Distributed Individual-Based Environmental Simulation

This paper describes the development and construction of a distributed model allowing the simulation of a large population. Particular attention will be paid to allowing the modelling of an individual's behaviour, communication and interaction with a shared environment. Individual based modelling is not a new concept, nor is the idea of distributed simulations, the system detailed here offers a means of combining these two paradigms into one large-scale modelling environment. A key concept in this system is that each individual being modelled is implemented as a separate process. This atomisation of the model allows the simulation a greater flexibility, individuals can be rapidly developed and the simulation can be spread over a wide number of machines of varying architectures. In an attempt to produce a flexible, extensible, individual based model of a large number of individual subjects the client-server paradigm has been employed. Combining the individual-based modelling techniques with a client-server network architecture has been found to be quite straightforward with the added bonus of having communication between individuals included for free. The idea of considering the problem as one of interaction between an individual and the environment means that the problems normally associated with distributed simulations, those of continuity of world-views for different clients and of communication between clients, are easily solved. Although this system has been developed originally to allow simulations of the Mountain Gorilla (Gorilla Gorilla Beringe) population, the modelling methods employed have meant that almost any entity can be simulated with very little change to the basic simulation processes

Algorithm Portfolio for Individual-based Surrogate-Assisted Evolutionary Algorithms

Surrogate-assisted evolutionary algorithms (SAEAs) are powerful optimisation tools for computationally expensive problems (CEPs). However, a randomly selected algorithm may fail in solving unknown problems due to no free lunch theorems, and it will cause more computational resource if we re-run the algorithm or try other algorithms to get a much solution, which is more serious in CEPs. In this paper, we consider an algorithm portfolio for SAEAs to reduce the risk of choosing an inappropriate algorithm for CEPs. We propose two portfolio frameworks for very expensive problems in which the maximal number of fitness evaluations is only 5 times of the problem's dimension. One framework named Par-IBSAEA runs all algorithm candidates in parallel and a more sophisticated framework named UCB-IBSAEA employs the Upper Confidence Bound (UCB) policy from reinforcement learning to help select the most appropriate algorithm at each iteration. An effective reward definition is proposed for the UCB policy. We consider three state-of-the-art individual-based SAEAs on different problems and compare them to the portfolios built from their instances on several benchmark problems given limited computation budgets. Our experimental studies demonstrate that our proposed portfolio frameworks significantly outperform any single algorithm on the set of benchmark problems

Invasion and adaptive evolution for individual-based spatially structured populations

The interplay between space and evolution is an important issue in population dynamics, that is in particular crucial in the emergence of polymorphism and spatial patterns. Recently, biological studies suggest that invasion and evolution are closely related. Here we model the interplay between space and evolution starting with an individual-based approach and show the important role of parameter scalings on clustering and invasion. We consider a stochastic discrete model with birth, death, competition, mutation and spatial diffusion, where all the parameters may depend both on the position and on the trait of individuals. The spatial motion is driven by a reflected diffusion in a bounded domain. The interaction is modelled as a trait competition between individuals within a given spatial interaction range. First, we give an algorithmic construction of the process. Next, we obtain large population approximations, as weak solutions of nonlinear reaction-diffusion equations with Neumann's boundary conditions. As the spatial interaction range is fixed, the nonlinearity is nonlocal. Then, we make the interaction range decrease to zero and prove the convergence to spatially localized nonlinear reaction-diffusion equations, with Neumann's boundary conditions. Finally, simulations based on the microscopic individual-based model are given, illustrating the strong effects of the spatial interaction range on the emergence of spatial and phenotypic diversity (clustering and polymorphism) and on the interplay between invasion and evolution. The simulations focus on the qualitative differences between local and nonlocal interactions

Pattern formation in individual-based systems with time-varying parameters

We study the patterns generated in finite-time sweeps across symmetry-breaking bifurcations in individual-based models. Similar to the well-known Kibble-Zurek scenario of defect formation, large-scale patterns are generated when model parameters are varied slowly, whereas fast sweeps produce a large number of small domains. The symmetry breaking is triggered by intrinsic noise, originating from the discrete dynamics at the micro-level. Based on a linear-noise approximation, we calculate the characteristic length scale of these patterns. We demonstrate the applicability of this approach in a simple model of opinion dynamics, a model in evolutionary game theory with a time-dependent fitness structure, and a model of cell differentiation. Our theoretical estimates are confirmed in simulations. In further numerical work, we observe a similar phenomenon when the symmetry-breaking bifurcation is triggered by population growth.Comment: 16 pages, 9 figures. Published version. Corrected missing appendix link from previous versio

Outlook for tuberculosis elimination in California: An individual-based stochastic model.

RationaleAs part of the End TB Strategy, the World Health Organization calls for low-tuberculosis (TB) incidence settings to achieve pre-elimination (<10 cases per million) and elimination (<1 case per million) by 2035 and 2050, respectively. These targets require testing and treatment for latent tuberculosis infection (LTBI).ObjectivesTo estimate the ability and costs of testing and treatment for LTBI to reach pre-elimination and elimination targets in California.MethodsWe created an individual-based epidemic model of TB, calibrated to historical cases. We evaluated the effects of increased testing (QuantiFERON-TB Gold) and treatment (three months of isoniazid and rifapentine). We analyzed four test and treat targeting strategies: (1) individuals with medical risk factors (MRF), (2) non-USB, (3) both non-USB and MRF, and (4) all Californians. For each strategy, we estimated the effects of increasing test and treat by a factor of 2, 4, or 10 from the base case. We estimated the number of TB cases occurring and prevented, and net and incremental costs from 2017 to 2065 in 2015 U.S. dollars. Efficacy, costs, adverse events, and treatment dropout were estimated from published data. We estimated the cost per case averted and per quality-adjusted life year (QALY) gained.Measurements and main resultsIn the base case, 106,000 TB cases are predicted to 2065. Pre-elimination was achieved by 2065 in three scenarios: a 10-fold increase in the non-USB and persons with MRF (by 2052), and 4- or 10-fold increase in all Californians (by 2058 and 2035, respectively). TB elimination was not achieved by any intervention scenario. The most aggressive strategy, 10-fold in all Californians, achieved a case rate of 8 (95% UI 4-16) per million by 2050. Of scenarios that reached pre-elimination, the incremental net cost was $20 billion (non-USB and MRF) to$48 billion. These had an incremental cost per QALY of $657,000 to$3.1 million. A more efficient but somewhat less effective single-lifetime test strategy reached as low as $80,000 per QALY.ConclusionsSubstantial gains can be made in TB control in coming years by scaling-up current testing and treatment in non-USB and those with medical risks

Fisher Waves: an individual based stochastic model

The propagation of a beneficial mutation in a spatially extended population is usually studied using the phenomenological stochastic Fisher-Kolmogorov (SFKPP) equation. We derive here an individual based, stochastic model founded on the spatial Moran process where fluctuations are treated exactly. At high selection pressure, the results of this model are different from the classical FKPP. At small selection pressure, the front behavior can be mapped into a Brownian motion with drift, the properties of which can be derived from microscopic parameters of the Moran model. Finally, we show that the diffusion coefficient and the noise amplitude of SFKPP are not independent parameters but are both determined by the dispersal kernel of individuals