Related papers: Determining distances and consensus between mutati…
The minimum linear arrangement problem on a network consists of finding the minimum sum of edge lengths that can be achieved when the vertices are arranged linearly. Although there are algorithms to solve this problem on trees in polynomial…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
We study how to utilize (possibly erroneous) predictions in a model for computing under uncertainty in which an algorithm can query unknown data. Our aim is to minimize the number of queries needed to solve the minimum spanning tree…
We consider the message complexity of verifying whether a given subgraph of the communication network forms a tree with specific properties both in the KT-$\rho$ (nodes know their $\rho$-hop neighborhood, including node IDs) and the KT-$0$…
Topological structures such as the merge tree provide an abstract and succinct representation of scalar fields. They facilitate effective visualization and interactive exploration of feature-rich data. A merge tree captures the topology of…
The decision tree recursively partitions the input space into regions and derives axis-aligned decision boundaries from data. Despite its simplicity and interpretability, decision trees lack parameterized representation, which makes it…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
Results for estimating the convergence rate of non-stationary distributed consensus algorithms are provided, on the basis of qualitative (mainly topological) as well as basic quantitative information (lower-bounds on the matrix entries).…
The analysis of the internal structure of trees is highly important for both forest experts, biological scientists, and the wood industry. Traditionally, CT-scanners are considered as the most efficient way to get an accurate inner…
Physical phenomena in science and engineering are frequently modeled using scalar fields. In scalar field topology, graph-based topological descriptors such as merge trees, contour trees, and Reeb graphs are commonly used to characterize…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
Several real-world and abstract structures and systems are characterized by marked hierarchy to the point of being expressed as trees. Because the study of these entities often involves sampling (or discovering) the tree nodes in a specific…
CONTEXT. Attack treesare a recommended threat modeling tool, but there is no established method to compare them. OBJECTIVE. We aim to establish a method to compare "real" attack trees, based on both the structure of the tree itself and the…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
We present improved learning-augmented algorithms for finding an approximate minimum spanning tree (MST) for points in an arbitrary metric space. Our work follows a recent framework called metric forest completion (MFC), where the learned…
Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type. One of the main goals in analyzing these mutations is the identification of mutations associated…
In this paper we study several problems concerning the number of homomorphisms of trees. We give an algorithm for the number of homomorphisms from a tree to any graph by the Transfer-matrix method. By using this algorithm and some…
We establish maximal trees and graphs for the difference of average distance and proximity proving thus the corresponding conjecture posed in [4]. We also establish maximal trees for the difference of average eccentricity and remoteness and…
Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet most reconstruction methods like ML do not explicitly maximize this accuracy. To address this problem, we propose a…