Related papers: Species Trees Forcing Parsimony to Fail

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…

Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…

Decision tree optimization is fundamental to interpretable machine learning. The most popular approach is to greedily search for the best feature at every decision point, which is fast but provably suboptimal. Recent approaches find the…

The shrinking operation converts a hypergraph into a graph by choosing, from each hyperedge, two endvertices of a corresponding graph edge. A hypertree is a hypergraph which can be shrunk to a tree on the same vertex set. Klimo\v{s}ov\'{a}…

Imagine being able to ask questions to a black box model such as "Which adversarial examples exist?", "Does a specific attribute have a disproportionate effect on the model's prediction?" or "What kind of predictions could possibly be made…

A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…

We show that every connected graph $G$ has a tree decomposition indexed by a tree $T$ such that $T$ is a subgraph of $G$ and the width of the tree decomposition is bounded from above by a function of the pathwidth of $G$. This answers a…

In classification and forecasting with tabular data, one often utilizes tree-based models. Those can be competitive with deep neural networks on tabular data and, under some conditions, explainable. The explainability depends on the depth…

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…

This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…

Let $T$ be a tree on $n$ vertices. We can regard the edges of $T$ as transpositions of the vertex set; their product (in any order) is a cyclic permutation. All possible cyclic permutations arise (each exactly once) if and only if the tree…

The rooted tree is an important data structure, and the subtree size, height, and depth are naturally defined attributes of every node. We consider the problem of the existence of a k-ary tree given a list of attribute sequences. We give…

We prove a lower bound on the number of spanning two-forests in a graph, in terms of the number of vertices, edges, and spanning trees. This implies an upper bound on the average cut size of a random two-forest. The main tool is an identity…

A permutation $\sigma\in\mathfrak{S}_n$ is simsun if for all $k$, the subword of $\sigma$ restricted to $\{1,...,k\}$ does not have three consecutive decreasing elements. The permutation $\sigma$ is double simsun if both $\sigma$ and…

The arboricity $\Gamma(G)$ of an undirected graph $G = (V,E)$ is the minimal number such that $E$ can be partitioned into $\Gamma(G)$ forests. Nash-Williams' formula states that $k = \lceil \gamma(G) \rceil$, where $\gamma(G)$ is the…

In any given machine learning problem, there may be many models that could explain the data almost equally well. However, most learning algorithms return only one of these models, leaving practitioners with no practical way to explore…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

We analyze the trade-off between model complexity and accuracy for random forests by breaking the trees up into individual classification rules and selecting a subset of them. We show experimentally that already a few rules are sufficient…

Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…

In this thesis we consider ordered graphs (that is, graphs with a fixed linear ordering on their vertices). We summarize and further investigations on the number of edges an ordered graph may have while avoiding a fixed forbidden ordered…