Related papers: ERA: Efficient Serial and Parallel Suffix Tree Con…

This paper introduces new algorithms and data structures for quick counting for machine learning datasets. We focus on the counting task of constructing contingency tables, but our approach is also applicable to counting the number of…

Adders are fundamental building blocks in modern digital systems, and their performance, power, and area (PPA) directly impact system efficiency. Contemporary adders typically use parallel-prefix architectures with established PPA…

The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an…

The Suffix Array SA(S) of a string S[1 ... n] is an array containing all the suffixes of S sorted by lexicographic order. The suffix array is one of the most well known indexing data structures, and it functions as a key tool in many string…

In this paper, we introduce zip-tries, which are simple, dynamic, memory-efficient data structures for strings. Zip-tries support search and update operations for $k$-length strings in $\mathcal{O}(k+\log n)$ time in the standard RAM model…

We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem…

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…

We present an algorithm for parallelising the TreePM code. We use both functional and domain decompositions. Functional decomposition is used to separate the computation of long range and short range forces, as well as the task of…

We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…

Across a wide range of hardware scenarios, the computational efficiency and physical size of the arithmetic units significantly influence the speed and footprint of the overall hardware system. Nevertheless, the effectiveness of prior…

Tree-based models underpin many modern semantic search engines and recommender systems due to their sub-linear inference times. In industrial applications, these models operate at extreme scales, where every bit of performance is critical.…

Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…

Modern deep learning models have high memory and computation cost. To make them fast and memory-cost efficient, structured model pruning is commonly used. We find that pruning a model using a common training accelerator with large systolic…

Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…

We describe a parallel version of our tree-code for the simulation of self-gravitating systems in Astrophysics. It is based on a dynamic and adaptive method for the domain decomposition, which exploits the hierarchical data arrangement used…

Huge DBMSs storing genomic information are being created and engineerized for doing large-scale, comprehensive and in-depth analysis of human beings and their diseases. However, recent regulations like the GDPR require that sensitive data…

This paper presents a fully synthesizable, treebased Address-Event Representation (AER) encoder designed for scalable neuromorphic computing systems. To achieve high throughput while maintaining strict compatibility with commercial EDA…

Graph-based Retrieval-Augmented Generation (Graph-RAG) enhances large language models (LLMs) by structuring retrieval over an external corpus. However, existing approaches typically assume a static corpus, requiring expensive full-graph…

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…

Indexes provide a method to access data in databases quickly. It can improve the response speed of subsequent queries by building a complete index in advance. However, it also leads to a huge overhead of the continuous updating during…