Related papers: Fast Arc-Annotated Subsequence Matching in Linear …
In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…
The area of sublinear algorithms have recently received a lot of attention. In this setting, one has to choose specific access model for the input, as the algorithm does not have time to pre-process or even to see the whole input. A…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
Real-time analysis of graphs containing temporal information, such as social media streams, Q&A networks, and cyber data sources, plays an important role in various applications. Among them, detecting patterns is one of the fundamental…
It is well-known that checking whether a given string $w$ matches a given regular expression $r$ can be done in quadratic time $O(|w|\cdot |r|)$ and that this cannot be improved to a truly subquadratic running time of $O((|w|\cdot…
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
In this work we describe an Adaptive Regularization using Cubics (ARC) method for large-scale nonconvex unconstrained optimization using Limited-memory Quasi-Newton (LQN) matrices. ARC methods are a relatively new family of optimization…
We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
The Transformer architecture, underpinned by the self-attention mechanism, has become the de facto standard for sequence modeling tasks. However, its core computational primitive scales quadratically with sequence length (O(N^2)), creating…
Range Minimum Query (RMQ) is an important building brick of many compressed data structures and string matching algorithms. Although this problem is essentially solved in theory, with sophisticated data structures allowing for constant time…
Given a large data graph, trimming techniques can reduce the search space by removing vertices without outgoing edges. One application is to speed up the parallel decomposition of graphs into strongly connected components (SCC…
Learning to remember long sequences remains a challenging task for recurrent neural networks. Register memory and attention mechanisms were both proposed to resolve the issue with either high computational cost to retain memory…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
Recently, span-based constituency parsing has achieved competitive accuracies with extremely simple models by using bidirectional RNNs to model "spans". However, the minimal span parser of Stern et al (2017a) which holds the current state…
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
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…