Related papers: Simplifying and Characterizing DAGs and Phylogenet…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
We propose a method to identify nonlinear acyclic networks in continuous time when the dynamics are located on the edges and all the nodes are excited. We show that it is necessary and sufficient to measure all the sinks to identify any…
We describe a new paradigm for implementing inference in belief networks, which relies on compiling a belief network into an arithmetic expression called a Query DAG (Q-DAG). Each non-leaf node of a Q-DAG represents a numeric operation, a…
Causal DAGs (also known as Bayesian networks) are a popular tool for encoding conditional dependencies between random variables. In a causal DAG, the random variables are modeled as vertices in the DAG, and it is stipulated that every…
Enumerating the directed acyclic graphs (DAGs) of a Markov equivalence class (MEC) is an important primitive in causal analysis. The central resource from the perspective of computational complexity is the delay, that is, the time an…
We establish a new framework for statistical estimation of directed acyclic graphs (DAGs) when data are generated from a linear, possibly non-Gaussian structural equation model. Our framework consists of two parts: (1) inferring the…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Bayesian causal discovery offers the power to quantify epistemic uncertainties among a broad range of structurally diverse causal theories potentially explaining the data, represented in forms of directed acyclic graphs (DAGs). However,…
To date, most directed acyclic graphs (DAGs) structure learning approaches require data to be stored in a central server. However, due to the consideration of privacy protection, data owners gradually refuse to share their personalized raw…
Learning the structure of causal directed acyclic graphs (DAGs) is useful in many areas of machine learning and artificial intelligence, with wide applications. However, in the high-dimensional setting, it is challenging to obtain good…
To measure the tree-likeness of a directed acyclic graph (DAG), a new width parameter that considers the directions of the arcs was recently introduced: scanwidth. We present the first algorithm that efficiently computes the exact scanwidth…
Context-specific Bayesian networks (i.e. directed acyclic graphs, DAGs) identify context-dependent relationships between variables, but the non-convexity induced by the acyclicity requirement makes it difficult to share information between…
This paper presents the current state of the art on attack and defense modeling approaches that are based on directed acyclic graphs (DAGs). DAGs allow for a hierarchical decomposition of complex scenarios into simple, easily understandable…
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…
We present practical linear and almost linear-time algorithms to compute a chain decomposition of a directed acyclic graph (DAG), $G=(V,E)$. The number of vertex-disjoint chains computed is very close to the minimum. The time complexity of…
Acyclic model, often depicted as a directed acyclic graph (DAG), has been widely employed to represent directional causal relations among collected nodes. In this article, we propose an efficient method to learn linear non-Gaussian DAG in…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
New biological assays like Perturb-seq link highly parallel CRISPR interventions to a high-dimensional transcriptomic readout, providing insight into gene regulatory networks. Causal gene regulatory networks can be represented by directed…
Learning directed acyclic graphs (DAGs) is long known a critical challenge at the core of probabilistic and causal modeling. The NoTears approach of (Zheng et al., 2018), through a differentiable function involving the matrix exponential…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…