Related papers: Innovation as Evolution: Case Study Phylomemetic o…
Most decision tree induction algorithms are based on a greedy top-down recursive partitioning strategy for tree growth. In this paper, we propose several methods for induction of decision trees and their ensembles based on evolutionary…
For many networks, the connection pattern (often called the topology) can vary in time, depending on the changing state, or mode, of the modules within the network. For example, "airplane mode" is the name for one communicative mode of a…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
In this paper we present a novel tool to evaluate problem solving systems. Instead of using a system to solve a problem, we suggest using the problem to evaluate the system. By finding a numerical representation of a problem's complexity,…
We propose a model of the evolution of a matrix along a phylogenetic tree, in which transformations affect either entire rows or columns of the matrix. This represents the change of both lexical and phonological aspects of linguistic data,…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Here I describe a view of the evolution of cellular automata that allows to operate on larger structures. Instead of calculating the next state of all cells in one step, the method here developed uses a time slice that can proceed at…
The explosion of mobile phone communications in the last years occurs at a moment where data processing power increases exponentially. Thanks to those two changes in a global scale, the road has been opened to use mobile phone…
We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the…
In today's instant communication era, mobile phones play an important role in the efficient communication with respect to both individual and official communication strata. With the drastic explosion in the quantity of calls received and…
We consider an information dissemination problem where the root of an undirected graph constantly updates its information. The goal is to keep every other node in the graph about the root as freshly informed as possible. Our synchronous…
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…
Mobile phone metadata is increasingly used for humanitarian purposes in developing countries as traditional data is scarce. Basic demographic information is however often absent from mobile phone datasets, limiting the operational impact of…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…
Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cell's phenotype and the discrete, a priori states that define various…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…