Related papers: Fixed-Parameter Algorithms for Longest Heapable Su…
We show how to chain maximal exact matches (MEMs) between a query string $Q$ and a labeled directed acyclic graph (DAG) $G=(V,E)$ to solve the longest common subsequence (LCS) problem between $Q$ and $G$. We obtain our result via a new…
For the well-known Survivable Network Design Problem (SNDP) we are given an undirected graph $G$ with edge costs, a set $R$ of terminal vertices, and an integer demand $d_{s,t}$ for every terminal pair $s,t\in R$. The task is to compute a…
In this paper we improve the approximation ratio for the problem of scheduling packets on line networks with bounded buffers, where the aim is that of maximizing the throughput. Each node in the network has a local buffer of bounded size…
We show an algorithm that, given an $n$-vertex graph $G$ and a parameter $k$, in time $2^{O(k \log k)} n^{O(1)}$ finds a tree decomposition of $G$ with the following properties: * every adhesion of the tree decomposition is of size at most…
A decision problem is called parameterized if its input is a pair of strings. One of these strings is referred to as a parameter. The problem: given a propositional logic program P and a non-negative integer k, decide whether P has a stable…
In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…
The task of finding an extension to a given partial drawing of a graph while adhering to constraints on the representation has been extensively studied in the literature, with well-known results providing efficient algorithms for…
Dynamic programming on path and tree decompositions of graphs is a technique that is ubiquitous in the field of parameterized and exponential-time algorithms. However, one of its drawbacks is that the space usage is exponential in the…
The bandwidth of a $n$-vertex graph $G$ is the smallest integer $b$ such that there exists a bijective function $f : V(G) \rightarrow \{1,...,n\}$, called a layout of $G$, such that for every edge $uv \in E(G)$, $|f(u) - f(v)| \leq b$. In…
A mixed dominating set is a collection of vertices and edges that dominates all vertices and edges of a graph. We study the complexity of exact and parameterized algorithms for \textsc{Mixed Dominating Set}, resolving some open questions.…
Optimal Morse matchings reveal essential structures of cell complexes which lead to powerful tools to study discrete geometrical objects, in particular discrete 3-manifolds. However, such matchings are known to be NP-hard to compute on…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
This paper considers an optimization problem for a dynamical system whose evolution depends on a collection of binary decision variables. We develop scalable approximation algorithms with provable suboptimality bounds to provide…
A DAG compression of a (typically dense) graph is a simple data structure that stores how vertex clusters are connected, where the clusters are described indirectly as sets of reachable sinks in a directed acyclic graph (DAG). They…
Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches…
We study the following general disjoint paths problem: given a supply graph $G$, a set $T\subseteq V(G)$ of terminals, a demand graph $H$ on the vertices $T$, and an integer $k$, the task is to find a set of $k$ pairwise vertex-disjoint…
We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We present deterministic…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…
In this paper we develop optimal algorithms in the binary-forking model for a variety of fundamental problems, including sorting, semisorting, list ranking, tree contraction, range minima, and ordered set union, intersection and difference.…