Related papers: Nucleotide String Indexing using Range Matching

Motivation: Building the histogram of occurrences of every $k$-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of $k$-mer counting. Its applications include developing de…

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…

Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…

Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…

Range-based set reconciliation is a simple approach to efficiently computing the union of two sets over a network, based on recursively partitioning the sets and comparing fingerprints of the partitions to probabilistically detect whether a…

Addressing the growing demands of artificial intelligence (AI) and data analytics requires new computing approaches. In this paper, we propose a reconfigurable hardware accelerator designed specifically for AI and data-intensive…

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…

Neuro-encoded expression programming(NEEP) that aims to offer a novel continuous representation of combinatorial encoding for genetic programming methods is proposed in this paper. Genetic programming with linear representation uses…

E-commerce information retrieval (IR) systems struggle to simultaneously achieve high accuracy in interpreting complex user queries and maintain efficient processing of vast product catalogs. The dual challenge lies in precisely matching…

Rank and select data structures seek to preprocess a bit vector to quickly answer two kinds of queries: rank(i) gives the number of 1 bits in slots 0 through i, and select(j) gives the first slot s with rank(s) = j. A succinct data…

Scalable ordered maps must ensure that range queries, which operate over many consecutive keys, provide intuitive semantics (e.g., linearizability) without degrading the performance of concurrent insertions and removals. These goals are…

Accurate and efficient entity resolution (ER) is a significant challenge in many data mining and analysis projects requiring integrating and processing massive data collections. It is becoming increasingly important in real-world…

We introduce \emph{Adaptive RAG Memory} (ARM), a retrieval-augmented generation (RAG) framework that replaces a static vector index with a \emph{dynamic} memory substrate governed by selective remembrance and decay. Frequently retrieved…

Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…

Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…

The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…

Deep Neural Networks are increasingly leveraging sparsity to reduce the scaling up of model parameter size. However, reducing wall-clock time through sparsity and pruning remains challenging due to irregular memory access patterns, leading…

We present bundled references, a new building block to provide linearizable range query operations for highly concurrent linked data structures. Bundled references allow range queries to traverse a path through the data structure that is…