Related papers: Isomorphic unordered labeled trees up to substitut…
We study three different kinds of embeddings of tree patterns: weakly-injective, ancestor-preserving, and lca-preserving. While each of them is often referred to as injective embedding, they form a proper hierarchy and their computational…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
A routing labeling scheme assigns a binary string, called a label, to each node in a network, and chooses a distinct port number from $\{1,\ldots,d\}$ for every edge outgoing from a node of degree $d$. Then, given the labels of $u$ and $w$…
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 $X$…
Graph Isomorphism (GI) is a fundamental algorithmic problem. Amongst graph classes for which the computational complexity of GI has been resolved, trees are arguably the most fundamental. Tree Isomorphism is complete for deterministic…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
The Graph Isomorphism problem restricted to graphs of bounded treewidth or bounded tree distance width are known to be solvable in polynomial time [Bod90],[YBFT99]. We give restricted space algorithms for these problems proving the…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
A foundational question in the theory of linear compartmental models is how to assess whether a model is structurally identifiable -- that is, whether parameter values can be inferred from noiseless data -- directly from the combinatorics…
We solve the subgraph isomorphism problem in planar graphs in linear time, for any pattern of constant size. Our results are based on a technique of partitioning the planar graph into pieces of small tree-width, and applying dynamic…
Sturmian words are infinite binary words with many equivalent definitions: They have a minimal factor complexity among all aperiodic sequences; they are balanced sequences (the labels 0 and 1 are as evenly distributed as possible) and they…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
We study the problem of learning a hierarchical tree representation of data from labeled samples, taken from an arbitrary (and possibly adversarial) distribution. Consider a collection of data tuples labeled according to their hierarchical…
Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
Integrated interpretability without sacrificing the prediction accuracy of decision making algorithms has the potential of greatly improving their value to the user. Instead of assigning a label to an image directly, we propose to learn…
In the theoretical study of distributed communication networks, "history trees" are a discrete structure that naturally models the concept that anonymous agents become distinguishable upon receiving different sets of messages from…
We estimate the size of a labelled tree by comparing the amount of (labelled) nodes with the size of the set of labels. Roughly speaking, a exponentially big labelled tree, is any labelled tree that has an exponential gap between its size,…
We study a class of combinatorial objects that we call "decorated trees". These consist of vertices, arrows and edges, where each edge is decorated by two integers (one near each of its endpoints), each arrow is decorated by an integer, and…
We consider sequences of finite weighted random graphs that converge locally to unimodular i.i.d. weighted random trees. When the weights are atomless, we prove that the matchings of maximal weight converge locally to a matching on the…