Related papers: A Fast Generic Sequence Matching Algorithm
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
In high-dimensional generalized linear models, it is crucial to identify a sparse model that adequately accounts for response variation. Although the best subset section has been widely regarded as the Holy Grail of problems of this type,…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…
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…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
The classical pattern matching paradigm is that of seeking occurrences of one string - the pattern, in another - the text, where both strings are drawn from an alphabet set $\Sigma$. Assuming the text length is $n$ and the pattern length is…
Schema matching is the process of identifying correspondences between the elements of two given schemata, essential for database management systems, data integration, and data warehousing. For datasets across different scenarios, the…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
Subgraph matching is a compute-intensive problem that asks to enumerate all the isomorphic embeddings of a query graph within a data graph. This problem is generally solved with backtracking, which recursively evolves every possible partial…
We introduce string2string, an open-source library that offers a comprehensive suite of efficient algorithms for a broad range of string-to-string problems. It includes traditional algorithmic solutions as well as recent advanced neural…
Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
Quantum computation represents a computational paradigm whose distinctive attributes confer the ability to devise algorithms with asymptotic performance levels significantly superior to those achievable via classical computation. Recent…
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…