Related papers: Reflections on kernelizing and computing unrooted …
We consider the well-studied problem of finding a spanning tree with minimum average distance between vertex pairs (called a MAD tree). This is a classic network design problem which is known to be NP-hard. While approximation algorithms…
Computing the rotation distance between two binary trees with $n$ internal nodes efficiently (in $poly(n)$ time) is a long standing open question in the study of height balancing in tree data structures. In this paper, we initiate the study…
Several novel mixed-integer linear and bilinear formulations are proposed for the optimum communication spanning tree problem. They implement the distance-based approach: graph distances are directly modeled by continuous, integral, or…
Machine learning is increasingly used to guide branch-and-cut (B&C) for mixed-integer linear programming by learning score-based policies for selecting branching variables and cutting planes. Many approaches train on local signals from…
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,…
We propose to prune a random forest (RF) for resource-constrained prediction. We first construct a RF and then prune it to optimize expected feature cost & accuracy. We pose pruning RFs as a novel 0-1 integer program with linear constraints…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
We study efficient preprocessing for the undirected Feedback Vertex Set problem, a fundamental problem in graph theory which asks for a minimum-sized vertex set whose removal yields an acyclic graph. More precisely, we aim to determine for…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
Computing the similarity between two data points plays a vital role in many machine learning algorithms. Metric learning has the aim of learning a good metric automatically from data. Most existing studies on metric learning for…
This paper investigates the a-posteriori analysis of Branch-and-Bound~(BB) trees to extract structural information about the feasible region of mixed-binary linear programs. We introduce three novel outer approximations of the feasible…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Retrieving relevant targets from an extremely large target set under computational limits is a common challenge for information retrieval and recommendation systems. Tree models, which formulate targets as leaves of a tree with trainable…
Given a digraph $D$, the Minimum Leaf Out-Branching problem (MinLOB) is the problem of finding in $D$ an out-branching with the minimum possible number of leaves, i.e., vertices of out-degree 0. We prove that MinLOB is polynomial-time…
We propose a novel architecture for Graph Neural Networks that is inspired by the idea behind Tree Kernels of measuring similarity between trees by taking into account their common substructures, named fragments. By imposing a series of…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…