Related papers: Internal Pattern Matching in Small Space and Appli…
Contrast pattern mining (CPM) aims to discover patterns whose support increases significantly from a background dataset compared to a target dataset. CPM is particularly useful for characterising changes in evolving systems, e.g., in…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
Given a string $T$ of length $n$, a substring $u = T[i..j]$ of $T$ is called a shortest unique substring (SUS) for an interval $[s,t]$ if (a) $u$ occurs exactly once in $T$, (b) $u$ contains the interval $[s,t]$ (i.e. $i \leq s \leq t \leq…
Given a set $\Pi$ of permutation patterns of length at most $k$, we present an algorithm for building $S_{\le n}(\Pi)$, the set of permutations of length at most $n$ avoiding the patterns in $\Pi$, in time $O(|S_{\le n - 1}(\Pi)| \cdot k +…
Sequential pattern mining (SPM) has excellent prospects and application spaces and has been widely used in different fields. The non-overlapping SPM, as one of the data mining techniques, has been used to discover patterns that have…
We study integer linear programs (ILP) of the form $\min\{c^\top x\ \vert\ Ax=b,l\le x\le u,x\in\mathbb Z^n\}$ and analyze their parameterized complexity with respect to their distance to the generalized matching problem, following the…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
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…
The Permutation Pattern Matching problem, asking whether a pattern permutation $\pi$ is contained in a permutation $\tau$, is known to be NP-complete. In this paper we present two polynomial time algorithms for special cases. The first…
The goal of data selection is to capture the most structural information from a set of data. This paper presents a fast and accurate data selection method, in which the selected samples are optimized to span the subspace of all data. We…
We introduce a data structure for counting pattern occurrences in texts compressed with any run-length context-free grammar. Our structure uses space proportional to the grammar size and counts the occurrences of a pattern of length $m$ in…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
We study the complexity of the decision problem known as Permutation Pattern Matching, or PPM. The input of PPM consists of a pair of permutations $\tau$ (the `text') and $\pi$ (the `pattern'), and the goal is to decide whether $\tau$…
Analog Ising machines (IMs) occupy an increasingly prominent area of computer architecture research, offering high-quality and low latency/energy solutions to intractable computing tasks. However, IMs have a fixed capacity, with little to…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
We study regular expression membership testing: Given a regular expression of size $m$ and a string of size $n$, decide whether the string is in the language described by the regular expression. Its classic $O(nm)$ algorithm is one of the…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
We study the classic set cover problem in the streaming model: the sets that comprise the instance are revealed one by one in a stream and the goal is to solve the problem by making one or few passes over the stream while maintaining a…