Related papers: Computing the original eBWT faster, simpler, and w…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
In 1994, Burrows and Wheeler developed a data compression algorithm which performs significantly better than Lempel-Ziv based algorithms. Since then, a lot of work has been done in order to improve their algorithm, which is based on a…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…
In this paper, we propose a new method for calculating the output layer in neural machine translation systems. The method is based on predicting a binary code for each word and can reduce computation time/memory requirements of the output…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
The emergence of large language models (LLMs) like GPT-4 has revolutionized natural language processing (NLP), enabling diverse, complex tasks. However, extensive token counts lead to high computational and financial burdens. To address…
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts…
Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
The Burrows-Wheeler-Transform (BWT) is an invertible permutation of a text known to be highly compressible but also useful for sequence analysis, what makes the BWT highly attractive for lossless data compression. In this paper, we present…
We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma * n) + o(\log \sigma * \sigma * n)$ bits of space. This is done by replacing the…
We present the first linear time algorithm to construct the $2n$-bit version of the Lyndon array for a string of length $n$ using only $o(n)$ bits of working space. A simpler variant of this algorithm computes the plain ($n\lg n$-bit)…
We consider the problem of finding repetitive structures and inherent patterns in a given string $\s{s}$ of length $n$ over a finite totally ordered alphabet. A border $\s{u}$ of a string $\s{s}$ is both a prefix and a suffix of $\s{s}$…
Large language models (LLMs) have shown remarkable progress in code generation, but their generated code often suffers from inefficiency, resulting in longer execution times and higher memory consumption. To address this issue, we propose…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…
Transformer-based models, exemplified by GPT-3, ChatGPT, and GPT-4, have recently garnered considerable attention in both academia and industry due to their promising performance in general language tasks. Nevertheless, these models…
We show the formal equivalence of linearised self-attention mechanisms and fast weight controllers from the early '90s, where a ``slow" neural net learns by gradient descent to program the ``fast weights" of another net through sequences of…
In neural machine translation (NMT), it is has become standard to translate using subword units to allow for an open vocabulary and improve accuracy on infrequent words. Byte-pair encoding (BPE) and its variants are the predominant approach…
Background: Baum-Welch training is an expectation-maximisation algorithm for training the emission and transition probabilities of hidden Markov models in a fully automated way. Methods and results: We introduce a linear space algorithm for…