,ci…〉}. A database might include more than one dictionary on such a set, for example, one indexed on the a ‘s, another on the b‘s, and so on. Once again, in a RAM, inserting into a set of L cross-referenced dictionaries takes O(L log n) time, as does deleting. The situation is moremore »interesting in external memory. On a Disk Access Machine (DAM), B-trees achieve O(logB N) I/Os for insertions and deletions on a single dictionary and K-element range queries take optimal O(logB N + K/B) I/Os. These bounds are also achievable by a B-tree on cross-referenced dictionaries, with a slowdown of an L factor on insertion and deletions. In recent years, both the theory and practice of external- memory dictionaries has been revolutionized by write- optimization techniques. A dictionary is write optimized if it is close to a B-tree for query time while beating B-trees on insertions. The best (and optimal) dictionaries achieve a substantially improved insertion and deletion cost of amortized I/Os on a single dictionary while maintaining optimal O(log1+B∊ N + K/B)- I/O range queries. Although write optimization still helps for insertions into cross-referenced dictionaries, its value for deletions would seem to be greatly reduced. A deletion into a cross- referenced dictionary only specifies a key a. It seems to be necessary to look up the associated values b, c … in order to delete them from the other dictionaries. This takes Ω(logB N) I/Os, well above the per-dictionary write-optimization budget of So the total deletion cost is In short, for deletions, write optimization offers an advantage over B-trees in that L multiplies a lower order term, but when L = 2, write optimization seems to offer no asymptotic advantage over B-trees. That is, no known query- optimal solution for pairs of cross-referenced dictionaries seem to beat B-trees for deletions. In this paper, we show a lower bound establishing that a pair of cross-referenced dictionaries that are optimal for range queries and that supports deletions cannot match the write optimization bound available to insert-only dictionaries. This result thus establishes a limit to the applicability of write-optimization techniques on which many new databases and file systems are based. Read More: http://epubs.siam.org/doi/10.1137/1.9781611974782.99« less
Blelloch, Guy E; Fineman, Jeremy T; Gibbons, Phillip B; Gu, Yan; Shun, Julian(
, 24th Annual European Symposium on Algorithms (ESA 2016))
In several emerging technologies for computer memory (main memory), the cost of reading is significantly cheaper than the cost of writing. Such asymmetry in memory costs poses a fundamentally different model from the RAM for algorithm design. In this paper we study lower and upper bounds for various problems under such asymmetric read and write costs. We consider both the case in which all but O(1) memory has asymmetric cost, and the case of a small cache of symmetric memory. We model both cases using the (M,w)-ARAM, in which there is a small (symmetric) memory of size M and amore »large unbounded (asymmetric) memory, both random access, and where reading from the large memory has unit cost, but writing has cost w >> 1. For FFT and sorting networks we show a lower bound cost of Omega(w*n*log_{w*M}(n)), which indicates that it is not possible to achieve asymptotic improvements with cheaper reads when w is bounded by a polynomial in M. Moreover, there is an asymptotic gap (of min(w,log(n)/log(w*M)) between the cost of sorting networks and comparison sorting in the model. This contrasts with the RAM, and most other models, in which the asymptotic costs are the same. We also show a lower bound for computations on an n*n diamond DAG of Omega(w*n^2/M) cost, which indicates no asymptotic improvement is achievable with fast reads. However, we show that for the minimum edit distance problem (and related problems), which would seem to be a diamond DAG, we can beat this lower bound with an algorithm with only O(w*n^2/(M*min(w^{1/3},M^{1/2}))) cost. To achieve this we make use of a "path sketch" technique that is forbidden in a strict DAG computation. Finally, we show several interesting upper bounds for shortest path problems, minimum spanning trees, and other problems. A common theme in many of the upper bounds is that they require redundant computation and a tradeoff between reads and writes.« less
Shawki, N.; Elseify, T.; Cap, T.; Shah, V.; Obeid, I.; Picone, J.(
, 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 describemore »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.« less
Ahmad, Zafar; Chowdhury, Rezaul; Das, Rathish; Ganapathi, Pramod; Gregory, Aaron; Javanmard, Mohammad Mahdi(
, Proc. 33st ACM on Symposium on Parallelism in Algorithms and Architectures (SPAA))
The binary-forking model is a parallel computation model, formally defined by Blelloch et al., in which a thread can fork a concurrent child thread, recursively and asynchronously. The model incurs a cost of Theta(log n) to spawn or synchronize n tasks or threads. The binary-forking model realistically captures the performance of parallel algorithms implemented using modern multithreaded programming languages on multicore shared-memory machines. In contrast, the widely studied theoretical PRAM model does not consider the cost of spawning and synchronizing threads, and as a result, algorithms achieving optimal performance bounds in the PRAM model may not be optimal in themore »binary-forking model. Often, algorithms need to be redesigned to achieve optimal performance bounds in the binary-forking model and the non-constant synchronization cost makes the task challenging. In this paper, we show that in the binary-forking model we can achieve optimal or near-optimal span with negligible or no asymptotic blowup in work for comparison-based sorting, Strassen's matrix multiplication (MM), and the Fast Fourier Transform (FFT). Our major results are as follows: (1) A randomized comparison-based sorting algorithm with optimal O(log n) span and O(nlog n) work, both w.h.p. in n. (2) An optimal O(log n) span algorithm for Strassen's matrix multiplication (MM) with only a loglog n - factor blow-up in work as well as a near-optimal O(log n loglog log n) span algorithm with no asymptotic blow-up in work. (3) A near-optimal O(log n logloglog n) span Fast Fourier Transform (FFT) algorithm with less than a log n-factor blow-up in work for all practical values of n (i.e., n le 10 ^10,000 ).« less
Bender, Michael, Goswami, Mayank, Medjedovic, Dzejla, Montes, Pablo, and Tsichlas, Kostas. Batched Predecessor and Sorting with Size-Priced Information in External Memory. Retrieved from https://par.nsf.gov/biblio/10298528. Latin American Theoretical Informatics Symposium .
Bender, Michael, Goswami, Mayank, Medjedovic, Dzejla, Montes, Pablo, & Tsichlas, Kostas. Batched Predecessor and Sorting with Size-Priced Information in External Memory. Latin American Theoretical Informatics Symposium, (). Retrieved from https://par.nsf.gov/biblio/10298528.
Bender, Michael, Goswami, Mayank, Medjedovic, Dzejla, Montes, Pablo, and Tsichlas, Kostas.
"Batched Predecessor and Sorting with Size-Priced Information in External Memory". Latin American Theoretical Informatics Symposium (). Country unknown/Code not available. https://par.nsf.gov/biblio/10298528.
@article{osti_10298528,
place = {Country unknown/Code not available},
title = {Batched Predecessor and Sorting with Size-Priced Information in External Memory},
url = {https://par.nsf.gov/biblio/10298528},
abstractNote = {In the unit-cost comparison model, a black box takes an input two items and outputs the result of the comparison. Problems like sorting and searching have been studied in this model, and it has been general- ized to include the concept of priced information, where different pairs of items (say database records) have different comparison costs. These comparison costs can be arbitrary (in which case no algorithm can be close to optimal (Charikar et al. STOC 2000)), structured (for exam- ple, the comparison cost may depend on the length of the databases (Gupta et al. FOCS 2001)), or stochastic (Angelov et al. LATIN 2008). Motivated by the database setting where the cost depends on the sizes of the items, we consider the problems of sorting and batched predecessor where two non-uniform sets of items A and B are given as input. (1) In the RAM setting, we consider the scenario where both sets have n keys each. The cost to compare two items in A is a, to compare an item of A to an item of B is b, and to compare two items in B is c. We give upper and lower bounds for the case a ≤ b ≤ c, the case that serves as a warmup for the generalization to the external-memory model. Notice that the case b = 1,a = c = ∞ is the famous “nuts and bolts” problem. ) In the Disk-Access Model (DAM), where transferring elements between disk and internal memory is the main bottleneck, we con- sider the scenario where elements in B are larger than elements in A. The larger items take more I/Os to be brought into memory, consume more space in internal memory, and are required in their entirety for comparisons. A key observation is that the complexity of sorting depends heavily on the interleaving of the small and large items in the final sorted order. If all large elements come after all small elements in the final sorted order, sorting each type separately and concatenating is optimal. However, if the set of predecessors of B in A has size k ≪ n, one must solve an associated batched predecessor problem in order to achieve optimality. We first give output-sensitive lower and upper bounds on the batched predecessor problem, and use these to derive bounds on the complexity of sorting in the two models. Our bounds are tight in most cases, and require novel generalizations of the classical lower bound techniques in external memory to accommodate the non-uniformity of keys.},
journal = {Latin American Theoretical Informatics Symposium},
author = {Bender, Michael and Goswami, Mayank and Medjedovic, Dzejla and Montes, Pablo and Tsichlas, Kostas},
}