Related papers: A massively parallel algorithm for constructing th…

In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…

The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…

The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the…

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…

Bloom filters are a fundamental data structure for approximate membership queries, with applications ranging from data analytics to databases and genomics. Several variants have been proposed to accommodate parallel architectures. GPUs,…

The Burrows-Wheeler transform (BWT) is used by the bzip2 family of compressors. In this paper, we present a hardware architecture that implements an inplace algorithm to compute the BWT. Our design does not have explicit storage for the…

We present PEANUT (ParallEl AligNment UTility), a highly parallel GPU-based read mapper with several distinguishing features, including a novel q-gram index (called the q-group index) with small memory footprint built on-the-fly over the…

In this paper, we design parallel write-efficient geometric algorithms that perform asymptotically fewer writes than standard algorithms for the same problem. This is motivated by emerging non-volatile memory technologies with read…

Among the many possible approaches for the parallelization of self-organizing networks, and in particular of growing self-organizing networks, perhaps the most common one is producing an optimized, parallel implementation of the standard…

High Bandwidth Memory (HBM) provides massive aggregated memory bandwidth by exposing multiple memory channels to the processing units. To achieve high performance, an accelerator built on top of an FPGA configured with HBM (i.e., FPGA-HBM…

Minimum Spanning Tree (MST) is an important graph algorithm that has wide ranging applications in the areas of computer networks, VLSI routing, wireless communications among others. Today virtually every computer is built out of multi-core…

Graph Neural Networks (GNNs) are powerful deep learning models to generate node embeddings on graphs. When applying deep GNNs on large graphs, it is still challenging to perform training in an efficient and scalable way. We propose a novel…

Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…

We develop and extensively evaluate highly scalable distributed-memory algorithms for computing minimum spanning trees (MSTs). At the heart of our solutions is a scalable variant of Boruvka's algorithm. For partitioned graphs with many…

While Large Language Models (LLMs) have achieved remarkable success in various fields, the efficiency of training and inference remains a major challenge. To address this issue, we propose SUBLLM, short for Subsampling-Upsampling-Bypass…

This article presents a new high-level parallel computational model named BSF - Bulk Synchronous Farm. The BSF model extends the BSP model to deal with the compute-intensive iterative numerical methods executed on distributed-memory…

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…

The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…

The most efficient algorithms for finding maximum independent sets in both theory and practice use reduction rules to obtain a much smaller problem instance called a kernel. The kernel can then be solved quickly using exact or heuristic…

There has been surprisingly little work on algorithms for sorting strings on distributed-memory parallel machines. We develop efficient algorithms for this problem based on the multi-way merging principle. These algorithms inspect only…