Related papers: External memory BWT and LCP computation for sequen…

We present a work-efficient parallel level-synchronous Breadth First Search (BFS) algorithm for shared-memory architectures which achieves the theoretical lower bound on parallel running time. The optimality holds regardless of the shape of…

The BDD package Adiar manipulates Binary Decision Diagrams (BDDs) in external memory. This enables handling big BDDs, but the performance suffers when dealing with moderate-sized BDDs. This is mostly due to initializing expensive external…

We describe a model that enables us to analyze the running time of an algorithm in a computer with a memory hierarchy with limited associativity, in terms of various cache parameters. Our model, an extension of Aggarwal and Vitter's I/O…

The problem of finding the longest common subsequence (LCS) for a set of sequences is a very interesting and challenging problem in computer science. This problem is NP-complete, but because of its importance, many heuristic algorithms have…

Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…

Much research has been devoted to optimizing algorithms of the Lempel-Ziv (LZ) 77 family, both in terms of speed and memory requirements. Binary search trees and suffix trees (ST) are data structures that have been often used for this…

Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…

At CPM 2017, Castelli et al. define and study a new variant of the Longest Common Subsequence Problem, termed the Longest Filled Common Subsequence Problem (LFCS). For the LFCS problem, the input consists of two strings $A$ and $B$ and a…

We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…

This paper introduces a novel approach, the Bounded-Cache Transformer (BCT), for building large language models with a predefined Key-Value (KV) cache capacity. The BCT addresses the excessive memory consumption issue in traditional KV…

Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…

We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…

As the performance gap between memory and processors has increased, then it leads to the poor performance. Efficient virtual memory can overcome this problem. And the efficiency of virtual memory depends on the replacement policy used for…

As the gap between compute and I/O performance tends to grow, modern High-Performance Computing (HPC) architectures include a new resource type: an intermediate persistent fast memory layer, called burst buffers. This is just one of many…

When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…

This paper presents a novel outer approximation algorithm for nonsmooth mixed-integer nonlinear programming (MINLP) problems. The method proceeds by fixing the integer variables and solving the resulting nonlinear convex subproblem. When…

Recurrent neural networks have achieved excellent performance in many applications. However, on portable devices with limited resources, the models are often too large to deploy. For applications on the server with large scale concurrent…

Transformers have reached remarkable success in sequence modeling. However, these models have efficiency issues as they need to store all the history token-level representations as memory. We present Memformer, an efficient neural network…

In a variety of applications, we need to keep track of the development of a data set over time. For maintaining and querying this multi version data I/O-efficiently, external memory data structures are required. In this paper, we present a…

In recent years we have witnessed an increase on the development of methods for submodular optimization, which have been motivated by the wide applicability of submodular functions in real-world data-science problems. In this paper, we…