15 papers · ranked by Valyu relevance
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…
Raghvendra Mall, Rocco Langone, Johan A. K. Suykens, Renaud Lambiotte
'Renaud Lambiotte'] Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time.…
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais + 2 more
'Saket Navlakha' 'Carl Kingsford'] Background Understanding the evolution of biological networks can provide insight into how their modular structure arises and how they are affected by environmental changes. One approach to studying the evolution of these networks is to reconstruct plausible common ancestors of…
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…
Stefano Giaimo, Jordi Arranz, Arne Traulsen, Sebastian Schreiber
Population structure can strongly affect evolutionary dynamics. The most general way to describe population structures are graphs. An important observable on evolutionary graphs is the probability that a novel mutation spreads through the entire population. But what drives this spread of a mutation towards fixation?…
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…
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 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…
Belgin Ergenç Bostanoğlu, Nourhan Abuzayed, Bilal Alatas
Frequent subgraph mining (FSM) is an essential and challenging graph mining task used in several applications of the modern data science. Some of the FSM algorithms have the objective of finding all frequent subgraphs whereas some of the algorithms focus on discovering frequent subgraphs approximately. On the other…
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…
Stanisław Saganowski, Piotr Bródka, Michał Koziarski, Przemysław Kazienko + 1 more
'Przemysław Kazienko' 'Siew Ann Cheong'] In the world, in which acceptance and the identification with social communities are highly desired, the ability to predict the evolution of groups over time appears to be a vital but very complex research problem. Therefore, we propose a new, adaptable, generic, and multistage…
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…
Christopher G Knight, John W Pinney
Our understanding of how evolution acts on biological networks remains patchy, as is our knowledge of how that action is best identified, modelled and understood. Starting with network structure and the evolution of protein-protein interaction networks, we briefly survey the ways in which network evolution is being…
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…