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Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…
We present a computational framework for piecewise constant functions (PCFs) and use this for several types of computations that are useful in statistics, e.g., averages, similarity matrices, and so on. We give a linear-time,…
In simultaneous localization and mapping (SLAM), image feature point matching process consume a lot of time. The capacity of low-power systems such as embedded systems is almost limited. It is difficult to ensure the timely processing of…
Approximate dictionary matching is a classic string matching problem (checking if a query string occurs in a collection of strings) with applications in, e.g., spellchecking, online catalogs, geolocation, and web searchers. We present a…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
In recent years, Discriminative Correlation Filter (DCF) based methods have significantly advanced the state-of-the-art in tracking. However, in the pursuit of ever increasing tracking performance, their characteristic speed and real-time…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
We study the allocation problem in the Massively Parallel Computation (MPC) model. This problem is a special case of $b$-matching, in which the input is a bipartite graph with capacities greater than $1$ in only one part of the bipartition.…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
Sorted lists of integers are commonly used in inverted indexes and database systems. They are often compressed in memory. We can use the SIMD instructions available in common processors to boost the speed of integer compression schemes. Our…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we…
Traditional Von Neumann computing is falling apart in the era of exploding data volumes as the overhead of data transfer becomes forbidding. Instead, it is more energy-efficient to fuse compute capability with memory where the data reside.…
Matched filters are widely used to localise signal patterns due to their high efficiency and interpretability. However, their effectiveness deteriorates for low signal-to-noise ratio (SNR) signals, such as those recorded on edge devices,…
In this paper, we consider the patient similarity matching problem over a cancer cohort of more than 220,000 patients. Our approach first leverages on Word2Vec framework to embed ICD codes into vector-valued representation. We then propose…
Counting the number of ones in a binary stream is a common operation in database, information-retrieval, cryptographic and machine-learning applications. Most processors have dedicated instructions to count the number of ones in a word…
Exact substring matching is a common task in many software applications. Despite the existence of several algorithms for finding whether or not a pattern string is present in a target string, the most common implementation is a na\"ive,…
We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized…
This paper presents implementation details and empirical results for a hybrid message passing and shared memory paralleliziation of the adaptive integral method (AIM). AIM is implemented on a (near) petaflop supercomputing cluster of…