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Phase Transitions of the Moran Process and Algorithmic Consequences [article]

Leslie Ann Goldberg, John Lapinskas, David Richerby
2019 arXiv   pre-print
The Moran process is a random process that models the spread of genetic mutations through graphs.  ...  In the course of proving our main result, we also establish a phase transition in the probability of fixation, depending on the fitness parameter r of the mutation.  ...  Phase transitions In a connected regular n-vertex digraph, such as the clique (which corresponds to the original Moran process of [23] ), the number of mutants in a fitness-r Moran process evolves as  ... 
arXiv:1804.02293v4 fatcat:lyxlzd77ivchdidjwblzanla2q

Spatiotemporal bounded noises and transitions induced by them in solutions of the real Ginzburg-Landau model

Sebastiano de Franciscis, Alberto d'Onofrio
2012 Physical Review E  
The boundedness of these noises has some consequences on their equilibrium distributions.  ...  The observed phase transitions phenomenology is quite different from the one observed when the perturbations are unbounded.  ...  of the Moran index of the field ψ p , I ψ , and the bivariate Moran index I ξψ between the noise field ξ p and the GL one ψ p .  ... 
doi:10.1103/physreve.86.021118 pmid:23005733 fatcat:cfap7jacofgsznttxhj6ctirqi

An accurate model for genetic hitch-hiking [article]

A. Eriksson, P. Fernstrom, B. Mehlig, S. Sagitov
2007 arXiv   pre-print
Only when Ns < 10 (N is the population size and s denotes the selection coefficient), are discrepancies between our approximation and direct numerical simulations of a Moran model noticeable.  ...  Our model describes the gene genealogies of a contiguous segment of neutral loci close to the selected one, and it does not assume that the selective sweep happens instantaneously.  ...  The algorithm is divided into a forward and a backward phase.  ... 
arXiv:0705.2286v1 fatcat:vojr6mubk5ep5onum2tfzvwxkm

An Accurate Model for Genetic Hitchhiking

Anders Eriksson, Pontus Fernström, Bernhard Mehlig, Serik Sagitov
2008 Genetics  
Only when Ns , 10 (N is the population size and s denotes the selection coefficient) are discrepancies between our approximation and direct numerical simulations of a Moran model notable.  ...  Our model describes the gene genealogies of a contiguous segment of neutral loci close to the selected one, and it does not assume that the selective sweep happens instantaneously.  ...  The algorithm is divided into a forward and a backward phase.  ... 
doi:10.1534/genetics.107.076018 pmid:18202386 pmcid:PMC2206092 fatcat:dw4mst3o55e4fdkrl7gsu5u3bq

A Markov chain model of evolution in asexually reproducing populations: insight and analytical tractability in the evolutionary process [article]

Daniel Nichol, Peter Jeavons, Robert Bonomo, Philip K. Maini, Jerome L. Paul, Robert A. Gatenby, Alexander R.A. Anderson, Jacob G. Scott
2013 arXiv   pre-print
The evolutionary process has been modelled in many ways using both stochastic and deterministic models.  ...  Further, we show how the algebraic properties of the Markov Chain model can give insight into the evolutionary process and allow for analysis using familiar linear algebraic methods.  ...  Acknowledgment and Supplementary Information The authors would like to thank Arne Traulsen at the Max Planck Institute for helpful discussions.  ... 
arXiv:1301.4193v1 fatcat:5gl2dbsbnjejrl3jd5bwbitcna

Amplifiers for the Moran Process

Andreas Galanis, Andreas Göbel, Leslie Ann Goldberg, John Lapinskas, David Richerby
2017 Journal of the ACM  
The Moran process, as studied by Lieberman, Hauert and Nowak, is a randomised algorithm modelling the spread of genetic mutations in populations.  ...  Finally, we prove that our analysis of megastars is fairly tightthere is no infinite family of megastars such that the Moran algorithm gives a smaller extinction probability (up to logarithmic factors)  ...  of randomised algorithms and stochastic processes.  ... 
doi:10.1145/3019609 fatcat:ch5fpwywv5bkbcktsj2xux2j74

Inequality's Arrow: The Role of Greed and Order in Genetic Algorithms [chapter]

Anil Menon
2004 Lecture Notes in Computer Science  
It is also shown that with respect to the majorization-theoretic definition, the standard GA is a moderated greedy algorithm. Some consequences of this result are discussed.  ...  This notion can be made precise by using the majorizationtheoretic approach to greedy algorithms. Majorization is the study of pre-orderings induced by doubly stochastic matrices.  ...  I would like to thank the reviewers for their constructive and thought-provoking comments.  ... 
doi:10.1007/978-3-540-24854-5_129 fatcat:c422nus6u5hg7gxfatmmfxo3he

Distinct progressions of neuronal activity changes underlie the formation and consolidation of a gustatory associative memory [article]

Elor Arieli, Nadia Younis, Anan Moran
2021 bioRxiv   pre-print
However, the specific mapping between the known phases of memory and the observed changes in neuronal activity remains unknown.  ...  The population response changed continuously; these changes, however, were only reflected in the population mean amplitude during the acquisition and consolidation phases, and in the known quickening of  ...  This is also true for learned aversion; measured 24 hours after CTA training, the processing of the conditioned taste becomes quicker (Moran and Katz, 2014) .  ... 
doi:10.1101/2021.08.08.455552 fatcat:joly6oybfrf4thifj3wdz5ijau

Phase Diagram for the Methane-Ethane System and its Implications for Titan's Lakes [article]

Anna E. Engle, Jennifer Hanley, Shyanne Dustrud, Garrett Thompson, Gerrick E. Lindberg, William M. Grundy, Stephen C. Tegler
2021 arXiv   pre-print
In addition to mapping the binary system, we looked at the solid-solid transitions of pure ethane and found that, when cooling, the transition of solid I-III occurred at 89.45±0.2 K.  ...  The warming sequence showed transitions of solid III-II occurring at 89.85±0.2 K and solid II-I at 89.65±0.2 K.  ...  Sugata Tan, Jordan Steckloff, Daniel Matthew, Helen Maynard-Casely, and Paul Jagodzinski were also instrumental to the development of this paper through insightful discussion.  ... 
arXiv:2103.15978v1 fatcat:vmtjmdyvpvegnmsz36vr7372nu

Transition probabilities for general birth–death processes with applications in ecology, genetics, and evolution

Forrest W. Crawford, Marc A. Suchard
2011 Journal of Mathematical Biology  
In this paper, we first revisit the theory of continued fractions to obtain expressions for the Laplace transforms of these transition probabilities and make explicit an important derivation connecting  ...  Currently no robust and efficient method exists to evaluate the finite-time transition probabilities in a general birth-death process with arbitrary birth and death rates.  ...  This work was supported by National Institutes of Health grants GM086887 and T32GM008185, and National  ... 
doi:10.1007/s00285-011-0471-z pmid:21984359 pmcid:PMC3310285 fatcat:6jsucqxg6zemfm3qhfgrspr7ju

Distributed Community Detection via Metastability of the 2-Choices Dynamics

Emilio Cruciani, Emanuele Natale, Giacomo Scornavacca
In the context of evolutionary biology, dynamics such as the Moran process have been used to model the spread of mutations in genetic populations (Lieberman, Hauert, and Nowak 2005); our result shows that  ...  , when the probability of adoption of a given mutation by a node of the evolutionary graph depends super-linearly on the frequency of the mutation in the neighborhood of the node and the underlying evolutionary  ...  The Moran process has since then attracted the attention of the computer science community due to the algorithmic questions associated to its fixation probability (Giakkoupis 2016; Galanis et al. 2017  ... 
doi:10.1609/aaai.v33i01.33016046 fatcat:j5rn4hzidvhdpjhzvehdfagasu

The Evolving Moran Genealogy [article]

Johannes Wirtz, Thomas Wiehe
2019 arXiv   pre-print
We derive a number of properties of this process, and show that they are in agreement with existing results on the infinite-population limit of the Moran Model.  ...  We study the evolution of the population genealogy in the classic neutral Moran Model of finite size and in discrete time.  ...  This work was financially supported by the German Research Foundation (DFG-SPP1590).  ... 
arXiv:1808.10809v2 fatcat:ngobddfwtndxjlxc7jfjrkesnu

Prediction of freezing of gait using analysis of brain effective connectivity

A. M. Ardi Handojoseno, James M. Shine, Moran Gilat, Tuan N. Nguyen, Yvonne Tran, Simon J. G. Lewis, Hung T. Nguyen
2014 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
In this study, directed transfer function (DTF) and partial directed coherence (PDC) were used to calculate the effective connectivity of neural networks, as the input features for systems that can detect  ...  The sensitivity, specificity and accuracy obtained in subject dependent analysis were 82%, 77%, and 78%, respectively.  ...  Shine, Moran Gilat and Simon J.G.  ... 
doi:10.1109/embc.2014.6944530 pmid:25570898 dblp:conf/embc/HandojosenoSGNT14 fatcat:yocyoxy5qvdudpf5giiw6cvbi4

Punishment in public goods games leads to meta-stable phase transitions and hysteresis

Arend Hintze, Christoph Adami
2015 Physical Biology  
In terms of this synergy parameter, the transition from defection to cooperation can be viewed as a phase transition with the synergy as the critical parameter.  ...  We show here that punishment reduces the critical value at which cooperation occurs, but also creates the possibility of meta-stable phase transitions, where populations can "tunnel" into the cooperating  ...  We wish to acknowledge the support of the Michigan State University High Performance Computing Center and the Institute for Cyber-Enabled Research.  ... 
doi:10.1088/1478-3975/12/4/046005 pmid:26031571 fatcat:schixw73rbf7xbgt7x32dr3y64

Quantification of subclonal selection in cancer from bulk sequencing data [article]

Marc J Williams, Benjamin Werner, Christina Curtis, Chris Barnes, Andrea Sottoriva, Trevor A Graham
2016 bioRxiv   pre-print
Our approach simultaneously determines the subclonal architecture of a tumour sample, and measures the mutation rate, the selective advantage, and the time of appearance of subclones.  ...  Simulations demonstrate the accuracy of the method, and revealed the degree to which evolutionary dynamics are recorded in the genome.  ...  However simulating a tumour that grows logisitically and transitions into a moran model B, even when the population followed a moran model for 20 times longer than it was in the growth phase, the main  ... 
doi:10.1101/096305 fatcat:xxmhrhkkivci7lyd5mgc4xcgii
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