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We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
A resolving set $S$ of a graph $G$ is a subset of its vertices such that no two vertices of $G$ have the same distance vector to $S$. The Metric Dimension problem asks for a resolving set of minimum size, and in its decision form, a…
Depth first search (DFS) tree is a fundamental data structure for solving various problems in graphs. It is well known that it takes $O(m+n)$ time to build a DFS tree for a given undirected graph $G=(V,E)$ on $n$ vertices and $m$ edges. We…
We introduce the concept of Most, and Least, Compact Spanning Trees - denoted respectively by $T^*(G)$ and $T^\#(G)$ - of a simple, connected, undirected and unweighted graph $G(V, E, W)$. For a spanning tree $T(G) \in \mathcal{T}(G)$ to be…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
The Tree Evaluation Problem ($\mathsf{TreeEval}$) is a computational problem originally proposed as a candidate to prove a separation between complexity classes $\mathsf{P}$ and $\mathsf{L}$. Recently, this problem has gained significant…
We study two fundamental decremental dynamic graph problems. In both problems, we need to maintain a vertex-weighted forest of size $n$ under edge deletions, weight updates, and a certain information-retrieval query. Both problems can be…
We present a simple $O(n^4)$-time algorithm for computing optimal search trees with two-way comparisons. The only previous solution to this problem, by Anderson et al., has the same running time, but is significantly more complicated and is…
When using graph transformation rules to implement graph algorithms, a challenge is to match the efficiency of programs in conventional languages. To help overcome that challenge, the graph programming language GP 2 features rooted rules…
The study of structural graph width parameters like tree-width, clique-width and rank-width has been ongoing during the last five decades, and their algorithmic use has also been increasing [Cygan et al., 2015]. New width parameters…
An $\alpha$-thin tree $T$ of a graph $G$ is a spanning tree such that every cut of $G$ has at most an $\alpha$ proportion of its edges in $T$. The Thin Tree Conjecture proposes that there exists a function $f$ such that for any $\alpha >…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
An algorithm on weighted graphs is called universally optimal if it is optimal for every input graph, in the worst case taken over all weight assignments. Informally, this means the algorithm is competitive even with algorithms that are…
We present two new and efficient algorithms for computing all-pairs shortest paths. The algorithms operate on directed graphs with real (possibly negative) weights. They make use of directed path consistency along a vertex ordering d. Both…
An algorithm is developed for finding a close to optimal junction tree of a given graph G. The algorithm has a worst case complexity O(c^k n^a) where a and c are constants, n is the number of vertices, and k is the size of the largest…
For many algorithmic problems on graphs of treewidth $t$, a standard dynamic programming approach gives an algorithm with time and space complexity $2^{\mathcal{O}(t)}\cdot n^{\mathcal{O}(1)}$. It turns out that when one considers the more…
The minimum degree spanning tree (MDST) problem requires the construction of a spanning tree $T$ for graph $G=(V,E)$ with $n$ vertices, such that the maximum degree $d$ of $T$ is the smallest among all spanning trees of $G$. In this paper,…