Related papers: Practical algorithms for Hierarchical overlap grap…
Graph neural networks (GNNs) have achieved success in various inference tasks on graph-structured data. However, common challenges faced by many GNNs in the literature include the problem of graph node embedding under various geometries and…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
In this paper we raise the question of how to compress sparse graphs. By introducing the idea of redundancy, we find a way to measure the overlap of neighbors between nodes in networks. We exploit symmetry and information by making use of…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
Classification in the dissimilarity space has become a very active research area since it provides a possibility to learn from data given in the form of pairwise non-metric dissimilarities, which otherwise would be difficult to cope with.…
This study presents a hierarchical mining framework for high-dimensional imbalanced data, leveraging a depth graph model to address the inherent performance limitations of conventional approaches in handling complex, high-dimensional data…
A fundamental problem in shape matching and geometric similarity is computing the maximum area overlap between two polygons under translation. For general simple polygons, the best-known algorithm runs in $O((nm)^2 \log(nm))$ time [Mount,…
As a distributed hash table (DHT) routing overlay, Skip Graph is used in a variety of peer-to-peer (P2P) systems including cloud storage, social networks, and search engines. The overlay connectivity of P2P systems is negatively affected by…
Finding an optimal parameter of a black-box function is important for searching stable material structures and finding optimal neural network structures, and Bayesian optimization algorithms are widely used for the purpose. However, most of…
Many real-world data can be represented as heterogeneous graphs with different types of nodes and connections. Heterogeneous graph neural network model aims to embed nodes or subgraphs into low-dimensional vector space for various…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
Given a hypergraph $H$, the Minimum Connectivity Inference problem asks for a graph on the same vertex set as $H$ with the minimum number of edges such that the subgraph induced by every hyperedge of $H$ is connected. This problem has…
In a random intersection graph $G_{n,m,p}$, each of $n$ vertices selects a random subset of a set of $m$ labels by including each label independently with probability $p$ and edges are drawn between vertices that have at least one label in…
We consider the task of drawing a graph on multiple horizontal layers, where each node is assigned a layer, and each edge connects nodes of different layers. Known algorithms determine the orders of nodes on each layer to minimize crossings…
Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large…
Hierarchical clustering is a popular unsupervised data analysis method. For many real-world applications, we would like to exploit prior information about the data that imposes constraints on the clustering hierarchy, and is not captured by…
Scalable addressing of high dimensional constrained combinatorial optimization problems is a challenge that arises in several science and engineering disciplines. Recent work introduced novel application of graph neural networks for solving…
Given a hypergraph, influence maximization (IM) is to discover a seed set containing $k$ vertices that have the maximal influence. Although the existing vertex-based IM algorithms perform better than the hyperedge-based algorithms by…