A method for system of systems definition and modeling using patterns of collective behavior

The Department of Defense ship and aircraft acquisition process, with its capability-based assessments and fleet synthesis studies, relies heavily on the assumption that a functional decomposition of higher-level system of systems (SoS) capabilities into lower-level system and subsystem behaviors is both possible and practical. However, SoS typically exhibit “non-decomposable” behaviors (also known as emergent behaviors) for which no widely-accepted representation exists. The presence of unforeseen emergent behaviors, particularly undesirable ones, can make systems vulnerable to attacks, hacks, or other exploitation, or can cause delays in acquisition program schedules and cost overruns in order to mitigate them. The International Council on Systems Engineering has identified the development of methods for predicting and managing emergent behaviors as one of the top research priorities for the Systems Engineering profession. Therefore, this thesis develops a method for rendering quantifiable SoS emergent properties and behaviors traceable to patterns of interaction of their constitutive systems, so that exploitable patterns identified during the early stages of design can be accounted for. This method is designed to fill two gaps in the literature. First, the lack of an approach for mining data to derive a model (i.e. an equation) of the non-decomposable behavior. Second, the lack of an approach for qualitatively and quantitatively associating emergent behaviors with the components that cause the behavior. A definition for emergent behavior is synthesized from the literature, as well as necessary conditions for its identification. An ontology of emergence that enables studying the emergent behaviors exhibited by self-organized systems via numerical simulations is adapted for this thesis in order to develop the mathematical approach needed to satisfy the research objective. Within the confines of two carefully qualified assumptions (that the model is valid, and that the model is efficient), it is argued that simulated emergence is bona-fide emergence, and that simulations can be used for experimentation without sacrificing rigor. This thesis then puts forward three hypotheses: The first hypothesis is that self-organized structures imply the presence of a form of data compression, and this compression can be used to explicitly calculate an upper bound on the number of emergent behaviors that a system can possess. The second hypothesis is that the set of numerical criteria for detecting emergent behavior derived in this research constitutes sufficient conditions for identifying weak and functional emergent behaviors. The third hypothesis states that affecting the emergent properties of these systems will have a bigger impact on the system’s performance than affecting any single component of that system. Using the method developed in this thesis, exploitable properties are identified and component behaviors are modified to attempt the exploit. Changes in performance are evaluated using problem-specific measures of merit. The experiments find that Hypothesis 2 is false (the numerical criteria are not sufficient conditions) by identifying instances where the numerical criteria produce a false-positive. As a result, a set of sufficient conditions for emergent behavior identification remains to be found. Hypothesis 1 was also falsified based on a worst-case scenario where the largest possible number of obtainable emergent behaviors was compared against the upper bound computed from the smallest possible data compression of a self-organized system. Hypothesis 3, on the other hand, was supported, as it was found that new behavior rules based on component-level properties provided less improvement to performance against an adversary than rules based on system-level properties. Overall, the method is shown to be an effective, systematic approach to non-decomposable behavior exploitation, and an improvement over the modern, largely ad hoc approach.Ph.D

Prevalence and patterns of higher-order drug interactions in Escherichia coli.

Interactions and emergent processes are essential for research on complex systems involving many components. Most studies focus solely on pairwise interactions and ignore higher-order interactions among three or more components. To gain deeper insights into higher-order interactions and complex environments, we study antibiotic combinations applied to pathogenic Escherichia coli and obtain unprecedented amounts of detailed data (251 two-drug combinations, 1512 three-drug combinations, 5670 four-drug combinations, and 13608 five-drug combinations). Directly opposite to previous assumptions and reports, we find higher-order interactions increase in frequency with the number of drugs in the bacteria's environment. Specifically, as more drugs are added, we observe an elevated frequency of net synergy (effect greater than expected based on independent individual effects) and also increased instances of emergent antagonism (effect less than expected based on lower-order interaction effects). These findings have implications for the potential efficacy of drug combinations and are crucial for better navigating problems associated with the combinatorial complexity of multi-component systems

Emergent states in dense systems of active rods: from swarming to turbulence

Dense suspensions of self-propelled rod-like particles exhibit a fascinating variety of non-equilibrium phenomena. By means of computer simulations of a minimal model for rigid self-propelled colloidal rods with variable shape we explore the generic diagram of emerging states over a large range of rod densities and aspect ratios. The dynamics is studied using a simple numerical scheme for the overdamped noiseless frictional dynamics of a many-body system in which steric forces are dominant over hydrodynamic ones. The different emergent states are identified by various characteristic correlation functions and suitable order parameter fields. At low density and aspect ratio, a disordered phase with no coherent motion precedes a highly-cooperative swarming state at large aspect ratio. Conversely, at high densities weakly anisometric particles show a distinct jamming transition whereas slender particles form dynamic laning patterns. In between there is a large window corresponding to strongly vortical, turbulent flow. The different dynamical states should be verifiable in systems of swimming bacteria and artificial rod-like micro-swimmers.Comment: 14 pages, 8 figure

A strategic perspective for managing socio-technical systems: the missing link

Most man-made systems around us are mainly socio-technical systems. As such it is imperative that to manage such systems effectively we need to understand their properties at both the micro and macro level and the holistic functioning of such systems. Such an approach is important in understanding the emergent properties that are exhibited by such system. We already have been delving into the micro level and the intricacies of the different subsystems without actually having the broader view of the whole system. This current approach came from the fact that reductionism is the ‘mantra’ of our scientific nature and endeavours, and dictates how a problem is solved. In this paper a strategic approach is put forward, making use of the force field theory as a necessary missing component for designing and managing socio-technical systems. With this proposed strategic approach the true understanding of solving these emergent properties will be reinforced with what we already know and also help in solving some disorder exhibited in these systems, without creating more uncertainties. This paper sets out the framework and its usefulness to understanding the socio-technical systems around us

Development and validation of computational models of cellular interaction

In this paper we take the view that computational models of biological systems should satisfy two conditions – they should be able to predict function at a systems biology level, and robust techniques of validation against biological models must be available. A modelling paradigm for developing a predictive computational model of cellular interaction is described, and methods of providing robust validation against biological models are explored, followed by a consideration of software issues

The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors

Background: A deep understanding of what causes the phenotypic variation arising from biological patterning processes, cannot be claimed before we are able to recreate this variation by mathematical models capable of generating genotype-phenotype maps in a causally cohesive way. However, the concept of pattern in a multicellular context implies that what matters is not the state of every single cell, but certain emergent qualities of the total cell aggregate. Thus, in order to set up a genotype-phenotype map in such a spatiotemporal pattern setting one is actually forced to establish new pattern descriptors and derive their relations to parameters of the original model. A pattern descriptor is a variable that describes and quantifies a certain qualitative feature of the pattern, for example the degree to which certain macroscopic structures are present. There is today no general procedure for how to relate a set of patterns and their characteristic features to the functional relationships, parameter values and initial values of an original pattern-generating model. Here we present a new, generic approach for explorative analysis of complex patterning models which focuses on the essential pattern features and their relations to the model parameters. The approach is illustrated on an existing model for Delta-Notch lateral inhibition over a two-dimensional lattice. Results: By combining computer simulations according to a succession of statistical experimental designs, computer graphics, automatic image analysis, human sensory descriptive analysis and multivariate data modelling, we derive a pattern descriptor model of those macroscopic, emergent aspects of the patterns that we consider of interest. The pattern descriptor model relates the values of the new, dedicated pattern descriptors to the parameter values of the original model, for example by predicting the parameter values leading to particular patterns, and provides insights that would have been hard to obtain by traditional methods. Conclusion: The results suggest that our approach may qualify as a general procedure for how to discover and relate relevant features and characteristics of emergent patterns to the functional relationships, parameter values and initial values of an underlying pattern-generating mathematical model

Investigating biocomplexity through the agent-based paradigm.

Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex