Related papers: Practical colinear chaining on sequences revisited
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
The {\it matrix-chain multiplication} problem is a classic problem that is widely taught to illustrate dynamic programming. The textbook solution runs in $\theta(n^3)$ time. However, there is a complex $O(n \log n)$-time method \cite{HU82},…
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…
In this paper we describe COLIN, a forward-chaining heuristic search planner, capable of reasoning with COntinuous LINear numeric change, in addition to the full temporal semantics of PDDL. Through this work we make two advances to the…
We provide a deterministic algorithm that outputs an $O(n^{3/4} \log n)$-approximation for the Longest Common Subsequence (LCS) of two input sequences of length $n$ in near-linear time. This is the first deterministic approximation…
In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…
The product of a matrix chain consisting of $n$ matrices can be computed in $C_{n-1}$ (Catalan's number) different ways, each identified by a distinct parenthesisation of the chain. The best algorithm to select a parenthesisation that…
Longest common extension queries (LCE queries) and runs are ubiquitous in algorithmic stringology. Linear-time algorithms computing runs and preprocessing for constant-time LCE queries have been known for over a decade. However, these…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
We present the first $\mathrm{o}(n)$-space polynomial-time algorithm for computing the length of a longest common subsequence. Given two strings of length $n$, the algorithm runs in $\mathrm{O}(n^{3})$ time with $\mathrm{O}\left(\frac{n…
We consider the classic problem of computing the Longest Common Subsequence (LCS) of two strings of length $n$. While a simple quadratic algorithm has been known for the problem for more than 40 years, no faster algorithm has been found…
We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. Several classical textbook algorithms have quite efficient expected-runtime complexity, whereas…
Monotonicity is a simple yet significant qualitative characteristic. We consider the problem of segmenting a sequence in up to K segments. We want segments to be as monotonic as possible and to alternate signs. We propose a quality metric…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
Correlation clustering is arguably the most natural formulation of clustering. Given n objects and a pairwise similarity measure, the goal is to cluster the objects so that, to the best possible extent, similar objects are put in the same…
The generalized egg dropping problem is a classic challenge in sequential decision-making. Standard dynamic programming evaluates the minimax minimum number of tests in $\mathcal{O}(K \cdot N^2)$ time. A known approach formulates the…
Markov chain methods are remarkably successful in computational physics, machine learning, and combinatorial optimization. The cost of such methods often reduces to the mixing time, i.e., the time required to reach the steady state of the…
Canonical orderings [STOC'88, FOCS'92] have been used as a key tool in graph drawing, graph encoding and visibility representations for the last decades. We study a far-reaching generalization of canonical orderings to non-planar graphs…