To Calibrate & Validate an Agent-Based Simulation Model - An Application of the Combination Framework of BI solution & Multi-agent platform

National audienceIntegrated environmental modeling approaches, especially the agent-based modeling one, are increasingly used in large-scale decision support systems. A major consequence of this trend is the manipulation and generation of huge amount of data in simulations, which must be efficiently managed. Furthermore, calibration and validation are also challenges for Agent-Based Modelling and Simulation (ABMS) approaches when the model has to work with integrated systems involving high volumes of input/output data. In this paper, we propose a calibration and validation approach for an agent-based model, using a Combination Framework of Business intelligence solution and Multi-agent platform (CFBM). The CFBM is a logical framework dedicated to the management of the input and output data in simulations, as well as the corresponding empirical datasets in an integrated way. The calibration and validation of Brown Plant Hopper Prediction model are presented and used throughout the paper as a case study to illustrate the way CFBM manages the data used and generated during the life-cycle of simulation and validation

Inland dry season saline intrusion in the Vietnamese Mekong River Delta is driving the identification and implementation of alternative crops to rice

CONTEXT: Inland saline intrusion is occurring during the dry season in the Mekong River Delta (MRD), Vietnam. Rising sea levels, tidal fluctuations, drought, and changes to upstream flow contribute to extensive salinisation of rice producing areas of the MRD, leading to substantial rice crop losses. OBJECTIVE: The identification, evaluation and implementation of alternative crop and soil management solutions are required to complement on-going rice production in the region. METHODS: A review of scientific and grey literature was conducted regarding the nature and extent of salinisation in the MRD and the adoption and management of alternative crops to rice. RESULTS: Familiar crops in Vietnam (e.g., maize, soybean), as well as novel crops to the MRD (e.g., quinoa, cowpea) were explored as potential options to replace dry season rice. Management options including surface soil mulches and plastic coverings help maintain soil moisture and reduce salinity damage to plants, and the use of drainage and seed preparation techniques can improve plant establishment and yield. Factors contributing to the success of alternative crops include salt tolerance, timing and efficiency of water use, ability to grow in the dry growing season, tolerance to pests and diseases, labour intensiveness and the crops' marketability. SIGNIFICANCE: The identification of suitable alternative crops to replace dry season rice in saline affected areas of the MRD, combined with management practices like mulching and soil moisture monitoring, could provide farmers with income opportunities to offset rice losses. Documenting the factors contributing to successful crop diversification can assist with decision-making and support initiatives among farmers, agribusiness, and government agencies

To Develop a Database Management Tool for Multi-Agent Simulation Platform

Depuis peu, la Modélisation et Simulation par Agents (ABMs) est passée d'une approche dirigée par les modèles à une approche dirigée par les données (Data Driven Approach, DDA). Cette tendance vers l’utilisation des données dans la simulation vise à appliquer les données collectées par les systèmes d’observation à la simulation (Edmonds and Moss, 2005; Hassan, 2009). Dans la DDA, les données empiriques collectées sur les systèmes cibles sont utilisées non seulement pour la simulation des modèles mais aussi pour l’initialisation, la calibration et l’évaluation des résultats issus des modèles de simulation, par exemple, le système d’estimation et de gestion des ressources hydrauliques du bassin Adour-Garonne Français (Gaudou et al., 2013) et l’invasion des rizières du delta du Mékong au Vietnam par les cicadelles brunes (Nguyen et al., 2012d). Cette évolution pose la question du « comment gérer les données empiriques et celles simulées dans de tels systèmes ». Le constat que l’on peut faire est que, si la conception et la simulation actuelles des modèles ont bénéficié des avancées informatiques à travers l’utilisation des plateformes populaires telles que Netlogo (Wilensky, 1999) ou GAMA (Taillandier et al., 2012), ce n'est pas encore le cas de la gestion des données, qui sont encore très souvent gérées de manière ad-hoc. Cette gestion des données dans des Modèles Basés Agents (ABM) est une des limitations actuelles des plateformes de simulation multiagents (SMA). Autrement dit, un tel outil de gestion des données est actuellement requis dans la construction des systèmes de simulation par agents et la gestion des bases de données correspondantes est aussi un problème important de ces systèmes. Dans cette thèse, je propose tout d’abord une structure logique pour la gestion des données dans des plateformes de SMA. La structure proposée qui intègre des solutions de l’Informatique Décisionnelle et des plateformes multi-agents s’appelle CFBM (Combination Framework of Business intelligence and Multi-agent based platform), elle a plusieurs objectifs : (1) modéliser et exécuter des SMAs, (2) gérer les données en entrée et en sortie des simulations, (3) intégrer les données de différentes sources, et (4) analyser les données à grande échelle. Ensuite, le besoin de la gestion des données dans les simulations agents est satisfait par une implémentation de CFBM dans la plateforme GAMA. Cette implémentation présente aussi une architecture logicielle pour combiner entrepôts deIv données et technologies du traitement analytique en ligne (OLAP) dans les systèmes SMAs. Enfin, CFBM est évaluée pour la gestion de données dans la plateforme GAMA à travers le développement de modèles de surveillance des cicadelles brunes (BSMs), où CFBM est utilisé non seulement pour gérer et intégrer les données empiriques collectées depuis le système cible et les résultats de simulation du modèle simulé, mais aussi calibrer et valider ce modèle. L'intérêt de CFBM réside non seulement dans l'amélioration des faiblesses des plateformes de simulation et de modélisation par agents concernant la gestion des données mais permet également de développer des systèmes de simulation complexes portant sur de nombreuses données en entrée et en sortie en utilisant l’approche dirigée par les données.Recently, there has been a shift from modeling driven approach to data driven approach inAgent Based Modeling and Simulation (ABMS). This trend towards the use of data-driven approaches in simulation aims at using more and more data available from the observation systems into simulation models (Edmonds and Moss, 2005; Hassan, 2009). In a data driven approach, the empirical data collected from the target system are used not only for the design of the simulation models but also in initialization, calibration and evaluation of the output of the simulation platform such as e.g., the water resource management and assessment system of the French Adour-Garonne Basin (Gaudou et al., 2013) and the invasion of Brown Plant Hopper on the rice fields of Mekong River Delta region in Vietnam (Nguyen et al., 2012d). That raises the question how to manage empirical data and simulation data in such agentbased simulation platform. The basic observation we can make is that currently, if the design and simulation of models have benefited from advances in computer science through the popularized use of simulation platforms like Netlogo (Wilensky, 1999) or GAMA (Taillandier et al., 2012), this is not yet the case for the management of data, which are still often managed in an ad hoc manner. Data management in ABM is one of limitations of agent-based simulation platforms. Put it other words, such a database management is also an important issue in agent-based simulation systems. In this thesis, I first propose a logical framework for data management in multi-agent based simulation platforms. The proposed framework is based on the combination of Business Intelligence solution and a multi-agent based platform called CFBM (Combination Framework of Business intelligence and Multi-agent based platform), and it serves several purposes: (1) model and execute multi-agent simulations, (2) manage input and output data of simulations, (3) integrate data from different sources; and (4) analyze high volume of data. Secondly, I fulfill the need for data management in ABM by the implementation of CFBM in the GAMA platform. This implementation of CFBM in GAMA also demonstrates a software architecture to combine Data Warehouse (DWH) and Online Analytical Processing (OLAP) technologies into a multi-agent based simulation system. Finally, I evaluate the CFBM for data management in the GAMA platform via the development of a Brown Plant Hopper Surveillance Models (BSMs), where CFBM is used ii not only to manage and integrate the whole empirical data collected from the target system and the data produced by the simulation model, but also to calibrate and validate the models.The successful development of the CFBM consists not only in remedying the limitation of agent-based modeling and simulation with regard to data management but also in dealing with the development of complex simulation systems with large amount of input and output data supporting a data driven approach

To Develop a Database Management Tool for Multi-Agent Simulation Platform

Depuis peu, la Modélisation et Simulation par Agents (ABMs) est passée d'une approche dirigée par les modèles à une approche dirigée par les données (Data Driven Approach, DDA). Cette tendance vers l’utilisation des données dans la simulation vise à appliquer les données collectées par les systèmes d’observation à la simulation (Edmonds and Moss, 2005; Hassan, 2009). Dans la DDA, les données empiriques collectées sur les systèmes cibles sont utilisées non seulement pour la simulation des modèles mais aussi pour l’initialisation, la calibration et l’évaluation des résultats issus des modèles de simulation, par exemple, le système d’estimation et de gestion des ressources hydrauliques du bassin Adour-Garonne Français (Gaudou et al., 2013) et l’invasion des rizières du delta du Mékong au Vietnam par les cicadelles brunes (Nguyen et al., 2012d). Cette évolution pose la question du « comment gérer les données empiriques et celles simulées dans de tels systèmes ». Le constat que l’on peut faire est que, si la conception et la simulation actuelles des modèles ont bénéficié des avancées informatiques à travers l’utilisation des plateformes populaires telles que Netlogo (Wilensky, 1999) ou GAMA (Taillandier et al., 2012), ce n'est pas encore le cas de la gestion des données, qui sont encore très souvent gérées de manière ad-hoc. Cette gestion des données dans des Modèles Basés Agents (ABM) est une des limitations actuelles des plateformes de simulation multiagents (SMA). Autrement dit, un tel outil de gestion des données est actuellement requis dans la construction des systèmes de simulation par agents et la gestion des bases de données correspondantes est aussi un problème important de ces systèmes. Dans cette thèse, je propose tout d’abord une structure logique pour la gestion des données dans des plateformes de SMA. La structure proposée qui intègre des solutions de l’Informatique Décisionnelle et des plateformes multi-agents s’appelle CFBM (Combination Framework of Business intelligence and Multi-agent based platform), elle a plusieurs objectifs : (1) modéliser et exécuter des SMAs, (2) gérer les données en entrée et en sortie des simulations, (3) intégrer les données de différentes sources, et (4) analyser les données à grande échelle. Ensuite, le besoin de la gestion des données dans les simulations agents est satisfait par une implémentation de CFBM dans la plateforme GAMA. Cette implémentation présente aussi une architecture logicielle pour combiner entrepôts deIv données et technologies du traitement analytique en ligne (OLAP) dans les systèmes SMAs. Enfin, CFBM est évaluée pour la gestion de données dans la plateforme GAMA à travers le développement de modèles de surveillance des cicadelles brunes (BSMs), où CFBM est utilisé non seulement pour gérer et intégrer les données empiriques collectées depuis le système cible et les résultats de simulation du modèle simulé, mais aussi calibrer et valider ce modèle. L'intérêt de CFBM réside non seulement dans l'amélioration des faiblesses des plateformes de simulation et de modélisation par agents concernant la gestion des données mais permet également de développer des systèmes de simulation complexes portant sur de nombreuses données en entrée et en sortie en utilisant l’approche dirigée par les données.Recently, there has been a shift from modeling driven approach to data driven approach inAgent Based Modeling and Simulation (ABMS). This trend towards the use of data-driven approaches in simulation aims at using more and more data available from the observation systems into simulation models (Edmonds and Moss, 2005; Hassan, 2009). In a data driven approach, the empirical data collected from the target system are used not only for the design of the simulation models but also in initialization, calibration and evaluation of the output of the simulation platform such as e.g., the water resource management and assessment system of the French Adour-Garonne Basin (Gaudou et al., 2013) and the invasion of Brown Plant Hopper on the rice fields of Mekong River Delta region in Vietnam (Nguyen et al., 2012d). That raises the question how to manage empirical data and simulation data in such agentbased simulation platform. The basic observation we can make is that currently, if the design and simulation of models have benefited from advances in computer science through the popularized use of simulation platforms like Netlogo (Wilensky, 1999) or GAMA (Taillandier et al., 2012), this is not yet the case for the management of data, which are still often managed in an ad hoc manner. Data management in ABM is one of limitations of agent-based simulation platforms. Put it other words, such a database management is also an important issue in agent-based simulation systems. In this thesis, I first propose a logical framework for data management in multi-agent based simulation platforms. The proposed framework is based on the combination of Business Intelligence solution and a multi-agent based platform called CFBM (Combination Framework of Business intelligence and Multi-agent based platform), and it serves several purposes: (1) model and execute multi-agent simulations, (2) manage input and output data of simulations, (3) integrate data from different sources; and (4) analyze high volume of data. Secondly, I fulfill the need for data management in ABM by the implementation of CFBM in the GAMA platform. This implementation of CFBM in GAMA also demonstrates a software architecture to combine Data Warehouse (DWH) and Online Analytical Processing (OLAP) technologies into a multi-agent based simulation system. Finally, I evaluate the CFBM for data management in the GAMA platform via the development of a Brown Plant Hopper Surveillance Models (BSMs), where CFBM is used ii not only to manage and integrate the whole empirical data collected from the target system and the data produced by the simulation model, but also to calibrate and validate the models.The successful development of the CFBM consists not only in remedying the limitation of agent-based modeling and simulation with regard to data management but also in dealing with the development of complex simulation systems with large amount of input and output data supporting a data driven approach

Simulations and Modelling for Biological Invasions

Biological invasions are characterized by the movement of organisms from their native geographic region to new, distinct regions in which they may have significant impacts. Biological invasions pose one of the most serious threats to global biodiversity, and hence significant resources are invested in predicting, preventing, and managing them. Biological systems and processes are typically large, complex, and inherently difficult to study naturally because of their immense scale and complexity. Hence, computational modelling and simulation approaches can be taken to study them. In this dissertation, I applied computer simulations to address two important problems in invasion biology. First, in invasion biology, the impact of genetic diversity of introduced populations on their establishment success is unknown. We took an individual-based modelling approach to explore this, leveraging an ecosystem simulation called EcoSim to simulate biological invasions. We conducted reciprocal transplants of prey individuals across two simulated environments, over a gradient of genetic diversity. Our simulation results demonstrated that a harsh environment with low and spatially-varying resource abundance mediated a relationship between genetic diversity and short-term establishment success of introduced populations rather than the degree of difference between native and introduced ranges. We also found that reducing Allee effects by maintaining compactness, a measure of spatial density, was key to the establishment success of prey individuals in EcoSim, which were sexually reproducing. Further, we found evidence of a more complex relationship between genetic diversity and long-term establishment success, assuming multiple introductions were occurring. Low-diversity populations seemed to benefit more strongly from multiple introductions than high-diversity populations. Our results also corroborated the evolutionary imbalance hypothesis: the environment that yielded greater diversity produced better invaders and itself was less invasible. Finally, our study corroborated a mechanical explanation for the evolutionary imbalance hypothesis – the populations evolved in a more intense competitive environment produced better invaders. Secondly, an important advancement in invasion biology is the use of genetic barcoding or metabarcoding, in conjunction with next-generation sequencing, as a potential means of early detection of aquatic introduced species. Barcoding and metabarcoding invariably requires some amount of computational DNA sequence processing. Unfortunately, optimal processing parameters are not known in advance and the consequences of suboptimal parameter selection are poorly understood. We aimed to determine the optimal parameterization of a common sequence processing pipeline for both early detection of aquatic nonindigenous species and conducting species richness assessments. We then aimed to determine the performance of optimized pipelines in a simulated inoculation of sequences into community samples. We found that early detection requires relatively lenient processing parameters. Further, optimality depended on the research goal – what was optimal for early detection was suboptimal for estimating species richness and vice-versa. Finally, with optimal parameter selection, fewer than 11 target sequences were required in order to detect 90% of nonindigenous species