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This paper initiates the study of I/O algorithms (minimizing cache misses) from the perspective of fine-grained complexity (conditional polynomial lower bounds). Specifically, we aim to answer why sparse graph problems are so hard, and why…
The all-pairs suffix-prefix (APSP) problem is a classical problem in string processing which has important applications in bioinformatics. Given a set $\mathcal{S} = \{S_1, \ldots, S_k\}$ of $k$ strings, the APSP problem asks one to compute…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
This paper presents constant-time and near-constant-time distributed algorithms for a variety of problems in the congested clique model. We show how to compute a 3-ruling set in expected $O(\log \log \log n)$ rounds and using this, we…
One of the most critical problems in the field of string algorithms is the longest common subsequence problem (LCS). The problem is NP-hard for an arbitrary number of strings but can be solved in polynomial time for a fixed number of…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
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…
This paper discusses the odds problem, proposed by Bruss in 2000, and its variants. A recurrence relation called a dynamic programming (DP) equation is used to find an optimal stopping policy of the odds problem and its variants. In 2013,…
Integer Linear Programming with $n$ binary variables and $m$ many $0/1$-constraints can be solved in time $2^{\tilde O(m^2)} \text{poly}(n)$ and it is open whether the dependence on $m$ is optimal. Several seemingly unrelated problems,…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
Integer linear programs $\min\{c^T x : A x = b, x \in \mathbb{Z}^n_{\ge 0}\}$, where $A \in \mathbb{Z}^{m \times n}$, $b \in \mathbb{Z}^m$, and $c \in \mathbb{Z}^n$, can be solved in pseudopolynomial time for any fixed number of constraints…
Since many real-world problems arising in the fields of compiler optimisation, automated software engineering, formal proof systems, and so forth are equivalent to the Halting Problem--the most notorious undecidable problem--there is a…
Subset-Sum is an NP-complete problem where one must decide if a multiset of $n$ integers contains a subset whose elements sum to a target value $m$. The best-known classical and quantum algorithms run in time $\tilde{O}(2^{n/2})$ and…
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…
Non-parametric entropy estimation on sequential data is a fundamental tool in signal processing, capturing information flow within or between processes to measure predictability, redundancy, or similarity. Methods based on longest common…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
In a sequence of recent results (PODC 2015 and PODC 2016), the running time of the fastest algorithm for the \emph{minimum spanning tree (MST)} problem in the \emph{Congested Clique} model was first improved to $O(\log \log \log n)$ from…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
We study the problem of clustering networks whose nodes have imputed or physical positions in a single dimension, for example prestige hierarchies or the similarity dimension of hyperbolic embeddings. Existing algorithms, such as the…