相关论文: Inferring DAGs and Phylogenetic Networks from Leas…
Rooted phylogenetic networks, or more generally, directed acyclic graphs (DAGs), are widely used to model species or gene relationships that traditional rooted trees cannot fully capture, especially in the presence of reticulate processes…
Directed acyclic graphs (DAGs) are fundamental structures used across many scientific fields. A key concept in DAGs is the least common ancestor (LCA), which plays a crucial role in understanding hierarchical relationships. Surprisingly…
The AP-LCA problem asks, given an $n$-node directed acyclic graph (DAG), to compute for every pair of vertices $u$ and $v$ in the DAG a lowest common ancestor (LCA) of $u$ and $v$ if one exists. In this paper we study several interesting…
We explore the connections between clusters and least common ancestors (LCAs) in directed acyclic graphs (DAGs), focusing on the interplay between so-called $I$-lca-relevant DAGs and DAGs with the $I$-lca-property. Here, $I$ denotes a set…
We investigate the connections between clusters and least common ancestors (LCAs) in directed acyclic graphs (DAGs). We focus on the class of DAGs having unique least common ancestors for certain subsets of their minimal elements since…
Let $G=(V,E)$ be an $n$-vertex directed acyclic graph (DAG). A lowest common ancestor (LCA) of two vertices $u$ and $v$ is a common ancestor $w$ of $u$ and $v$ such that no descendant of $w$ has the same property. In this paper, we consider…
Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…
Phylogenetic networks provide a framework for representing evolutionary histories involving reticulate events such as hybridization or horizontal gene transfer. A central problem is to infer such networks from local structural information.…
We define and study analogs of probabilistic tree embedding and tree cover for directed graphs. We define the notion of a DAG cover of a general directed graph $G$: a small collection $D_1,\dots D_g$ of DAGs so that for all pairs of…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
A DAG compression of a (typically dense) graph is a simple data structure that stores how vertex clusters are connected, where the clusters are described indirectly as sets of reachable sinks in a directed acyclic graph (DAG). They…
A directed acyclic graph (DAG) partially represents the conditional independence structure among observations of a system if the local Markov condition holds, that is, if every variable is independent of its non-descendants given its…
Let $T$ be a rooted tree in which a set $M$ of vertices are marked. The lowest common ancestor (LCA) of $M$ is the unique vertex $\ell$ with the following property: after failing (i.e., deleting) any single vertex $x$ from $T$, the root…
In this work, we present a neural approach to reconstructing rooted tree graphs describing hierarchical interactions, using a novel representation we term the Lowest Common Ancestor Generations (LCAG) matrix. This compact formulation is…
A growing body of work has begun to study intervention design for efficient structure learning of causal directed acyclic graphs (DAGs). A typical setting is a causally sufficient setting, i.e. a system with no latent confounders, selection…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
A directed acyclic graph (DAG) is the most common graphical model for representing causal relationships among a set of variables. When restricted to using only observational data, the structure of the ground truth DAG is identifiable only…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
The recent works on causal discovery have followed a similar trend of learning partial ancestral graphs (PAGs) since observational data constrain the true causal directed acyclic graph (DAG) only up to a Markov equivalence class. This…
The Maximum Leaf Spanning Arborescence problem (MLSA) is defined as follows: Given a directed graph $G$ and a vertex $r\in V(G)$ from which every other vertex is reachable, find a spanning arborescence rooted at $r$ maximizing the number of…