Related papers: Relaxed Agreement Forests
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
In this paper the minimum spanning tree problem with uncertain edge costs is discussed. In order to model the uncertainty a discrete scenario set is specified and a robust framework is adopted to choose a solution. The min-max, min-max…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Recently, a new vector encoding, Ordered Leaf Attachment (OLA), was introduced that represents $n$-leaf phylogenetic trees as $n-1$ length integer vectors by recording the placement location of each leaf. Both encoding and decoding of trees…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
Sparse residual tree (SRT) is an adaptive exploration method for multivariate scattered data approximation. It leads to sparse and stable approximations in areas where the data is sufficient or redundant, and points out the possible local…
Trust in counterfactual explanations depends critically on whether their recommended changes are truly minimal: suboptimal explanations may vastly overshoot the actual changes needed to alter a decision, and heuristic errors can affect…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
Given a set $P$ of terminals in the plane and a partition of $P$ into $k$ subsets $P_1, ..., P_k$, a two-level rectilinear Steiner tree consists of a rectilinear Steiner tree $T_i$ connecting the terminals in each set $P_i$ ($i=1,...,k$)…
For an $m$-edge connected simple graph $G$, finding a spanning tree of $G$ with the maximum number of leaves is MAXSNP-complete. The problem remains NP-complete even if $G$ is planar and the maximal degree of $G$ is at most four. Lu and…
In this work, we present an $\Omega\left(\min\{\log \Delta, \sqrt{\log n}\}\right)$ lower bound for Maximal Matching (MM) in $\Delta$-ary trees against randomized algorithms. By a folklore reduction, the same lower bound applies to Maximal…
The goal of branch length estimation in phylogenetic inference is to estimate the divergence time between a set of sequences based on compositional differences between them. A number of software is currently available facilitating branch…
We study the robustness verification problem for tree-based models, including decision trees, random forests (RFs) and gradient boosted decision trees (GBDTs). Formal robustness verification of decision tree ensembles involves finding the…
The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification…
Random forest (RF) stands out as a highly favored machine learning approach for classification problems. The effectiveness of RF hinges on two key factors: the accuracy of individual trees and the diversity among them. In this study, we…
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…