Biomedical subjects

Hiroki Sayama

Publications and source records attributed to Hiroki Sayama.

6 recordsLinked to original sources

PubMed2006

Visualizing evolutionary dynamics of self-replicators: a graph-based approach.

We present a general approach for evaluating and visualizing evolutionary dynamics of self-replicators using a graph-based representation for genealogy. Through a transformation from the space of species and mutations to the space of nodes and links, evolutionary dynamics are understood as a flow in graph space. A formalism is introduced to quantify such genealogical flows in terms of the complete history of localized evolutionary events recorded at the finest level of detail. Represented in a multidimensional viewing space, collective dynamical properties of an evolving genealogy are characterized in the form of aggregate flows. We demonstrate the effectiveness of this approach by using it to compare the evolutionary exploration behavior of self-replicating loops under two different environmental settings.

Artificial Intelligence↗

PubMed2004

Evolutionary dynamics of cellular automata-based self-replicators in hostile environments.

In this paper we investigate population dynamics, genealogy and complexity-increase of locally interacting populations of cellular automata-based evolving self-replicating loops (evoloops). We outline experiments indicating that the evolutionary growth in complexity, known to be achievable in principle given the complete genetic accessibility granted by universal construction, may be achievable in practice using much simpler replicating structures. By introducing evoloop populations to hostile environments, we demonstrate that selection pressures toward smaller species can be mediated to enable evolutionary accessibility to larger species, which themselves roam a much more vast portion of genetic state-space. We show that this growth in size results from intrinsically biased genealogy inherent in the rules of the evoloop CA, normally suppressed by selection pressures from direct competition favouring the smallest species. This shows that, in populations of simple self-replicating structures, a limited form of complexity-increase may result from a process which is driven by biased genealogical connectivity--a purely emergent property arising out of bottom-up evolutionary dynamics--and not just by adaptation . Implications of this result are discussed and contrasted with other self-replication studies in Artificial Life and Biology.

Cells↗

PubMed2004

Self-protection and diversity in self-replicating cellular automata.

The concept of self-protection, a capability of an organism to protect itself from exogenous attacks, is introduced into the design of artificial evolutionary systems as a possible method to create and maintain diversity in the population. Three different mechanisms of self-protection are considered and implemented on a cellular-automaton-based evolutionary system, the evoloop. Simulation results imply a positive effect of those mechanisms on diversity maintenance, especially when the self-protection is moderate so that it conserves both the attacker and the attacked. This letter briefly reports the models and the simulation results obtained using those models.

Biodiversity↗

PubMed2003

Dynamics and genealogy of strains in spatially extended host-pathogen models.

We examine the dynamics of evolution in a generic spatial model of a pathogen infecting a population of hosts, or an analogous predator-prey system. Previous studies of this model have found a range of interesting phenomena that differ from the well-mixed version. We extend these studies by examining the spatial and temporal dynamics of strains using genealogical tracing. When transmissibility can evolve by mutation, strains of intermediate transmissibility dominate even though high-transmissibility mutants have a short-term reproductive advantage. Mutant strains continually arise and grow rapidly for many generations but eventually go extinct before dominating the system. We find that, after a number of generations, the mutant pathogen characteristics strongly impact the spatial distribution of their local host environment, even when there are diverse types coexisting. Extinction is due to the depletion of susceptibles in the local environment of these mutant strains. Studies of spatial and genealogical relatedness reveal the self-organized spatial clustering of strains that enables their impact on the local environment. Thus, we find that selection acts against the high-transmissibility strains on long time-scales as a result of the feedback due to environmental change. Our study shows that averages over space or time should not be assumed to adequately describe the evolutionary dynamics of spatially distributed host-pathogen systems.

Animals↗

PubMed2003

Optimization of robustness and connectivity in complex networks.

Scale-free networks rely on a relatively small number of highly connected nodes to achieve a high degree of interconnectivity and robustness to random failure, but suffer from a high sensitivity to directed attack. In this paper we describe a parameterized family of networks and analyze their connectivity and sensitivity, identifying a network that has an interconnectedness closer to that of a scale-free network, a robustness to attack closer to that of an exponential network, and a resistance to failure better than that of either of those networks.

Models, Biological↗

PubMed2002

Spontaneous pattern formation and genetic invasion in locally mating and competing populations.

We present a theoretical model of evolution of spatially distributed populations in which organisms mate with and compete against each other only locally. We show using both analysis and numerical simulation that the typical dynamics of population density variation is a spontaneous formation of isolated groups due to competition for resources. The resulting spatial separation between groups strongly affects the process of genetic invasion by local reproductive mixing, and spatially inhomogeneous genetic distributions are possible in the final states. We then consider a specific version of this model in the presence of disruptive selection, favoring two fittest types against their genetic intermediates. This case can be simplified to a system that involves just two nonconserved order parameters: population density and type difference. Since the coexistence of two fittest types is unstable in this case, symmetry breaking and coarsening occur in type difference, implying eventual dominance by one type over another for finite populations. However, such coarsening patterns may be pinned by the spontaneously generated spatial separation between isolated groups. The long-term evolution of genetic composition is found to be sensitive to the ratio of the mating and competition ranges, and other parameters. Our model may provide a theoretical basis for consideration of various properties of spatially extended evolutionary processes, including spontaneous formation of subpopulations and lateral invasion of different types.

Journal Article↗