Related papers: On Longest Repeat Queries Using GPU
We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution…
In the reordering buffer management problem, a sequence of requests must be executed by a service station, where a cost occurs for each pair of consecutive requests with different attributes. A reordering buffer management algorithm aims to…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
Local search is a successful approach for solving combinatorial optimization and constraint satisfaction problems. With the progressing move toward multi and many-core systems, GPUs and the quest for Exascale systems, parallelism has become…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
This paper investigates the usage of FPGA devices for energy-efficient exact kNN search in high-dimension latent spaces. This work intercepts a relevant trend that tries to support the increasing popularity of learned representations based…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
While well-known methods to list the intersections of either a list of segments or a complex polygon aim at achieving optimal time-complexity they often do so at the cost of memory comsumption and complex code. Real-life software…
We consider computing a longest palindrome in the streaming model, where the symbols arrive one-by-one and we do not have random access to the input. While computing the answer exactly using sublinear space is not possible in such a…
Recurrent neural networks (RNNs) have shown outstanding performance on processing sequence data. However, they suffer from long training time, which demands parallel implementations of the training procedure. Parallelization of the training…
The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…
In this paper we solve on GPUs massive problems with large amount of data, which are not appropriate for solution with the SIMD technology. For the given problem we consider a three-level parallelization. The multithreading of CPU is used…
As the size of artificial intelligence and machine learning (AI/ML) models and datasets grows, the memory bandwidth becomes a critical bottleneck. The paper presents a novel extended memory hierarchy that addresses some major memory…
In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…
Recurrent Neural Networks (RNNs) are powerful tools for solving sequence-based problems, but their efficacy and execution time are dependent on the size of the network. Following recent work in simplifying these networks with model pruning…
Graphics Processing Units (GPUs) with high computational capabilities used as modern parallel platforms to deal with complex computational problems. We use this platform to solve large-scale linear programing problems by revised simplex…
We propose a fast, parallel maximum clique algorithm for large sparse graphs that is designed to exploit characteristics of social and information networks. The method exhibits a roughly linear runtime scaling over real-world networks…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…