11 papers · ranked by Valyu relevance
Fabio Cumbo, Kabir Dhillon, Jayadev Joshi, Davide Chicco + 2 more
Viral species classification is crucial for understanding viral evolution, epidemiology, and developing effective diagnostics and treatments. Traditional methods often rely on sequence similarity, which can be challenging for rapidly evolving viruses. Pangenomes, offering a comprehensive representation of species’…
Anders Høst-Madsen, Jun Zhang
—This paper has dual aims. First is to develop practical universal coding methods for unlabeled graphs. Second is to use these for graph anomaly detection. The paper develops two coding methods for unlabeled graphs: one based on the degree distribution, the second based on the triangle distribution. It is shown that…
Hung T. Nguyen, Pierre Jinghong Liang, Leman Akoglu
Within a large database G containing graphs with labeled nodes and directed, multi-edges; how can we detect the anomalous graphs? Most existing work are designed for plain (unlabeled) and/or simple (unweighted) graphs. We introduce CODEtect, the first approach that addresses the anomaly detection task for graph…
Mojtaba Abolfazli, Anders Høst-Madsen, Jun Zhang, András Bratincsák
—Many multivariate data such as social and biological data exhibit complex dependencies that are best characterized by graphs. Unlike sequential data, graphs are, in general, unordered structures. This means we can no longer use classic, sequential-based compression methods on these graph-based data. Therefore, it is…
Giorgos Bouritsas, Andreas Loukas, Nikolaos Karalias, Michael M. Bronstein
'Michael M. Bronstein'] Can we use machine learning to compress graph data? The absence of ordering in graphs poses a significant challenge to conventional compression algorithms, limiting their attainable gains as well as their ability to discover relevant patterns. On the other hand, most graph compression approaches…
Lloyd Allison
TR #2014/2771 . This report concerns the information content of a graph, optionally conditional on one or more background, "common knowledge" graphs. It describes an algorithm to estimate this information content, and includes some examples based on chemical compounds. keywords: Graph, network, complexity, information…
Md Toki Tahmid, Tanjeem Azwad Zaman, Mohammad Saifur Rahman
Understanding complex graph-structured data is a cornerstone of modern research in fields like cheminformatics and bioinformatics, where molecules and biological systems are naturally represented as graphs. However, traditional graph neural networks (GNNs) often fall short by focusing mainly on node features while…
Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani + 6 more
Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic data sets can be challenging to work at. These challenges have impeded…
Peter Heringer, Daniel Doerr
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly…
Zhiyuan Ding, Alex Baras
Recent advances in computation pathology have seen the development of various forms of foundational models that have enabled high-quality, generalpurpose feature extraction from tissue patches. However, most of these models are somewhat limited in their ability to capture cell-to-cell spatial relationships essential…
Ian T. Hoffecker, Yunshi Yang, Giulio Bernardinelli, Pekka Orponen + 1 more
Barcoded DNA polony amplification techniques provide a means to impart a unique sequence identity onto specific locations of a surface wafer or chip. We describe a method whereby micro-scale spatial information such as the relative positions of biomolecules on a surface can be transferred to a sequence-based format and…