@article {1513, title = {Dynamic trade-offs in granulocyte colony-stimulating factor (G-CSF) administration during chemotherapy}, journal = {System Dynamics Review}, volume = {36}, year = {2021}, pages = {397{\textendash}446}, abstract = {

Chemotherapeutic treatment of cancer comes with side effects on the immune system, such as Chemotherapy-Induced Neutropenia (CIN). A recombinant form of Granulocyte Colony-Stimulating Factor (G-CSF) has been used to alleviate CIN. This is a challenging task due to the feedback complexity of the hematological system. A System Dynamics model is constructed to study this system and to derive practical insights for the management of CIN. Stimulation of neutrophil production via G-CSF is observed to propose crucial trade-offs. On one hand, production by stem cells and mobilization from bone marrow should be stimulated to compensate for the impairment caused by chemotherapy. On the other hand, it is important to avoid overstimulation, which reduces the regenerative capacity, as well as draining the much-needed bone-marrow reservoir. Our analysis supports the intuition that the response to G-CSF administration is conditional to patient characteristics, and {\textquotedblleft}one for all{\textquotedblright} treatment protocols are impractical. {\textcopyright} 2021 System Dynamics Society.

}, issn = {10991727}, doi = {10.1002/sdr.1671}, author = {{\.I}rsoy, Orkun and G{\"u}z, {\c S}anser and Akan, Naz Beril and G{\"o}nen{\c c} Y{\"u}cel} } @article {1417, title = {Analysis of an individual-based influenza epidemic model using random forest metamodels and adaptive sequential sampling}, journal = {Systems Research and Behavioral Science}, volume = {37}, year = {2020}, pages = {936-958}, abstract = {

Abstract This study proposes a three-step procedure for the analysis of input{\textendash}response relationships of dynamic models, which enables the analyst to develop a better understanding about the dynamics of the system. The main building block of the procedure is a random forest metamodel capturing the input{\textendash}output relationships. We utilize an active learning approach as the second step to improve the accuracy of the metamodel. In the last step, we develop a novel way to present the information captured by the metamodel as a set of intelligible IF{\textendash}THEN rules. For illustration, we use the FluTE model, which is an individual-based influenza epidemic model. We observe that the number of daily applicable vaccines determines the success of an intervention strategy the most. Another critical observation is that when the daily available vaccines are constrained, nonpharmaceutical strategies should be incorporated to reduce the extent of the outbreak.

}, keywords = {adaptive sequential sampling, FluTE, individual-based modelling, Metamodeling, Rule Extraction}, doi = {https://doi.org/10.1002/sres.2763}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/sres.2763}, author = {Edali, Mert and G{\"o}nen{\c c} Y{\"u}cel} } @article {1415, title = {Classification of generic system dynamics model outputs via supervised time series pattern discovery}, journal = {Turkish Journal of Electrical Engineering \& Computer Sciences}, volume = {27}, year = {2019}, pages = {832{\textendash}846}, author = {Edali, Mert and Mustafa Gokce Baydogan and G{\"o}nen{\c c} Y{\"u}cel} } @article {1416, title = {Exploring the behavior space of agent-based simulation models using random forest metamodels and sequential sampling}, journal = {Simulation Modelling Practice and Theory}, volume = {92}, year = {2019}, pages = {62-81}, abstract = {

Agent-based modeling is an effective way of understanding and analyzing complex adaptive phenomena. In this respect, discovering the relationship between inputs and outputs of agent-based models is the ultimate way of providing insights into understanding the dynamics of the system being modeled. Therefore, there are many approaches in the literature to clarify these relationships including sampling and metamodeling. Emphasizing the weaknesses and disadvantages of current methods, we present a metamodel-guided sequential sampling technique which combines random forests and uncertainty sampling. Experimental results on two well-known agent-based models show that the presented technique yields metamodels of higher accuracy compared to metamodels trained with randomly selected input{\textendash}output data. Contrary to the previous studies emphasizing only the improvement in the metamodel accuracy, we also focus on input parameter combinations selected by the sequential sampling technique, and we observe that sequential sampling is able to capture the boundaries of tipping point behaviors as well as the points exhibiting counter-intuitive behavior, thus, potentially aiding verification, validation, and understanding of agent-based models. Additionally, we propose a novel two-step method for the categorization of the agent-based model outputs prior to metamodel training, which helps the analyst to decide on whether preserving numerical model outputs or continuing the metamodel training procedure with qualitative categorical agent-based model outputs.

}, keywords = {Active learning, Agent-based modeling, Metamodeling, Output categorization, Random forest, Sequential sampling}, issn = {1569-190X}, doi = {https://doi.org/10.1016/j.simpat.2018.12.006}, url = {https://www.sciencedirect.com/science/article/pii/S1569190X18301941}, author = {Mert Edali and G{\"o}nen{\c c} Y{\"u}cel} } @article {1414, title = {Automated Analysis of Regularities Between Model Parameters and Output Using Support Vector Regression in Conjunction with Decision Trees}, journal = {Journal of Artificial Societies and Social Simulation}, volume = {21}, year = {2018}, pages = {1}, abstract = {

Opening the black-box of nonlinear relationships between model inputs and outputs, significantly contributes to the understanding of the dynamic problem being studied. Considering the weaknesses and disadvantages of human-guided and systematic techniques offered in the literature, this paper presents a model analysis and exploration tool for agent-based models. The tool first approximates input-output relationships by developing a metamodel, a simplified representation of the original agent-based model. For this purpose, it utilizes support vector regression, which is capable of approximating highly nonlinear systems accurately. Following metamodel fitting, the tool incorporates a tree-based method to extract knowledge embedded in the metamodel. The resulting tree is then expressed as a set of IF-THEN rules that have high comprehensibility compared to complex metamodel function. We utilized the tool for the exploration of Traffic Basic model and the results show the relationship between model input and output. Furthermore, rules extracted from the metamodel point out certain counter-intuitive results of the model which are not easily inferred from the raw input-output data. We also discuss potential uses of our tool and provide the R script which makes the analysis repeatable for other agent-based models.

}, keywords = {decision tree, MetaModel, R, Rule Extraction, Support Vector Regression, Traffic}, issn = {1460-7425}, doi = {10.18564/jasss.3786}, url = {http://jasss.soc.surrey.ac.uk/21/4/1.html}, author = {Edali, Mert and G{\"o}nen{\c c} Y{\"u}cel} } @article {1160, title = {Accelerating Transition Dynamics in City Regions: A Qualitative Modeling Perspective}, journal = {Sustainability}, volume = {9}, year = {2017}, pages = {1254}, author = {Valkering, Pieter and G{\"o}nen{\c c} Y{\"u}cel and Gebetsroither-Geringer, Ernst and Markvica, Karin and Meynaerts, Erika and Frantzeskaki, Niki} } @article {1159, title = {Influence maximization based on partial network structure information: A comparative analysis on seed selection heuristics}, journal = {International Journal of Modern Physics C}, volume = {28}, year = {2017}, pages = {1750122}, author = {{\c S}irag Erkol and G{\"o}nen{\c c} Y{\"u}cel} } @article {Yavas2014, title = {Impact of Homophily on Diffusion Dynamics Over Social Networks}, journal = {Social Science Computer Review}, volume = {32}, number = {3}, year = {2014}, month = {mar}, abstract = {

The purpose of this study is to analyze the impact of homophily on diffusion over social networks. An agent-based simulation model is developed to serve as the experimental ground for this analysis. Diffusion dynamics of a nonsticky innovation is investigated by varying homophily levels in the social network depicted in the model as the primary control variable. First of all, the results show that homophily is self-reinforcing. Second, starting from a nonhomophilous network, early increases in the level of homophily have a positive effect on the extent of diffusion, whereas further increases have a negative impact. Finally, several local minima and maxima are observed in the relation between the homophily level and the extent of diffusion. Our analysis focuses on node properties such as connect- edness and average degrees in order to explain the observed regular relationship between homophily and diffusion. We argue that (i) homophily increases the connectedness of different status groups separately and (ii) increasing levels of homophily decreases the marginal importance of a single homo- philous tie by increasing the sources of valuable information. Future research involves investigating the coevolution of social behavior and networks by allowing the adopted innovation to lead to value homophily, exploration of different diffusion initiation types, and different adoption heuristics.

}, issn = {0894-4393}, doi = {10.1177/0894439313512464}, url = {http://ssc.sagepub.com/cgi/doi/10.1177/0894439313512464}, author = {Yava{\c s}, Mustafa and G{\"o}nen{\c c} Y{\"u}cel} } @inbook {Yucel2013a, title = {The actor-option framework: a general framework for modelling socio-technical systems in transitions}, booktitle = {Infranomics: Sustainability, Engineering Design and Governance}, series = {Topics in Safety, Risk, Reliability and Quality}, volume = {24}, year = {2013}, pages = {407{\textendash}418}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, keywords = {modelling, simulation, socio-technical transitions}, isbn = {978-3-319-02492-9}, doi = {10.1007/978-3-319-02493-6}, url = {http://link.springer.com/10.1007/978-3-319-02493-6}, author = {G{\"o}nen{\c c} Y{\"u}cel}, editor = {Gheorghe, Adrian V. and Masera, Marcelo and Katina, Polinpapilinho F.} } @proceedings {nisa1, title = {Evaluation of Alternative Dynamic Behavior Representations for Automated Model Output Classification and Clustering}, journal = {31st International Conference of the System Dynamics Society}, year = {2013}, author = {Nisa {\"O}nsel and E. {\"O}nsel and G{\"o}nen{\c c} Y{\"u}cel} } @article {Yucel2013, title = {Extent of inertia caused by the existing building stock against an energy transition in the Netherlands}, journal = {Energy and Buildings}, volume = {56}, year = {2013}, pages = {134{\textendash}145}, keywords = {residential energy consumption}, issn = {03787788}, doi = {10.1016/j.enbuild.2012.09.022}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0378778812004720}, author = {G{\"o}nen{\c c} Y{\"u}cel} } @article {Kwakkel2012, title = {An Exploratory Analysis of the Dutch Electricity System in Transition}, journal = {Journal of the Knowledge Economy}, year = {2012}, pages = {1{\textendash}16}, publisher = {Springer US}, abstract = {

Recent contextual developments constitute a backdrop of change for the Dutch electricity system. Institutional change driven by liberalization, changing economic competitiveness of the dominant fuels, new technologies, and changing end-user preferences regarding electricity supply are some exam- ples of these developments. This paper explores plausible transition trajectories in the face of these developments given technological uncertainty about invest- ment and operating costs, and fuel efficiency of various alternative technolo- gies; political uncertainty about future CO2 abatement policies such as emission trading; and socio-economic uncertainty about fuel prices, investment decisions of suppliers, and load curves. Various alternative developments for these uncertainties are specified. The consequences of each of these alternative developments are assessed using an agent-based model of the Dutch electricity system. The outputs are analyzed using various data-mining and data visualization techniques in order to reveal arch-typical transition trajectories and their conditions for occurring. Policy recommendations are derived from this. The results indicate that most transition trajectories point towards a future energy supply system that is reliant on clean coal and gas. Under the explored uncertainties, only rarely a transition to renewables occurs. The various sustainable energy support programs appear to be ineffective in steering the energy supply system towards a more sustainable mode of functioning across the various uncertainties.

}, keywords = {Electricity supply, Exploratory model, Transitions}, issn = {1868-7865}, doi = {10.1007/s13132-012-0128-1}, url = {http://dx.doi.org/10.1007/s13132-012-0128-1}, author = {Kwakkel, Jan and G{\"o}nen{\c c} Y{\"u}cel} } @article {Yucel2012, title = {A simulation-based analysis of transition pathways for the Dutch electricity system}, journal = {Energy Policy}, volume = {42}, year = {2012}, pages = {557{\textendash}568}, issn = {03014215}, doi = {10.1016/j.enpol.2011.12.024}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0301421511010299}, author = {G{\"o}nen{\c c} Y{\"u}cel and van Daalen, Cornelia} } @article {Yucel2011, title = {Automated parameter specification in dynamic feedback models based on behavior pattern features}, journal = {System Dynamics Review}, volume = {27}, number = {2}, year = {2011}, pages = {195{\textendash}215}, publisher = {Wiley Online Library}, keywords = {Calibration}, doi = {10.1002/sdr}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sdr.457/full}, author = {G{\"o}nen{\c c} Y{\"u}cel and Yaman Barlas} } @article {Yucel2011a, title = {Exploratory analysis of the impact of information dynamics on innovation diffusion}, journal = {Technological Forecasting and Social Change}, volume = {78}, number = {2}, year = {2011}, pages = {358{\textendash}372}, publisher = {Elsevier Inc.}, keywords = {diffusion of innovations, information diffusion, negative word-of-mouth, Simulation model}, issn = {00401625}, doi = {10.1016/j.techfore.2010.11.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0040162510002684}, author = {G{\"o}nen{\c c} Y{\"u}cel and van Daalen, Cornelia} } @article {Yucel2010, title = {Dynamics of the North{\textendash}South welfare gap and global sustainability}, journal = {Technological Forecasting and Social Change}, volume = {77}, number = {4}, year = {2010}, pages = {594{\textendash}614}, publisher = {Elsevier Inc.}, keywords = {north, south welfare gap}, issn = {00401625}, doi = {10.1016/j.techfore.2009.11.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0040162509001887}, author = {G{\"o}nen{\c c} Y{\"u}cel and Yaman Barlas} } @article {Yucel2009, title = {An objective-based perspective on assessment of model-supported policy processes}, journal = {Journal of Artificial Societies and Social Simulation}, volume = {12}, number = {4}, year = {2009}, pages = {3}, keywords = {model assessment, model typology, policy analysis, simulation, validation}, url = {http://jasss.soc.surrey.ac.uk/12/4/3.html}, author = {G{\"o}nen{\c c} Y{\"u}cel and van Daalen, Cornelia} } @article {Yucel2008, title = {Studying transition dynamics via focusing on underlying feedback interactions}, journal = {Computational and Mathematical Organization Theory}, volume = {14}, number = {4}, year = {2008}, pages = {320{\textendash}349}, issn = {1381-298X}, doi = {10.1007/s10588-008-9032-4}, url = {http://www.springerlink.com/index/10.1007/s10588-008-9032-4}, author = {G{\"o}nen{\c c} Y{\"u}cel and Chiong Meza, Catherine Miluska} }