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Direct Multisearch (DMS) is a Derivative-free Optimization class of algorithms suited for computing approximations to the complete Pareto front of a given Multiobjective Optimization problem. It has a well-supported convergence analysis and…

Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and…

Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for…

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…

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…

This PhD thesis summarizes research works on the design of exact algorithms that provide a worst-case (time or space) guarantee for NP-hard scheduling problems. Both theoretical and practical aspects are considered with three main results…

In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…

Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…

Performance tools for emerging heterogeneous exascale platforms must address two principal challenges when analyzing execution measurements. First, measurement of large-scale executions may record mountains of performance data. Second,…

Mixed-precision algorithms have been proposed as a way for scientific computing to benefit from some of the gains seen for artificial intelligence (AI) on recent high performance computing (HPC) platforms. A few applications dominated by…

Advances in life sciences over the last few decades have lead to the generation of a huge amount of biological data. Computing research has become a vital part in driving biological discovery where analysis and categorization of biological…

With multi-core processors a ubiquitous building block of modern supercomputers, it is now past time to enable applications to embrace these developments in processor design. To achieve exascale performance, applications will need ways of…

More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…

The approximate minimum degree algorithm is widely used before numerical factorization to reduce fill-in for sparse matrices. While considerable attention has been given to the numerical factorization process, less focus has been placed on…

In this paper, we present a fast and strong neural approach for general purpose text matching applications. We explore what is sufficient to build a fast and well-performed text matching model and propose to keep three key features…

OpenMP has been the de facto standard for single node parallelism for more than a decade. Recently, asynchronous many-task runtime (AMT) systems have increased in popularity as a new programming paradigm for high performance computing…

The growing demands of processing massive datasets have promoted irresistible trends of running machine learning applications on MapReduce. When processing large input data, it is often of greater values to produce fast and accurate enough…

String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…

Streaming graphs are drawing increasing attention in both academic and industrial communities as many graphs in real applications evolve over time. Continuous subgraph matching (shorted as CSM) aims to report the incremental matches of a…

We present the submatrix method, a highly parallelizable method for the approximate calculation of inverse p-th roots of large sparse symmetric matrices which are required in different scientific applications. We follow the idea of…