Related papers: Phylogenetic tree calculations using the Grid with…

Causal DAGs(Directed Acyclic Graphs) are usually considered in a 2D plane. Edges indicate causal effects' directions and imply their corresponding time-passings. Due to the natural restriction of statistical models, effect estimation is…

Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…

With the rapid advancement of Artificial Intelligence, the Graphics Processing Unit (GPU) has become increasingly essential across a growing number of safety-critical application domains. Applying a GPU is indispensable for parallel…

Counting and uniform sampling of directed acyclic graphs (DAGs) from a Markov equivalence class are fundamental tasks in graphical causal analysis. In this paper, we show that these tasks can be performed in polynomial time, solving a…

We study the problem of broadcasting packets in wireless networks. At each time slot, a network controller activates non-interfering links and forwards packets to all nodes at a common rate; the maximum rate is referred to as the broadcast…

Weighted graphs are ubiquitous throughout biology, chemistry, and the social sciences, motivating the development of generative models for abstract weighted graph data using deep neural networks. However, most current deep generative models…

The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…

Our goal is to infer the topology of a network when (i) we can send probes between sources and receivers at the edge of the network and (ii) intermediate nodes can perform simple network coding operations, i.e., additions. Our key intuition…

Directed acyclic graphs (DAGs) are central to science and engineering applications including causal inference, scheduling, and neural architecture search. In this work, we introduce the DAG Convolutional Network (DCN), a novel graph neural…

Extracting signals through alpha factor mining is a fundamental challenge in quantitative finance. Existing automated methods primarily follow two paradigms: Decoupled Factor Generation, which treats factor discovery as isolated events, and…

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…

Directed Acyclic Graphs (DAGs) are widely used to represent structured knowledge in scientific and technical domains. However, datasets for real-world DAGs remain scarce because constructing them typically requires expert interpretation of…

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that…

Directed acyclic graphs (DAGs) constitute a central modeling tool to enable principled reasoning about cause-effect interactions in complex systems. However, since the causal structure underlying a group of variables is often unknown and…

We establish a novel framework for learning a directed acyclic graph (DAG) when data are generated from a Gaussian, linear structural equation model. It consists of two parts: (1) introduce a permutation matrix as a new parameter within a…

We describe a new paradigm for implementing inference in belief networks, which consists of two steps: (1) compiling a belief network into an arithmetic expression called a Query DAG (Q-DAG); and (2) answering queries using a simple…

In this paper, we study classes of graphs with three types of edges that capture the modified independence structure of a directed acyclic graph (DAG) after marginalisation over unobserved variables and conditioning on selection variables…

The search space of Bayesian Network structures is usually defined as Acyclic Directed Graphs (DAGs) and the search is done by local transformations of DAGs. But the space of Bayesian Networks is ordered by DAG Markov model inclusion and it…

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package…