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We present an approach for efficiently taking snapshots of the state of a collection of CAS objects. Taking a snapshot allows later operations to read the value that each CAS object had at the time the snapshot was taken. Taking a snapshot…
We study the problem of finding maximal exact matches (MEMs) between a query string $Q$ and a labeled graph $G$. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their…
We consider the problem of implementing a space-efficient dynamic trie, with an emphasis on good practical performance. For a trie with $n$ nodes with an alphabet of size $\sigma$, the information-theoretic lower bound is $n \log \sigma +…
The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
This paper proposed a storing approach for trie structures, called coordinate hash trie. The basic idea is using a global hash table with a special hash function to store all edges of a trie. For a trie with $n$ nodes and an alphabet with…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
Hashing is one of the most popular methods for similarity search because of its speed and efficiency. Dense binary hashing is prevalent in the literature. Recently, insect olfaction was shown to be structurally and functionally analogous to…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…
Tensor network methods provide a scalable solution to represent high-dimensional data. However, their efficacy is often limited by static, expert-defined structures that fail to adapt to evolving data correlations. We address this…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
Stereo matching is the key step in estimating depth from two or more images. Recently, some tree-based non-local stereo matching methods have been proposed, which achieved state-of-the-art performance. The algorithms employed some tree…
We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…
Tree projections provide a unifying framework to deal with most structural decomposition methods of constraint satisfaction problems (CSPs). Within this framework, a CSP instance is decomposed into a number of sub-problems, called views,…
As a fundamental issue in network analysis, structural node similarity has received much attention in academia and is adopted in a wide range of applications. Among these proposed structural node similarity measures, role similarity stands…
We describe a substring search problem that arises in group presentation simplification processes. We suggest a two-level searching model: skip and match levels. We give two timestamp algorithms which skip searching parts of the text where…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
The convolution between a text string $S$ of length $N$ and a pattern string $P$ of length $m$ can be computed in $O(N \log m)$ time by FFT. It is known that various types of approximate string matching problems are reducible to…