On agent-based modeling and computational social science

BharatSim: An agent-based modelling framework for India

BharatSim is an open-source agent-based modelling framework for the Indian population. It can simulate populations at multiple scales, from small communities to states. BharatSim uses a synthetic population created by applying statistical methods and machine learning algorithms to survey data from multiple sources, including the Census of India, the India Human Development Survey, the National Sample Survey, and the Gridded Population of the World. This synthetic population defines individual agents with multiple attributes, among them age, gender, home and work locations, pre-existing health conditions, and socio-economic and employment status. BharatSim's domain-specific language provides a framework for the simulation of diverse models. Its computational core, coded in Scala, supports simulations of a large number of individual agents, up to 50 million. Here, we describe the design and implementation of BharatSim, using it to address three questions motivated by the COVID-19 pandemic in India: (i) When can schools be safely reopened given specified levels of hybrid immunity?, (ii) How do new variants alter disease dynamics in the background of prior infections and vaccinations? and (iii) How can the effects of varied non-pharmaceutical interventions (NPIs) be quantified for a model Indian city? Through its India-specific synthetic population, BharatSim allows disease modellers to address questions unique to this country. It should also find use in the computational social sciences, potentially providing new insights into emergent patterns in social behaviour.

How the Complexity of Psychological Processes Reframes the Issue of Reproducibility in Psychological Science

In the past decade, various recommendations have been published to enhance the methodological rigor and publication standards in psychological science. However, adhering to these recommendations may have limited impact on the reproducibility of causal effects as long as psychological phenomena continue to be viewed as decomposable into separate and additive statistical structures of causal relationships. In this article, we show that (a) psychological phenomena are patterns emerging from nondecomposable and nonisolable complex processes that obey idiosyncratic nonlinear dynamics, (b) these processual features jeopardize the chances of standard reproducibility of statistical results, and (c) these features call on researchers to reconsider what can and should be reproduced, that is, the psychological processes per se, and the signatures of their complexity and dynamics. Accordingly, we argue for a greater consideration of process causality of psychological phenomena reflected by key properties of complex dynamical systems (CDSs). This implies developing and testing formal models of psychological dynamics, which can be implemented by computer simulation. The scope of the CDS paradigm and its convergences with other paradigms are discussed regarding the reproducibility issue. Ironically, the CDS approach could account for both reproducibility and nonreproducibility of the statistical effects usually sought in mainstream psychological science.

In silico study of heterogeneous tumour-derived organoid response to CAR T-cell therapy

Chimeric antigen receptor (CAR) T-cell therapy is a promising immunotherapy for treating cancers. This method consists in modifying the patients' T-cells to directly target antigen-presenting cancer cells. One of the barriers to the development of this type of therapies, is target antigen heterogeneity. It is thought that intratumour heterogeneity is one of the leading determinants of therapeutic resistance and treatment failure. While understanding antigen heterogeneity is important for effective therapeutics, a good therapy strategy could enhance the therapy efficiency. In this work we introduce an agent-based model (ABM), built upon a previous ABM, to rationalise the outcomes of different CAR T-cells therapies strategies over heterogeneous tumour-derived organoids. We found that one dose of CAR T-cell therapy should be expected to reduce the tumour size as well as its growth rate, however it may not be enough to completely eliminate it. Moreover, the amount of free CAR T-cells (i.e. CAR T-cells that did not kill any cancer cell) increases as we increase the dosage, and so does the risk of side effects. We tested different strategies to enhance smaller dosages, such as enhancing the CAR T-cells long-term persistence and multiple dosing. For both approaches an appropriate dosimetry strategy is necessary to produce "effective yet safe" therapeutic results. Moreover, an interesting emergent phenomenon results from the simulations, namely the formation of a shield-like structure of cells with low antigen expression. This shield turns out to protect cells with high antigen expression. Finally we tested a multi-antigen recognition therapy to overcome antigen escape and heterogeneity. Our studies suggest that larger dosages can completely eliminate the organoid, however the multi-antigen recognition increases the risk of side effects. Therefore, an appropriate small dosages dosimetry strategy is necessary to improve the outcomes. Based on our results, it is clear that a proper therapeutic strategy could enhance the therapies outcomes. In that direction, our computational approach provides a framework to model treatment combinations in different scenarios and to explore the characteristics of successful and unsuccessful treatments.

Can Generative AI improve social science?

Generative AI that can produce realistic text, images, and other human-like outputs is currently transforming many different industries. Yet it is not yet known how such tools might influence social science research. I argue Generative AI has the potential to improve survey research, online experiments, automated content analyses, agent-based models, and other techniques commonly used to study human behavior. In the second section of this article, I discuss the many limitations of Generative. I examine how bias in the data used to train these tools can negatively impact social science research-as well as a range of other challenges related to ethics, replication, environmental impact, and the proliferation of low-quality research. I conclude by arguing that social scientists can address many of these limitations by creating open-source infrastructure for research on human behavior. Such infrastructure is not only necessary to ensure broad access to high-quality research tools, I argue, but also because the progress of AI will require deeper understanding of the social forces that guide human behavior.

Agent-based social simulations for health crises response: utilising the everyday digital health perspective

There is increasing recognition of the role that artificial intelligence (AI) systems can play in managing health crises. One such approach, which allows for analysing the potential consequences of different policy interventions is agent-based social simulations (ABSS). Here, the actions and interactions of autonomous agents are modelled to generate virtual societies that can serve as a "testbed" for investigating and comparing different interventions and scenarios. This piece focuses on two key challenges of ABSS in collaborative policy interventions during the COVID-19 pandemic. These were defining valuable scenarios to simulate and the availability of appropriate data. This paper posits that drawing on the research on the "everyday" digital health perspective in designing ABSS before or during health crises, can overcome aspects of these challenges. The focus on digital health interventions reflects a rapid shift in the adoption of such technologies during and after the COVID-19 pandemic, and the new challenges this poses for policy makers. It is argued that by accounting for the everyday digital health in modelling, ABSS would be a more powerful tool in future health crisis management.

Agent-based simulation and child protection systems: Rationale, implementation, and verification

BACKGROUND AND OBJECTIVE

Simulation models are an important tool used in health care and other disciplines to support operational research and decision-making. In the child protection literature, simulation models are an under-utilized source of research evidence.

PARTICIPANTS AND SETTING

In this paper, we describe the rationale for and the development of an agent-based simulation of a child protection system in the US. Using the investigation, prevention service, and placement histories of 600,000 children served in an urban child welfare system, we walk the reader through the development of a prototype known as OSPEDALE.

METHODS

The governing equations built into OSPEDALE probabilistically simulate the onset of investigations. Then, drawing from empirical survival distributions, the governing equations trace the probability of subsequent interactions with the system (recurrence of maltreatment, service referrals, and placement) conditional on the characteristics of children, their assessed risk level, and prior child protection system involvement.

RESULTS

As an initial test of OSPEDALE's utility, we compare empirical admission counts with counts generated from OSPEDALE. Though the verification step is admittedly simple, the comparison shows that OSPEDALE replicates the empirical count of new admissions closely enough to justify further investment in OSPEDALE.

CONCLUSIONS

Management of public child protection systems is increasingly research evidence-dependent. The emphasis on research evidence as a decision-support tool has elevated evidence acquired through randomized clinical trials. Though important, the evidence from clinical trials represents only one type of research evidence. Properly specified, simulation models are another source of evidence with real-world relevance.

An integrated framework of mobile crowd estimation for the 2019, July 1st rally in Hong Kong

Traditional approach of mobile crowd estimation involves counting a group of individuals at a specific place, manually, in real-time. It is a laborious exercise that can be physically and mentally demanding. In Hong Kong, a large rally can last more than six hours, making the manual count method susceptible to human errors. While crowd counting using object detection and tracking has been well-established in computer vision, such application has remained relatively small scale within a controlled indoor setting (e.g. counting people at fixed gateways in a mall). No attempt to date has applied the automatic crowd counting method to count hundreds of thousands of people along an open stretch of rally route within the complex urban outdoor landscape. This research proposed an integrated approach that combines the capture-recapture method in statistics and a Convolutional Neural Network (CNN) method in computer vision to count the mobile crowd. The research teams implemented the integrative approach and counted 276,970 people with a 95% confidence interval of 263,663 to 290,276 in the 2019, July 1st Rally in Hong Kong. This work counted the attendance of a large-scale rally as a proof of concept to fill in a gap in the empirical studies. The intellectual merits and research findings shed useful insights to improve mobile population estimation and leverage alternative data sources to support related scientific applications.

Synergistic Integration Between Machine Learning and Agent-Based Modeling: A Multidisciplinary Review

Agent-based modeling (ABM) involves developing models in which agents make adaptive decisions in a changing environment. Machine-learning (ML) based inference models can improve sequential decision-making by learning agents' behavioral patterns. With the aid of ML, this emerging area can extend traditional agent-based schemes that hardcode agents' behavioral rules into an adaptive model. Even though there are plenty of studies that apply ML in ABMs, the generalized applicable scenarios, frameworks, and procedures for implementations are not well addressed. In this article, we provide a comprehensive review of applying ML in ABM based on four major scenarios, i.e., microagent-level situational awareness learning, microagent-level behavior intervention, macro-ABM-level emulator, and sequential decision-making. For these four scenarios, the related algorithms, frameworks, procedures of implementations, and multidisciplinary applications are thoroughly investigated. We also discuss how ML can improve prediction in ABMs by trading off the variance and bias and how ML can improve the sequential decision-making of microagent and macrolevel policymakers via a mechanism of reinforced behavioral intervention. At the end of this article, future perspectives of applying ML in ABMs are discussed with respect to data acquisition and quality issues, the possible solution of solving the convergence problem of reinforcement learning, interpretable ML applications, and bounded rationality of ABM.

Testing the Social Function of Metacognition for Common-Pool Resource Use

Metacognition, the ability to monitor and evaluate our own cognitive processes, confers advantages to individuals and their own judgment. A more recent hypothesis, however, states that explicit metacognition may also enhance the collective judgment of groups, and may enhance human collaboration and coordination. Here, we investigate this social function hypothesis of metacognition with arguably one of the oldest collaboration problems humans face, common-pool resource use. Using an agent-based model that simulates repeated group interactions and the forming of collective judgments about resource extraction, we show that (1) in "kind" environments (where confidence and judgment accuracy correlate positively), explicit metacognition may allow groups to reach more accurate judgments compared to groups exchanging object-level information only; while (2) in "wicked" environments (where confidence and judgment accuracy correlate negatively), explicit metacognition may protect groups from the large judgment errors yielded by groups using metacognitive information for individual-level learning only (implicit metacognition). With explicit metacognition, this research highlights a novel mechanism which, among others, provides a testable explanation of the often-observed finding that groups all over the world communicate to enhance common property use.

NorMASS: A normative MAS-based modeling approach for simulating incentive mechanisms of Q&A communities

Incentive mechanisms steer users in Q&A communities to achieve community goals, which need to be cautiously reviewed and revised before actual industrial application. Simulating incentive mechanisms is significant for predicting how changes in incentive mechanisms will affect community emergence, such as user answering patterns. However, due to the complexity of Q&A communities, the challenge faced by simulating incentive mechanisms lies in the difficulty of establishing micro-macro connections in the communities to simulate their emergence. To fill this gap, this paper proposes a Normative Multi-Agent System based Simulation (NorMASS) approach to simulate community emergence. The NorMASS models a Q&A community as a normative multi-agent system and adopts agents to formally express community users. Moreover, the approach provides an open-source simulator with a data generator to simulate community emergence. An evaluation of the NorMASS comparing simulation emergence with the counterpart of an actual community demonstrates that the proposed approach provides an effective solution for simulating incentive mechanisms of Q&A communities, with a similarity of 80% or above.

A research agenda for the study of social norm change

Social norms have been investigated across many disciplines for many years, but until recently, studies mainly provided indirect, implicit and correlational support for the role of social norms in driving behaviour. To understand how social norms, and in particular social norm change, can generate a large-scale behavioural change to deal with some of the most pressing challenges of our current societies, such as climate change and vaccine hesitancy, we discuss and review several recent advances in social norm research that enable a more precise underpinning of the role of social norms: how to identify their existence, how to establish their causal effect on behaviour and when norm change may pass tipping points. We advocate future research on social norms to study norm change through a mechanism-based approach that integrates experimental and computational methods in theory-driven, empirically calibrated agent-based models. As such, social norm research may move beyond unequivocal praising of social norms as the missing link between self-interested behaviour and observed cooperation or as the explanation for (the lack of) social tipping. It provides the toolkit to understand explicitly where, when and how social norms can be a solution to solve large-scale problems, but also to recognize their limits. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Social integration as a determinant of inequalities in green space usage: Insights from a theoretical agent-based model

Visiting urban green spaces (UGS) benefits physical and mental health. However, socio-economic and geographical inequalities in visits persist and their causes are under-explored. Perceptions of, and attitudes to, other UGS users have been theorised as a determinant of visiting. In the absence of data on these factors, we created a spatial agent-based model (ABM) of four cities in Scotland to investigate intra- and inter-city inequalities in UGS visiting. The ABM focused on the plausibility of a 'social integration hypothesis' whereby the primary factor in decisions to visit UGS is an assessment of who else is likely to be using the space. The model identified the conditions under which this mechanism was sufficient to reproduce the observed inequalities. The addition of environmental factors, such as neighbourhood walkability and green space quality, increased the ability of the model to reproduce observed phenomena. The model identified the potential for unanticipated adverse effects on both overall visit numbers and inequalities of interventions targeting those in lower socio-economic groups.

Agent-Based Models for Assessing Complex Statistical Models: An Example Evaluating Selection and Social Influence Estimates from SIENA

Although agent-based models (ABMs) have been increasingly accepted in social sciences as a valid tool to formalize theory, propose mechanisms able to recreate regularities, and guide empirical research, we are not aware of any research using ABMs to assess the robustness of our statistical methods. We argue that ABMs can be extremely helpful to assess models when the phenomena under study are complex. As an example, we create an ABM to evaluate the estimation of selection and influence effects by SIENA, a stochastic actor-oriented model proposed by Tom A. B. Snijders and colleagues. It is a prominent network analysis method that has gained popularity during the last 10 years and been applied to estimate selection and influence for a broad range of behaviors and traits such as substance use, delinquency, violence, health, and educational attainment. However, we know little about the conditions for which this method is reliable or the particular biases it might have. The results from our analysis show that selection and influence are estimated by SIENA asymmetrically and that, with very simple assumptions, we can generate data where selection estimates are highly sensitive to misspecification, suggesting caution when interpreting SIENA analyses.

Data-Driven Computational Social Network Science: Predictive and Inferential Models for Web-Enabled Scientific Discoveries

The ultimate goal of the social sciences is to find a general social theory encompassing all aspects of social and collective phenomena. The traditional approach to this is very stringent by trying to find causal explanations and models. However, this approach has been recently criticized for preventing progress due to neglecting prediction abilities of models that support more problem-oriented approaches. The latter models would be enabled by the surge of big Web-data currently available. Interestingly, this problem cannot be overcome with methods from computational social science (CSS) alone because this field is dominated by simulation-based approaches and descriptive models. In this article, we address this issue and argue that the combination of big social data with social networks is needed for creating prediction models. We will argue that this alliance has the potential for gradually establishing a causal social theory. In order to emphasize the importance of integrating big social data with social networks, we call this approach data-driven computational social network science (DD-CSNS).

Using a Modeling-Based Approach to Assess and Optimize HIV Linkage to Care Services

Evidence-based linkage to care interventions (LTCs) help recently diagnosed HIV+ individuals engage in care in a timely manner yet are heavily impacted by the systems in which they are embedded. We developed a prototype agent-based model informed by data from an established LTC program targeting youth and young adults aged 13-24 in Memphis, Tennessee. We then tested two interventions to improve LTC in a simulated environment: expanding testing sites versus using current testing sites but improving direct referral to LTC staff from organizations providing testing, to understand the impact on timely linkage to care. Improving direct referral to the LTC program decreased days to successful linkage from an average of 30 to 23 days but expanding testing sites increased average days to 31 days unless those sites also made direct referrals. We demonstrated how LTC is impacted by the system and interventions for shortening days to linkage to care.

Healthcare and education networks interaction as an indicator of social services stability following natural disasters

Healthcare and education systems have been identified by various national and international organizations as the main pillars of communities' stability. Understanding the correlation between these main social services institutions is critical to determining the tipping point of communities following natural disasters. Despite being defined as social services stability indicators, to date, no studies have been conducted to determine the level of interdependence between schools and hospitals and their collective influence on their recoveries following extreme events. In this study, we devise an agent-based model to investigate the complex interaction between healthcare and education networks and their overall recovery, while considering other physical, social, and economic factors. We employ comprehensive models to simulate the functional processes within each facility and to optimize their recovery trajectories after earthquake occurrence. The results highlight significant interdependencies between hospitals and schools, including direct and indirect relationships, suggesting the need for collective coupling of their recovery to achieve full functionality of either of the two systems following natural disasters. Recognizing this high level of interdependence, we then establish a social services stability index, which can be used by policymakers and community leaders to quantify the impact of healthcare and education services on community resilience and social services stability.

Advances in the agent-based modeling of economic and social behavior

In this review we discuss advances in the agent-based modeling of economic and social systems. We show the state of the art of the heuristic design of agents and how behavioral economics and laboratory experiments have improved the modeling of agent behavior. We further discuss how economic networks and social systems can be modeled and we discuss novel methodology and data sources. Lastly, we present an overview of estimation techniques to calibrate and validate agent-based models and show avenues for future research.

Analyzing the effects of memory biases and mood disorders on social performance

Realistic models of decision-making and social interactions, considering the nature of memory and biases, continue to be an area of immense interest. Emotion and mood are a couple of key factors that play a major role in decisions, nature of social interactions, size of the social network, and the level of engagement. Most of the prior work in this direction focused on a single trait, behavior, or bias. However, this work builds an integrated model that considers multiple traits such as loneliness, the drive to interact, the memory, and mood biases in an agent. The agent system comprises of rational, manic, depressed, and bipolar agents. The system is modeled with an interconnected network, and the size of the personal network of each agent is based on its nature. We consider a game of iterated interactions where an agent cooperates based on its past experiences with the other agent. Through simulation, the effects of various biases and comparative performances of agent types is analyzed. Taking the performance of rational agents as the baseline, manic agents do much better, and depressed agents do much worse. The payoffs also exhibit an almost-linear relationship with the extent of mania. It is also observed that agents with stronger memory perform better than those with weaker memory. For rational agents, there is no significant difference between agents with a positive bias and those with a negative bias. Positive bias is linked with higher payoffs in manic and bipolar agents. In depressed agents, negative bias is linked with higher payoffs. In manic agents, an intermediate value of mood dependence offers the highest payoff. But the opposite is seen in depressed agents. In bipolar agents, agents with weak mood dependence perform the best.

A social engineering model for poverty alleviation

Poverty, the quintessential denominator of a developing nation, has been traditionally defined against an arbitrary poverty line; individuals (or countries) below this line are deemed poor and those above it, not so! This has two pitfalls. First, absolute reliance on a single poverty line, based on basic food consumption, and not on total consumption distribution, is only a partial poverty index at best. Second, a single expense descriptor is an exogenous quantity that does not evolve from income-expenditure statistics. Using extensive income-expenditure statistics from India, here we show how a self-consistent endogenous poverty line can be derived from an agent-based stochastic model of market exchange, combining all expenditure modes (basic food, other food and non-food), whose parameters are probabilistically estimated using advanced Machine Learning tools. Our mathematical study establishes a consumption based poverty measure that combines labor, commodity, and asset market outcomes, delivering an excellent tool for economic policy formulation.

Current inequality and market consumption modelling appears to be subjective. Here the authors combined all three axes of poverty modelling - Engel-Krishnakumar’s microeconomics, Aoki-Chattopadhyay’s mathematical precept and found that multivariate construction is a key component of economic data analysis, implying all modes of income and expenditure need to be considered to arrive at a proper weighted prediction of poverty.

Developing political-ecological theory: The need for many-task computing

Models of political-ecological systems can inform policies for managing ecosystems that contain endangered species. To increase the credibility of these models, massive computation is needed to statistically estimate the model’s parameters, compute confidence intervals for these parameters, determine the model’s prediction error rate, and assess its sensitivity to parameter misspecification. To meet this statistical and computational challenge, this article delivers statistical algorithms and a method for constructing ecosystem management plans that are coded as distributed computing applications. These applications can run on cluster computers, the cloud, or a collection of in-house workstations. This downloadable code is used to address the challenge of conserving the East African cheetah (Acinonyx jubatus). This demonstration means that the new standard of credibility that any political-ecological model needs to meet is the one given herein.

Modeling the Economic Impact of Substandard and Falsified Antimalarials in the Democratic Republic of the Congo

Substandard and falsified medicines pose significant risks to global health, including increased deaths, prolonged treatments, and growing drug resistance. Antimalarials are one of the most common medications to be of poor quality in low- and middle-income countries. We assessed the health and economic impact of substandard and falsified antimalarials for children less than 5 years of age in the Democratic Republic of the Congo, which has one of the world's highest malaria mortality rates. We developed an agent-based model to simulate patient care-seeking behavior and medicine supply chain processes to examine the impact of antimalarial quality in Kinshasa province and Katanga region. We simulated the impact of potential interventions to improve medicinal quality, reduce stockouts, or educate caregivers. We estimated that substandard and falsified antimalarials are responsible for $20.9 million (35% of $59.6 million; 95% CI: $20.7-$21.2 million) in malaria costs in Kinshasa province and $130 million (43% of $301 million; $129-$131 million) in malaria costs in the Katanga region annually. If drug resistance to artemisinin were to develop, total annual costs of malaria could increase by $17.9 million (30%; $17.7-$18.0 million) and $73 million (24%; $72.2-$72.8 million) in Kinshasa and Katanga, respectively. Replacing substandard and falsified antimalarials with good quality medicines had a larger impact than interventions that prevented stockouts or educated caregivers. The results highlight the importance of improving access to good quality antimalarials to reduce the burden of malaria and mitigate the development of antimalarial resistance.

Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae

This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.

Influence of Narratives of Vision and Identity on Collective Behavior Change

Profound societal transformations are needed to move society from unsustainability to greater sustainability under continually changing social and environmental conditions. A key challenge is to understand the influences on and the dynamics of collective behavior change toward sustainability. In this paper we describe our approach to (1) understanding how affective narrative expressions influence transitions to more sustainable collective behaviors and (2) how that understanding, as well as the potential for using narrative expressions in modeling of social movements, can become a basis for improving community responses to change in a rapidly changing world. Our focus is on narratives that express visions of desirable futures and narratives that reflect individual and social identities, on the cultures and contexts in which they are embedded, exchanged, and modified, and through which they influence the dynamics of social movements toward sustainability. Using an analytical categorization of narrative expressions of case studies in the Caribbean, Micronesia, and Africa, we describe insights derived from the narratives of vision and social identities in diverse communities. Finally, we suggest that narrative expressions may provide a basis for agent-based modeling to expand thinking about potential development pathways of social movements for sustainable futures.

Development of an agent-based model to assess the impact of substandard and falsified anti-malarials: Uganda case study

BACKGROUND

Global efforts to address the burden of malaria have stagnated in recent years with malaria cases beginning to rise. Substandard and falsified anti-malarial treatments contribute to this stagnation. Poor quality anti-malarials directly affect health outcomes by increasing malaria morbidity and mortality, as well as threaten the effectiveness of treatment by contributing to artemisinin resistance. Research to assess the scope and impact of poor quality anti-malarials is essential to raise awareness and allocate resources to improve the quality of treatment. A probabilistic agent-based model was developed to provide country-specific estimates of the health and economic impact of poor quality anti-malarials on paediatric malaria. This paper presents the methodology and case study of the Substandard and Falsified Antimalarial Research Impact (SAFARI) model developed and applied to Uganda.

RESULTS

The total annual economic impact of malaria in Ugandan children under age five was estimated at US$614 million. Among children who sought medical care, the total economic impact was estimated at $403 million, including $57.7 million in direct costs. Substandard and falsified anti-malarials were a significant contributor to this annual burden, accounting for $31 million (8% of care-seeking children) in total economic impact involving $5.2 million in direct costs. Further, 9% of malaria deaths relating to cases seeking treatment were attributable to poor quality anti-malarials. In the event of widespread artemisinin resistance in Uganda, we simulated a 12% yearly increase in costs associated with paediatric malaria cases that sought care, inflicting $48.5 million in additional economic impact annually.

CONCLUSIONS

Improving the quality of treatment is essential to combat the burden of malaria and prevent the development of drug resistance. The SAFARI model provides country-specific estimates of the health and economic impact of substandard and falsified anti-malarials to inform governments, policy makers, donors and the malaria community about the threat posed by poor quality medicines. The model findings are useful to illustrate the significance of the issue and inform policy and interventions to improve medicinal quality.

Agent-Based Modeling in Molecular Systems Biology

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease.

In Silico Modeling of Immunotherapy and Stroma-Targeting Therapies in Human Colorectal Cancer

Despite the fact that the local immunological microenvironment shapes the prognosis of colorectal cancer, immunotherapy has shown no benefit for the vast majority of colorectal cancer patients. A better understanding of the complex immunological interplay within the microenvironment is required. In this study, we utilized wet lab migration experiments and quantitative histological data of human colorectal cancer tissue samples (n = 20) including tumor cells, lymphocytes, stroma, and necrosis to generate a multiagent spatial model. The resulting data accurately reflected a wide range of situations of successful and failed immune surveillance. Validation of simulated tissue outcomes on an independent set of human colorectal cancer specimens (n = 37) revealed the model recapitulated the spatial layout typically found in human tumors. Stroma slowed down tumor growth in a lymphocyte-deprived environment but promoted immune escape in a lymphocyte-enriched environment. A subgroup of tumors with less stroma and high numbers of immune cells showed high rates of tumor control. These findings were validated using data from colorectal cancer patients (n = 261). Low-density stroma and high lymphocyte levels showed increased overall survival (hazard ratio 0.322, P = 0.0219) as compared with high stroma and high lymphocyte levels. To guide immunotherapy in colorectal cancer, simulation of immunotherapy in preestablished tumors showed that a complex landscape with optimal stroma permeabilization and immune cell activation is able to markedly increase therapy response in silico These results can help guide the rational design of complex therapeutic interventions, which target the colorectal cancer microenvironment. Cancer Res; 77(22); 6442-52. ©2017 AACR.

Towards Computational and Behavioral Social Science

Abstract. In the last few years, the study of social phenomena has hosted a renewal of interest in Computational Social Science (CSS). While this field is not new – Axelrod’s first computational work on the evolution of cooperation goes back to 1981 – CSS has recently resurged under the pressure of quantitative social science and the application of Big Data analytics to social datasets. However, Big Data is no panacea and the data deluge that it provides raises more questions than it answers. The aim of this paper is to present an overview in which CSS will be introduced and the costs of CSS will be balanced against its benefits, in an attempt to propose an integrative view of the new and the old practice of CSS. In particular, two routes to integration will be drawn. First, it will be advocated that social data mining and computational modeling need to be integrated. Second, we will introduce the generative approach, aimed to understand how social phenomena can be generated starting from the micro-components, including psychological mechanisms, and we will discuss the necessity of combining it with the anticipatory, data-driven objective. By these means, Computational Social Science will develop into a more comprehensive field of Computational Social and Behavioral Science in which data science, ICT, as well as the behavioral and social sciences will be fruitfully integrated.

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework

Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.