Related papers: Innovation as Evolution: Case Study Phylomemetic o…

We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as…

Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…

Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of…

In this paper we predict outgoing mobile phone calls using a machine learning approach. We analyze to which extent the activity of mobile phone users is predictable. The premise is that mobile phone users exhibit temporal regularity in…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…

Possibility to establish macroscopic phenomenological theory for biological systems, akin to the akin to the well-established framework of thermodynamics, is briefly reviewed. We introduce the concept of an evolutionary fluctuation-response…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

Mobile call networks have been widely used to investigate communication patterns and the network of interactions of humans at the societal scale. Yet, more detailed analysis is often hindered by having no information about the nature of the…

We study the asymptotic number of certain monotonically labeled increasing trees arising from a generalized evolution process. The main difference between the presented model and the classical model of binary increasing trees is that the…

Mobile phones are quickly becoming the primary source for social, behavioral, and environmental sensing and data collection. Today's smartphones are equipped with increasingly more sensors and accessible data types that enable the…

The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…

The dynamics of innovation are nonlinear and complex: geographical, technological, and economic selection environments can be expected to interact. Can patents provide an analytical lens to this process in terms of different attributes such…

Clustered cell-free networking, which dynamically partitions the whole network into nonoverlapping subnetworks, has been recently proposed to mitigate the cell-edge problem in cellular networks. However, prior works only focused on…

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…