Related papers: Polynomial-Time Solutions for Longest Common Subse…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Directed acyclic graphs (DAGs) are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical, as well as biological systems, where directed edges…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…
The problem of extending partial geometric graph representations such as plane graphs has received considerable attention in recent years. In particular, given a graph $G$, a connected subgraph $H$ of $G$ and a drawing $\mathcal{H}$ of $H$,…
The problem of finding multiple simple shortest paths in a weighted directed graph $G=(V,E)$ has many applications, and is considerably more difficult than the corresponding problem when cycles are allowed in the paths. Even for a single…
The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…
We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph $H$ to $n$-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…
Amiri and Wargalla (2020) proved the following local-to-global theorem in directed acyclic graphs (DAGs): if $G$ is a weighted DAG such that for each subset $S$ of 3 nodes there is a shortest path containing every node in $S$, then there…
We give the first polynomial-time algorithms on graphs of bounded maximum induced matching width (mim-width) for problems that are not locally checkable. In particular, we give $n^{\mathcal{O}(w)}$-time algorithms on graphs of mim-width at…
We present the first polynomial-time approximation schemes (PTASes) for the following subset-connectivity problems in edge-weighted graphs of bounded genus: Steiner tree, low-connectivity survivable-network design, and subset TSP. The…
The even cycle problem for both undirected and directed graphs has been the topic of intense research in the last decade. In this paper, we study the computational complexity of \emph{cycle length modularity problems}. Roughly speaking, in…
Graph representation learning is a fundamental problem for modeling relational data and benefits a number of downstream applications. Traditional Bayesian-based graph models and recent deep learning based GNN either suffer from…
The problem of finding longest common subsequence (LCS) is one of the fundamental problems in computer science, which finds application in fields such as computational biology, text processing, information retrieval, data compression etc.…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph nodes. A recent breakthrough…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
The clique-width is a measure of complexity of decomposing graphs into certain tree-like structures. The class of graphs with bounded clique-width contains bounded tree-width graphs. We give a polynomial time graph isomorphism algorithm for…
Bayesian networks are probabilistic graphical models with a wide range of application areas including gene regulatory networks inference, risk analysis and image processing. Learning the structure of a Bayesian network (BNSL) from discrete…