Related papers: Phylogenetic tree calculations using the Grid with…

Existing score-based methods for directed acyclic graph (DAG) learning from observational data struggle to recover the causal graph accurately and sample-efficiently. To overcome this, in this study, we propose DrBO (DAG recovery via…

In this paper, we propose a novel inference method for dynamic genetic networks which makes it possible to face with a number of time measurements n much smaller than the number of genes p. The approach is based on the concept of low order…

We propose a new differentiable probabilistic model over DAGs (DP-DAG). DP-DAG allows fast and differentiable DAG sampling suited to continuous optimization. To this end, DP-DAG samples a DAG by successively (1) sampling a linear ordering…

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…

Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…

We establish finite-sample guarantees for a polynomial-time algorithm for learning a nonlinear, nonparametric directed acyclic graphical (DAG) model from data. The analysis is model-free and does not assume linearity, additivity,…

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…

Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…

To represent the causal relationships between variables, a directed acyclic graph (DAG) is widely utilized in many areas, such as social sciences, epidemics, and genetics. Many causal structure learning approaches are developed to learn the…

We study a generalization of the well-known model of broadcasting on trees. Consider a directed acyclic graph (DAG) with a unique source vertex $X$, and suppose all other vertices have indegree $d\geq 2$. Let the vertices at distance $k$…

Learning the causal structure that underlies data is a crucial step towards robust real-world decision making. The majority of existing work in causal inference focuses on determining a single directed acyclic graph (DAG) or a Markov…

Random directed acyclic graphs (DAGs) based on imposing an order on Erd\H{o}s-R\'enyi and scale free random graphs are widely used for evaluating causal discovery algorithms. We show that in such DAGs, the set of nodes reachable via open…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a…

Learning the structure of directed acyclic graphs (DAGs) from observational data is a central problem in causal discovery, statistical signal processing, and machine learning. Under a linear Gaussian structural equation model (SEM) with…

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…

Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…

Estimating the structure of directed acyclic graphs (DAGs) from observational data remains a significant challenge in machine learning. Most research in this area concentrates on learning a single DAG for the entire population. This paper…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…