28 papers · ranked by Valyu relevance
Van Thuy Hoang, Hyeon-Ju Jeon, Eun-Soon You, Yoewon Yoon + 3 more
Graphs are data structures that effectively represent relational data in the real world. Graph representation learning is a significant task since it could facilitate various downstream tasks, such as node classification, link prediction, etc. Graph representation learning aims to map graph entities to low-dimensional…
Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth + 3 more
'David Broneske' 'Gunter Saake' 'Robert Heyer'] Title: Abstract The increasing amount and complexity of clinical data require an appropriate way of storing and analyzing those data. Traditional approaches use a tabular structure (relational databases) for storing data and thereby complicate storing and retrieving…
Dongqi Fu, Jingrui He
Graph structures have attracted much research attention for carrying complex relational information. Based on graphs, many algorithms and tools are proposed and developed for dealing with real-world tasks such as recommendation, fraud detection, molecule design, etc. In this paper, we first discuss three topics of…
Plácido A. Souza Neto
In the context of the DOING project, funded by APR-IA and based in the Val de Loire region of France, we've been developing a methodology (pipeline) to extract meaningful information from graph data. So, this work was funded by the DOING project. Our primary goal is to structure this information into a graph database…
Sotirios Panagiotis Chytas, Rudrasis Chakraborty, Vikas Singh
Recent results show that modern Large Language Models (LLM) are indeed capable of understanding and answering questions about structured data such as graphs. This new paradigm can lead to solutions that require less supervision while, at the same time, providing a model that can generalize and answer questions beyond…
Akhil Pandey Akella
Dimensionality reduction techniques map data represented on higher dimensions onto lower dimensions with varying degrees of information loss. Graph dimensionality reduction techniques adopt the same principle of providing latent representations of the graph structure with minor adaptations to the output representations…
Atsushi Yokoyama
In this paper, we propose a new type of graph, denoted as "embedded-graph", and its theory, which employs a distributed representation to describe the relations on the graph edges. Embedded-graphs can express linguistic and complicated relations, which cannot be expressed by the existing edge-graphs or weighted-graphs.…
Ping Yang, E. Adrian Henle, Xiaoli Fern, Cory M. Simon
Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are agriculturally and ecologically vital as pollinators. The development of new pesticides---driven by pest resistance to and demands to reduce negative environmental impacts of…
Tom C. Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee + 5 more
Quantitative and qualitative data derived from the analysis of genomes, genes, proteins or metabolites from tissue or cells are currently generated in huge volumes during biomedical research. Graphia is an open-source platform created for the graph-based analysis of such complex data, e.g. transcriptomics, proteomics…
Ine Melckenbeeck, Pieter Audenaert, Tom Michoel, Didier Colle + 2 more
'Mario Pickavet' 'Yongtang Shi'] Graphlets are small subgraphs, usually containing up to five vertices, that can be found in a larger graph. Identification of the graphlets that a vertex in an explored graph touches can provide useful information about the local structure of the graph around that vertex. Actually…
Authors not listed
Computational methods for predictive modeling have been increasingly utilized in the early stages of drug discovery to supplement high-throughput screening. The advent of highly efficient and complex machine learning architectures necessitates new methods of collating the plethora of topological, geometrical, and…
Ragini Kihlman, Ilkka Launonen, Mikko J Sillanpää, Patrik Waldmann + 1 more
'D-J de Koning'] Title: Abstract In genomics, use of deep learning (DL) is rapidly growing and DL has successfully demonstrated its ability to uncover complex relationships in large biological and biomedical data sets. With the development of high-throughput sequencing techniques, genomic markers can now be allocated…
Fawaz Dabbaghie
The representation of genomes and genomic sequences through graph structures has undergone a period of rapid development in recent years, particularly to accommodate the growing size of genome sequences that are being produced. Genome graphs have been employed extensively for a variety of purposes, including assembly…
Maryam Mohsenivatani, Samad Ali, Vismika Ranasinghe, Nandana Rajatheva + 1 more
'Nandana Rajatheva' 'Matti Latva‐aho'] Abstract—Wireless networks are inherently graph-structured, which can be utilized in graph representation learning to solve complex wireless network optimization problems. In graph representation learning, feature vectors for each entity in the network are calculated such that…
Zachary Humphreys, Xenophon Evangelopoulos, Stavros Gerolymatos, Edward O. Pyzer-Knapp + 1 more
Graph neural networks have recently met huge success in various inference tasks including materials property prediction amongst many others. Nevertheless, having an inherently locally-based representation capacity as they do, global representation of materials' structures can only only be achieved by expanding the…
Authors not listed
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…
Maxim Kolomeets, Vasily Desnitsky, Igor Kotenko, Andrey Chechulin + 3 more
'Brij B. Gupta' 'Guangtao Zhai' 'Alicia García-Holgado'] Currently, the methods and means of human-machine interaction and visualization as its integral part are being increasingly developed. In various fields of scientific knowledge and technology, there is a need to find and select the most effective visualization…
Wim Martens, Matthias Niewerth, Tina Popp, Stijn Vansummeren + 1 more
'Domagoj Vrgoč'] Modern graph database query languages such as GQL, SQL/PGQ, and their academic predecessor G-Core promote paths to first-class citizens in the sense that paths that match regular path queries can be returned to the user. This brings a number of challenges in terms of efficiency, caused by the fact that…
Sergey Kitaev
Letters x and y alternate in a word w if after deleting in w all letters but the copies of x and y we either obtain a word xyxy · · · (of even or odd length) or a word yxyx · · · (of even or odd length). A graph G = (V, E) is word-representable if and only if there exists a word w over the alphabet V such that letters…
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…
Mustafa Coşkun, Mehmet Koyutürk
Link prediction is an important and well-studied problem in computational biology, with a broad range of applications including disease gene prioritization, drug-disease associations, and drug response in cancer. The general principle in link prediction is to use the topological characteristics and the attributes–if…
Michael Hutcheon, Andrew Teale
Algorithms are presented for performing a topological analysis of an arbitrary function, evaluated on an arbitrary grid of points. These algorithms work strictly by post-processing the data and require no additional function evaluations. This is achieved by connecting the grid points with a neighbourhood graph…
Diane Duroux, Kristel Van Steen
Many problems in life sciences can be brought back to a comparison of graphs. Even though a multitude of such techniques exist, often, these assume prior knowledge about the partitioning or the number of clusters and fail to provide statistical significance of observed between-network heterogeneity. Addressing these…
Sergey Kitaev, Yangjing Long, Jun Ma, Hehui Wu
Letters x and y alternate in a word w if after deleting in w all letters but the copies of x and y we either obtain a word xyxy · · · (of even or odd length) or a word yxyx · · · (of even or odd length). A graph G = (V, E) is word-representable if and only if there exists a word w over the alphabet V such that letters…
Srijani Bagchi, Anasua Sarkar, Ujjwal Maulik
In times like this, it is imperative to be cautious about the effects of drugs or vaccination doses on patients who are already suffering from other serious diseases. It’s not only the virus which can affect the body metabolisms, drugs to encounter the virus may also end up having unwanted negative effects. Therapeutic…
Authors not listed
We present a unified, set–theoretic framework that extends molecular graphs to hypergraphs and superhypergraphs via iterated power sets. We define Molecular Graphs, Molecular HyperGraphs, and Molecular SuperHyperGraphs, and develop four complements over them: Weighted, Rough, Neural, and Multipolar frameworks. We prove…
Joshua Levy, Carly Bobak, Brock Christensen, Louis Vaickus + 1 more
Network analysis methods are useful to better understand and contextualize relationships between entities. While statistical and machine learning prediction models generally assume independence between actors, network-based statistical methods for social network data allow for dyadic dependence between actors. While…
Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck
The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of…