Related papers: Polynomial-Time Solutions for Longest Common Subse…
We initiate the study of a fundamental combinatorial problem: Given a capacitated graph $G=(V,E)$, find a shortest walk ("route") from a source $s\in V$ to a destination $t\in V$ that includes all vertices specified by a set…
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…
How to properly model graphs is a long-existing and important problem in NLP area, where several popular types of graphs are knowledge graphs, semantic graphs and dependency graphs. Comparing with other data structures, such as sequences…
A rerouting sequence is a sequence of shortest st-paths such that consecutive paths differ in one vertex. We study the the Shortest Path Rerouting Problem, which asks, given two shortest st-paths P and Q in a graph G, whether a rerouting…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…
Array-Based Comparative Genomic Hybridization (aCGH) is a method used to search for genomic regions with copy numbers variations. For a given aCGH profile, one challenge is to accurately segment it into regions of constant copy number.…
We raise some questions about graph polynomials, highlighting concepts and phenomena that may merit consideration in the development of a general theory. Our questions are mainly of three types: When do graph polynomials have reduction…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
Many natural computational problems, including e.g. Max Weight Independent Set, Feedback Vertex Set, or Vertex Planarization, can be unified under an umbrella of finding the largest sparse induced subgraph, that satisfies some property…
Many combinatorial optimization problems can be formulated as the search for a subgraph that satisfies certain properties and minimizes the total weight. We assume here that the vertices correspond to points in a metric space and can take…
We introduce loose graph simulations (LGS), a new notion about labelled graphs which subsumes in an intuitive and natural way subgraph isomorphism (SGI), regular language pattern matching (RLPM) and graph simulation (GS). Being a…
The quantum query complexity of subgraph-containment problems, which ask whether a given subgraph $H$ is present in an input graph $G$, has been the subject of considerable study. However, even for relatively simple subgraphs, such as paths…
We construct a polynomial-time algorithm which given a graph $\Gamma$ finds the full set of non-equivalent Cayley representations of $\Gamma$ over the group $D\cong C_p\times C_{p^k}$, where $p\in\{2,3\}$ and $k\geq 1$. This result implies…
Calculating the length of a longest common subsequence (LCS) of two strings $A$ and $B$ of length $n$ and $m$ is a classic research topic, with many worst-case oriented results known. We present two algorithms for LCS length calculation…
A straightforward dynamic programming method for the single-source shortest paths problem (SSSP) in an edge-weighted directed acyclic graph (DAG) processes the vertices in a topologically sorted order. First, we similarly iterate this…
Population-scale pangenome analysis increasingly requires representations that unify single-nucleotide and structural variation while remaining scalable across large cohorts. Existing formats are typically sequence-centric, path-centric, or…
Reconfiguration problems involve determining whether two given configurations can be transformed into each other under specific rules. The Token Sliding problem asks whether, given two different set of tokens on vertices of a graph $G$, we…
We introduce and study the problem of optimizing arbitrary functions over degree sequences of hypergraphs and multihypergraphs. We show that over multihypergraphs the problem can be solved in polynomial time. For hypergraphs, we show that…
In this paper, we show that the solution to a large class of "tiling" problems is given by a polynomial sequence of binomial type. More specifically, we show that the number of ways to place a fixed set of polyominos on an $n\times n$…