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…
Yazheng Liu, Xi Zhang, Sihong Xie
Graphs Authors: ['Yazheng Liu' 'Xi Zhang' 'Sihong Xie'] Graphs are ubiquitous in social networks and biochemistry, where Graph Neural Networks (GNN) are the state-of-the-art models for prediction. Graphs can be evolving and it is vital to formally model and understand how a trained GNN responds to graph evolution. We…
William Cappelletti, Étienne Voutaz, Pascal Frossard
Traditional change point detection in dynamic networks assumes abrupt transitions between stationary states, overlooking scenarios of continuous evolution which arise in most real-world applications, such as social networks or physical systems. We address this gap by formally defining regimes as periods of coherent…
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…
Carlos A. Alfaro, Juan Pablo Serrano, Ralihe R. Villagrán
The Abelian sandpile model was the first example of a self-organized critical system studied by Bak, Tang and Wiesenfeld. The dynamics of the sandpiles occur when the grains topple over a graph. In this study, we allow the graph to evolve over time and change the topology at each stage. This turns out in the occurrence…
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…
Yang Ping Kuo, Oana Carja, Christian Hilbe
To design population topologies that can accelerate rates of solution discovery in directed evolution problems or for evolutionary optimization applications, we must first systematically understand how population structure shapes evolutionary outcome. Using the mathematical formalism of evolutionary graph theory…
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…
Deukryeol Yoon, Dongjin Lee, Minyoung Choe, Kijung Shin
Counting the instances of each graphlet (i.e., an induced subgraph isomorphism class) has been successful in characterizing local structures of graphs, with many applications. While graphlets have been extended for temporal graphs, the extensions are designed for examining temporally-local subgraphs composed of edges…
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…
Nikhil Sharma, Suman G. Das, Joachim Krug, Arne Traulsen
Birth-death models are used to understand the interplay of genetic drift and natural selection. While well-mixed populations remain unaffected by the order of birth and death and where selection acts, evolutionary outcomes in spatially structured populations are affected by these choices. We show that the choice of…
Junya Wang, Yi-Jiao Zhang, Cong Xu, Jiaze Li + 5 more
'Jiarong Xie' 'Ling Feng' 'Tianshou Zhou' 'Yanqing Hu'] 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…
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…
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…
Mahdi Hajihashemi
Path of Fixation in evolutionary process highly depends on structure of underlying population. In this paper, we apply a machine learning method to predict the path of fixation in several complex graphs and two regular graphs. In our approach, the path of fixation is not used as the target variable in the machine…
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…
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…
Yang Ping Kuo, César Nombela-Arrieta, Oana Carja
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 or symmetrical structures that, most often, act as well-mixed populations. Other studies use network theory to study more…
Yang Ping Kuo, Oana Carja
Spatially-resolved datasets are revolutionizing knowledge in molecular biology, yet are under-utilized for questions in evolutionary biology. To gain insight from these large-scale datasets of spatial organization, we need mathematical representations and modeling techniques that can both capture their complexity, but…
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…
Authors not listed
Identifying synthesis routes from knowledge graphs poses challenges beyond retrosynthesis, including path–finding artifacts and data issues. We introduce “SynGPS”, a novel algorithm that overcomes these limitations by identifying viable routes even with common artifacts. SynGPS can resolve nonsensical cycles…
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…