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1. MCRapper: Monte-Carlo Rademacher Averages for Poset Families and Approximate Pattern Mining.

   Leonardo Pellegrina, Cyrus Cousins ( August 2020 , KDD: International Conference on Knowledge Discovery & Data Mining)

   We present MCRapper, an algorithm for efficient computation of Monte-Carlo Empirical Rademacher Averages (MCERA) for families of functions exhibiting poset (e.g., lattice) structure, such as those that arise in many pattern mining tasks. The MCERA allows us to compute upper bounds to the maximum deviation of sample means from their expectations, thus it can be used to find both statistically-significant functions (i.e., patterns) when the available data is seen as a sample from an unknown distribution, and approximations of collections of high-expectation functions (e.g., frequent patterns) when the available data is a small sample from a large dataset. This feature is a strong improvement over previously proposed solutions that could only achieve one of the two. MCRapper uses upper bounds to the discrepancy of the functions to efficiently explore and prune the search space, a technique borrowed from pattern mining itself. To show the practical use of MCRapper, we employ it to develop an algorithm TFP-R for the task of True Frequent Pattern (TFP) mining. TFP-R gives guarantees on the probability of including any false positives (precision) and exhibits higher statistical power (recall) than existing methods offering the same guarantees. We evaluate MCRapper and TFP-R and show that they outperformmore »the state-of-the-art for their respective tasks.« less
2. NTP-Miner: Nonoverlapping Three-Way Sequential Pattern Mining

   https://doi.org/10.1145/3480245  

   Wu, Youxi ; Luo, Lanfang ; Li, Yan ; Guo, Lei ; Fournier-Viger, Philippe ; Zhu, Xingquan ; Wu, Xindong ( June 2022 , ACM Transactions on Knowledge Discovery from Data)

   Nonoverlapping sequential pattern mining is an important type of sequential pattern mining (SPM) with gap constraints, which not only can reveal interesting patterns to users but also can effectively reduce the search space using the Apriori (anti-monotonicity) property. However, the existing algorithms do not focus on attributes of interest to users, meaning that existing methods may discover many frequent patterns that are redundant. To solve this problem, this article proposes a task called nonoverlapping three-way sequential pattern (NTP) mining, where attributes are categorized according to three levels of interest: strong, medium, and weak interest. NTP mining can effectively avoid mining redundant patterns since the NTPs are composed of strong and medium interest items. Moreover, NTPs can avoid serious deviations (the occurrence is significantly different from its pattern) since gap constraints cannot match with strong interest patterns. To mine NTPs, an effective algorithm is put forward, called NTP-Miner, which applies two main steps: support (frequency occurrence) calculation and candidate pattern generation. To calculate the support of an NTP, depth-first and backtracking strategies are adopted, which do not require creating a whole Nettree structure, meaning that many redundant nodes and parent–child relationships do not need to be created. Hence, time and spacemore »efficiency is improved. To generate candidate patterns while reducing their number, NTP-Miner employs a pattern join strategy and only mines patterns of strong and medium interest. Experimental results on stock market and protein datasets show that NTP-Miner not only is more efficient than other competitive approaches but can also help users find more valuable patterns. More importantly, NTP mining has achieved better performance than other competitive methods in clustering tasks. Algorithms and data are available at: https://github.com/wuc567/Pattern-Mining/tree/master/NTP-Miner .« less
3. Spiking Neural Networks Through the Lens of Streaming Algorithms

   Hitron, Y. ; Musco, C. ; Parter, M. ( January 2020 , 34th International Symposium on Distributed Computing (DISC))

   We initiate the study of biologically-inspired spiking neural networks from the perspective of streaming algorithms. Like computers, human brains face memory limitations, which pose a significant obstacle when processing large scale and dynamically changing data. In computer science, these challenges are captured by the well-known streaming model, which can be traced back to Munro and Paterson `78 and has had significant impact in theory and beyond. In the classical streaming setting, one must compute a function f of a stream of updates 𝒮 = {u₁,…,u_m}, given restricted single-pass access to the stream. The primary complexity measure is the space used by the algorithm. In contrast to the large body of work on streaming algorithms, relatively little is known about the computational aspects of data processing in spiking neural networks. In this work, we seek to connect these two models, leveraging techniques developed for streaming algorithms to better understand neural computation. Our primary goal is to design networks for various computational tasks using as few auxiliary (non-input or output) neurons as possible. The number of auxiliary neurons can be thought of as the "space" required by the network. Previous algorithmic work in spiking neural networks has many similarities with streaming algorithms.more »However, the connection between these two space-limited models has not been formally addressed. We take the first steps towards understanding this connection. On the upper bound side, we design neural algorithms based on known streaming algorithms for fundamental tasks, including distinct elements, approximate median, and heavy hitters. The number of neurons in our solutions almost match the space bounds of the corresponding streaming algorithms. As a general algorithmic primitive, we show how to implement the important streaming technique of linear sketching efficiently in spiking neural networks. On the lower bound side, we give a generic reduction, showing that any space-efficient spiking neural network can be simulated by a space-efficient streaming algorithm. This reduction lets us translate streaming-space lower bounds into nearly matching neural-space lower bounds, establishing a close connection between the two models.« less
4. Computing Maximal Unique Matches with the r-index

   https://doi.org/10.4230/LIPIcs.SEA.2022.22  

   Giuliani, Sara ; Romana, Giuseppe ; Rossi, Massimiliano ( January 2022 , SEA (International Symposium on Experimental Algorithms))

   In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique Matches (MUMs) have proven themselves to be useful in multiple bioinformatic contexts, for example short-read alignment and multiple-genome alignment. However, standard techniques using suffix trees and FM-indexes do not scale to a pangenomic level. Recently, Gagie et al. [JACM 20] introduced the r-index that is a Burrows-Wheeler Transform (BWT)-based index able to handle hundreds of human genomes. Later, Rossi et al. [JCB 22] enabled the computation of MEMs using the r-index, and Boucher et al. [DCC 21] showed how to compute them in a streaming fashion. In this paper, we show how to augment Boucher et al.'s approach to enable the computation of MUMs on the r-index, while preserving the space and time bounds. We add additional O(r) samples of the longest common prefix (LCP) array, where r is the number of equal-letter runs of the BWT, that permits the computation of the second longest match of the pattern suffix with respect to the input text, which in turn allows the computation of candidate MUMs. We implemented a proof-of-conceptmore »of our approach, that we call mum-phinder, and tested on real-world datasets. We compared our approach with competing methods that are able to compute MUMs. We observe that our method is up to 8 times smaller, while up to 19 times slower when the dataset is not highly repetitive, while on highly repetitive data, our method is up to 6.5 times slower and uses up to 25 times less memory.« less
5. MICCO: An Enhanced Multi-GPU Scheduling Framework for Many-Body Correlation Functions

   https://doi.org/10.1109/IPDPS53621.2022.00022  

   Wang, Qihan ; Ren, Bin ; Chen, Jie ; Edwards, Robert G. ( May 2022 , 2022 IEEE International Parallel and Distributed Processing Symposium (IPDPS))

   Calculation of many-body correlation functions is one of the critical kernels utilized in many scientific computing areas, especially in Lattice Quantum Chromodynamics (Lattice QCD). It is formalized as a sum of a large number of contraction terms each of which can be represented by a graph consisting of vertices describing quarks inside a hadron node and edges designating quark propagations at specific time intervals. Due to its computation- and memory-intensive nature, real-world physics systems (e.g., multi-meson or multi-baryon systems) explored by Lattice QCD prefer to leverage multi-GPUs. Different from general graph processing, many-body correlation function calculations show two specific features: a large number of computation-/data-intensive kernels and frequently repeated appearances of original and intermediate data. The former results in expensive memory operations such as tensor movements and evictions. The latter offers data reuse opportunities to mitigate the data-intensive nature of many-body correlation function calculations. However, existing graph-based multi-GPU schedulers cannot capture these data-centric features, thus resulting in a sub-optimal performance for many-body correlation function calculations. To address this issue, this paper presents a multi-GPU scheduling framework, MICCO, to accelerate contractions for correlation functions particularly by taking the data dimension (e.g., data reuse and data eviction) into account. This work firstmore »performs a comprehensive study on the interplay of data reuse and load balance, and designs two new concepts: local reuse pattern and reuse bound to study the opportunity of achieving the optimal trade-off between them. Based on this study, MICCO proposes a heuristic scheduling algorithm and a machine-learning-based regression model to generate the optimal setting of reuse bounds. Specifically, MICCO is integrated into a real-world Lattice QCD system, Redstar, for the first time running on multiple GPUs. The evaluation demonstrates MICCO outperforms other state-of-art works, achieving up to 2.25× speedup in synthesized datasets, and 1.49× speedup in real-world correlation functions.« less