27 papers · ranked by Valyu relevance
Evangelia Tsoukanara, Georgia Koloniari, Evaggelia Pitoura
In this paper, we focus on temporal property graphs, that is, property graphs whose labeled nodes and edges as well as the values of the properties associated with them may change with time. For instance, consider a bibliographic network, with nodes representing authors and conferences with properties such as gender…
Changmin Wu, Giannis Nikolentzos, Michalis Vazirgiannis
Neural networks for structured data like graphs have been studied extensively in recent years. To date, the bulk of research activity has focused mainly on static graphs. However, most real-world networks are dynamic since their topology tends to change over time. Predicting the evolution of dynamic graphs is a task of…
Evangelia Tsoukanara, Georgia Koloniari, Evaggelia Pitoura
Graphs offer a generic abstraction for modeling entities, and the interactions and relationships between them. Most real world graphs, such as social and cooperation networks evolve over time, and exploring their evolution may reveal important information. In this paper, we present TempoG-RAPHer, a system for…
Junya Wang, Yi-Jiao Zhang, Cong Xu, Jiaze Li + 5 more
The evolution processes of complex systems carry key information in the systems’ functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be extracted, including protein-protein interaction, ecology, and social network…
Leonid Bunimovich, Benjamin Webb
We introduce a method that can be used to evolve the topology of a network in a way that preserves both the network's spectral as well as local structure. This method is quite versatile in the sense that it can be used to evolve a network's topology over any collection of the network's elements. This evolution…
Xue Liu, Dan Sun, Wei Wei, Zhiming Zheng
—Autonomous individuals establish a structural complex system through pairwise connections and interactions. Notably, the evolution reflects the dynamic nature of each complex system since it recodes a series of temporal changes from the past, the present into the future. Different systems follow distinct evolutionary…
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…
Amit Verma, Manjish Pal
—A social network grows over a period of time with the formation of new connections and relations. In recent years we have witnessed a massive growth of online social networks like Facebook, Twitter etc. So it has become a problem of extreme importance to know the destiny of these networks. Thus predicting the…
Yang Ping Kuo, Oana Carja
To design population topologies that can accelerate rates of solution discovery in directed evolution problems or in evolutionary optimization applications, we must first systematically understand how population structure shapes evolutionary outcome. Using the mathematical formalism of evolutionary graph theory, recent…
Badhan Das, Lenwood S. Heath, Anna Bernasconi
The SARS-CoV-2 virus has undergone extensive mutations over time, resulting in considerable genetic diversity among circulating strains. This diversity directly affects important viral characteristics, such as transmissibility and disease severity. During a viral outbreak, the rapid mutation rate produces a large cloud…
Pedro J. Zufiria, Iker Barriales-Valbuena
Time evolving Random Network Models are presented as a mathematical framework for modelling and analyzing the evolution of complex networks. This framework allows the analysis over time of several network characterizing features such as link density, clustering coefficient, degree distribution, as well as entropy-based…
Nikhil Sharma, Suman G. Das, Joachim Krug, Arne Traulsen
Birth-death models have long been employed to understand the interplay of genetic drift and natural selection. While well-mixed populations remain unaffected by the choice of replacement rules, the evolutionary outcomes in spatially structured populations are strongly impacted by this choice. Moving parent individuals…
Badhan Das, Lenwood S. Heath
The SARS-CoV-2 virus has undergone mutations over time, leading to genetic diversity among circulating viral strains. This genetic diversity can affect the characteristics of the virus, including its transmissibility and the severity of symptoms in infected individuals. During the pandemic, this frequent mutation…
Saket Navlakha, Carl Kingsford, Joel S. Bader
What proteins interacted in a long-extinct ancestor of yeast? How have different members of a protein complex assembled together over time? Our ability to answer such questions has been limited by the unavailability of ancestral protein-protein interaction (PPI) networks. To overcome this limitation, we propose several…
Yang Ping Kuo, César Nombela Arrieta, Oana Carja
Understanding how the spatial arrangement of a population shapes its evolutionary dynamics has been of long-standing interest in population genetics. Most previous studies assume a small number of demes connected by migration corridors, symmetrical structures that most often act as well-mixed populations. Other studies…
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…
Abhinav Tamaskar, Bud Mishra
We present two main contributions which help us in leveraging the theory of graphons for modeling evolutionary processes. We show a generative model for digraphons using a finite basis of subgraphs, which is representative of biological networks with evolution by duplication[20]. We show a simple MAP estimate on the…
Sedigheh Yagoobi, Nikhil Sharma, Arne Traulsen
The structure of a population strongly influences its evolutionary dynamics. In various settings ranging from biology to social systems, individuals tend to interact more often with those present in their proximity and rarely with those far away. A common approach to model the structure of a population is Evolutionary…
Hirotaka Matsumoto, Motomu Matsui
With the determination of numerous viral and bacterial genome sequences, phylogeny-trait associations are now being studied. In these studies, phylogenetic trees were first reconstructed, and trait data were analyzed based on the reconstructed tree. However, in some cases, such as fast evolution sequences and…
Vaibhav Rajan, Carl Kingsford, Xiuwei Zhang
The study of the evolutionary history of biological networks enables deep functional understanding of various bio-molecular processes. Network growth models, such as the Duplication-Mutation with Complementarity (DMC) model, provide a principled approach to characterizing the evolution of protein-protein interactions…
Matthew Bailey, Mark Wilson
One of the critical tools of persistent homology is the persistence diagram. We demonstrate the applicability of a persistence diagram showing the existence of topological features (here rings in a 2D network) generated over time instead of space as a tool to analyse trajectories of biological networks. We show how the…
Francisco Herrerías-Azcué, Vicente Pérez-Muñuzuri, Tobias Galla, Natalia L. Komarova
'Natalia L. Komarova'] Seemingly minor details of mathematical and computational models of evolution are known to change the effect of population structure on the outcome of evolutionary processes. For example, birth-death dynamics often result in amplification of selection, while death-birth processes have been…
Alexander Smith, Spencer Runde, Alex Chew, Atharva Kelkar + 3 more
Molecular dynamics (MD) simulations are used in diverse scientific and engineering fields such as drug discovery, materials design, separations, biological systems, and reaction engineering. These simulations generate highly complex datasets that capture the 3D spatial positions, dynamics, and interactions of thousands…
Lionel Zoubritzky, François-Xavier Coudert
We present here an open-source Julia library for the topological identification of crystalline materials, with algorithmic and computational improvements over the previously available software in the field, resulting in a speed increase of one order of magnitude. This new algorithm and implementation can therefore be…
Authors not listed
SynTemp is a framework designed to extract and hierarchically cluster reaction templates from large-scale reaction data repositories. Reaction templates are partial Imaginary Transition State graphs representing the reaction center as well as surrounding context. These graphs are equivalent to Double Pushout graph…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Michael Statt, Brian Rohr, Dan Guevarra, Ja'Nya Breeden + 2 more
Materials knowledge is inherently hierarchical. While high-level descriptors such as composition and structure are valuable for contextualizing materials data, the data must ultimately be considered in the context of its low-level acquisition details. Graph databases offer an opportunity to represent hierarchical…