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

In recent years the Cache-Oblivious model of external memory computation has provided an attractive theoretical basis for the analysis of algorithms on massive datasets. Much progress has been made in discovering algorithms that are…

Memory-augmented neural networks consisting of a neural controller and an external memory have shown potentials in long-term sequential learning. Current RAM-like memory models maintain memory accessing every timesteps, thus they do not…

In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…

Suffix arrays and LCP arrays are one of the most fundamental data structures widely used for various kinds of string processing. We consider two problems for a read-only string of length $N$ over an integer alphabet $[1, \dots, \sigma]$ for…

In the area of Pattern Recognition and Matching, finding a Longest Common Subsequence plays an important role. In this paper, we have proposed one algorithm based on parallel computation. We have used OpenMP API package as middleware to…

For many algorithmic problems, traditional algorithms that optimise on the number of instructions executed prove expensive on I/Os. Novel and very different design techniques, when applied to these problems, can produce algorithms that are…

We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…

We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce computational costs when the input is…

We propose a novel approach to reduce memory consumption of the backpropagation through time (BPTT) algorithm when training recurrent neural networks (RNNs). Our approach uses dynamic programming to balance a trade-off between caching of…

The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…

Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…

For decades, computing the LZ factorization (or LZ77 parsing) of a string has been a requisite and computationally intensive step in many diverse applications, including text indexing and data compression. Many algorithms for LZ77 parsing…

A major limitation of exact inference algorithms for probabilistic graphical models is their extensive memory usage, which often puts real-world problems out of their reach. In this paper we show how we can extend inference algorithms,…

A priority queue is a fundamental data structure that maintains a dynamic set of (key, priority)-pairs and supports Insert, Delete, ExtractMin and DecreaseKey operations. In the external memory model, the current best priority queue…

Recent neural network models for algorithmic tasks have led to significant improvements in extrapolation to sequences much longer than training, but it remains an outstanding problem that the performance still degrades for very long or…

Effective attention modules have played a crucial role in the success of Transformer-based large language models (LLMs), but the quadratic time and memory complexities of these attention modules also pose a challenge when processing long…

Clustering is an unsupervised learning technique in which data or objects are grouped into sets based on some similarity measure. Most of the clustering algorithms assume that the main memory is infinite and can accommodate the set of…

We consider the dictionary problem in external memory and improve the update time of the well-known buffer tree by roughly a logarithmic factor. For any \lambda >= max {lg lg n, log_{M/B} (n/B)}, we can support updates in time O(\lambda /…

The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…

Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…