Related papers: Using Minimum Path Cover to Boost Dynamic Programm…
Bayesian networks represent relations between variables using a directed acyclic graph (DAG). Learning the DAG is an NP-hard problem and exact learning algorithms are feasible only for small sets of variables. We propose two scalable…
Causal structure learning, also known as causal discovery, aims to estimate causal relationships between variables as a form of a causal directed acyclic graph (DAG) from observational data. One of the major frameworks is the order-based…
Consider the execution of a sequential algorithm that requires the program to converge to an optimal state, and then terminate/stutter. To design such an algorithm, we need to ensure that the state space that it traverses forms a directed…
Directed Acylic Graphs with a single entry vertex and a single exit vertex (st-DAGs) have many applications. For instance, they are frequently used for modelling flow problems or precedence conditions among tasks, work packages, etc.. This…
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…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Graph Neural Networks (GNNs) are powerful deep learning models to generate node embeddings on graphs. When applying deep GNNs on large graphs, it is still challenging to perform training in an efficient and scalable way. We propose a novel…
Learning causal relationships between variables is a fundamental task in causal inference and directed acyclic graphs (DAGs) are a popular choice to represent the causal relationships. As one can recover a causal graph only up to its Markov…
Recent advances have established the identifiability of a directed acyclic graph (DAG) under additive noise models (ANMs), spurring the development of various causal discovery methods. However, most existing methods make restrictive model…
Estimating the structure of directed acyclic graphs (DAGs) of features (variables) plays a vital role in revealing the latent data generation process and providing causal insights in various applications. Although there have been many…
Given $n$ points in the plane, we propose algorithms to compile connected crossing-free geometric graphs into directed acyclic graphs (DAGs). The DAGs allow efficient counting, enumeration, random sampling, and optimization. Our algorithms…
Dense subgraph extraction is a fundamental problem in graph analysis and data mining, aimed at identifying cohesive and densely connected substructures within a given graph. It plays a crucial role in various domains, including social…
Learning directed acyclic graphs (DAGs) from data is a challenging task both in theory and in practice, because the number of possible DAGs scales superexponentially with the number of nodes. In this paper, we study the problem of learning…
In the $k$-Disjoint Shortest Paths ($k$-DSP) problem, we are given a weighted graph $G$ on $n$ nodes and $m$ edges with specified source vertices $s_1, \dots, s_k$, and target vertices $t_1, \dots, t_k$, and are tasked with determining if…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying local rearrangements to move a tree through its space as a…
This paper considers fully dynamic graph algorithms with both faster worst case update time and sublinear space. The fully dynamic graph connectivity problem is the following: given a graph on a fixed set of n nodes, process an online…
Graph embedding algorithms are used to efficiently represent (encode) a graph in a low-dimensional continuous vector space that preserves the most important properties of the graph. One aspect that is often overlooked is whether the graph…
The Graph Convolutional Network (GCN) model and its variants are powerful graph embedding tools for facilitating classification and clustering on graphs. However, a major challenge is to reduce the complexity of layered GCNs and make them…
We propose a general method for combinatorial online learning problems whose offline optimization problem can be solved efficiently via a dynamic programming algorithm defined by an arbitrary min-sum recurrence. Examples include online…