Related papers: Fast Exact String to D-Texts Alignments
Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
Despite the ability to produce human-level speech for in-domain text, attention-based end-to-end text-to-speech (TTS) systems suffer from text alignment failures that increase in frequency for out-of-domain text. We show that these failures…
In this paper, we present a fast and strong neural approach for general purpose text matching applications. We explore what is sufficient to build a fast and well-performed text matching model and propose to keep three key features…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
We study the problem of synthesizing string to string transformations from a set of input/output examples. The transformations we consider are expressed using deterministic finite automata (DFA) that read pairs of letters, one letter from…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
We present SentAlign, an accurate sentence alignment tool designed to handle very large parallel document pairs. Given user-defined parameters, the alignment algorithm evaluates all possible alignment paths in fairly large documents of…
We present Dynamic Skill Adaptation (DSA), an adaptive and dynamic framework to adapt novel and complex skills to Large Language Models (LLMs). Compared with previous work which learns from human-curated and static data in random orders, we…
We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
We discuss two classes of exact (in $\a'$) string solutions described by conformal sigma models. They can be viewed as two possibilities of constructing a conformal model out of the non-conformal one based on the metric of a $D$-dimensional…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
In this paper, we propose Dynamic Self-Attention (DSA), a new self-attention mechanism for sentence embedding. We design DSA by modifying dynamic routing in capsule network (Sabouretal.,2017) for natural language processing. DSA attends to…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…