On the Criticality of Adaptive Boolean Network Robots

Systems poised at a dynamical critical regime, between order and disorder, have been shown capable of exhibiting complex dynamics that balance robustness to external perturbations and rich repertoires of responses to inputs. This property has been exploited in artificial network classifiers, and preliminary results have also been attained in the context of robots controlled by Boolean networks. In this work, we investigate the role of dynamical criticality in robots undergoing online adaptation, i.e., robots that adapt some of their internal parameters to improve a performance metric over time during their activity. We study the behavior of robots controlled by random Boolean networks, which are either adapted in their coupling with robot sensors and actuators or in their structure or both. We observe that robots controlled by critical random Boolean networks have higher average and maximum performance than that of robots controlled by ordered and disordered nets. Notably, in general, adaptation by change of couplings produces robots with slightly higher performance than those adapted by changing their structure. Moreover, we observe that when adapted in their structure, ordered networks tend to move to the critical dynamical regime. These results provide further support to the conjecture that critical regimes favor adaptation and indicate the advantage of calibrating robot control systems at dynamical critical states

Towards a Boolean network-based Computational Model for Cell Differentiation and its applications to Robotics

Living organisms are the ultimate product of a series of complex processes that take place within—and among—biological cells. Most of these processes, such as cell differentiation, are currently poorly understood. Cell differentiation is the process by which cells progressively specialise. Being a fundamental process within cells, its dysregulations have dramatic implications in biological organisms ranging from developmental issues to cancer formation. The thesis objective is to contribute to the progress in the understanding of cell differentiation and explore the applications of its properties for designing artificial systems. The proposed approach, which relies on Boolean networks based modelling and on the theory of dynamical systems, aims at investigating the general mechanisms underlying cell differentiation. The results obtained contribute to taking a further step towards the formulation of a general theoretical framework—so far missing—for cellular differentiation. We conducted an in-depth analysis of the impact of self-loops in random Boolean networks ensembles. We proposed a new model of differentiation driven by a simplified bio-inspired methylation mechanism in Boolean models of genetic regulatory networks. On the artificial side, by introducing the conceptual metaphor of the “attractor landscape” and related proofs of concept that support its potential, we paved the way for a new research direction in robotics called behavioural differentiation robotics: a branch of robotics dealing with the designing of robots capable of expressing different behaviours in a way similar to that of biological cells that undergo differentiation. The implications of the results achieved may have beneficial effects on medical research. Indeed, the proposed approach can foster new questions, experiments and in turn, models that hopefully in the next future will take us to cure differentiation-related diseases such as cancer. Our work may also contribute to address questions concerning the evolution of complex behaviours and to help design robust and adaptive robots

Complexity Measures: Open Questions and Novel Opportunities in the Automatic Design and Analysis of Robot Swarms

Complexity measures and information theory metrics in general have recently been attracting the interest of multi-agent and robotics communities, owing to their capability of capturing relevant features of robot behaviors, while abstracting from implementation details. We believe that theories and tools from complex systems science and information theory may be fruitfully applied in the near future to support the automatic design of robot swarms and the analysis of their dynamics. In this paper we discuss opportunities and open questions in this scenario

The evolutionary origins of hierarchy

Hierarchical organization -- the recursive composition of sub-modules -- is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force--the cost of connections--promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.Comment: 32 page

Towards the control of cell states in gene regulatory networks by evolving Boolean networks

Biological cell behaviours emerge from complex patterns of interactions between genes and their products, known as gene regulatory networks (GRNs). More specifically, GRNs are complex dynamical structures that orchestrate the activities of biological cells by governing the expression of mRNA and proteins. Many computational models of these networks have been shown to be able to carry out complex computation in an efficient and robust manner, particularly in the domains of control and signal processing. GRNs play a central role within living organisms and efficient strategies for controlling their dynamics need to be developed. For instance, the ability to push a cell towards or away from certain behaviours, is an important aim in fields such as medicine and synthetic biology. This could, for example, help to find novel approaches in the design of therapeutic drugs. However, current approaches to controlling these networks exhibit poor scalability and limited generality. This thesis proposes a new approach and an alternative method for performing state space targeting in GRNs, by coupling an artificial GRN to an existing GRN. This idea is tested in simulation by coupling together Boolean networks that represent controlled and controller systems. Evolutionary algorithms are used to evolve the controller Boolean networks. Controller Boolean networks are applied to a range of controlled Boolean networks including Boolean models of actual biological circuits, each with different dynamics. The results show that controller Boolean networks can be optimised to control trajectories in the target networks. Also, the approach scales well as the target network size increases. The use of Boolean modelling is potentially advantageous from an implementation perspective, since synthetic biology techniques can be used to refine an optimised controller Boolean network into an in vivo form, which could then control a genetic network directly from within a cell

Attractor-Specific and Common Expression Values in Random Boolean Network Models (with a Preliminary Look at Single-Cell Data)

Random Boolean Networks (RBNs for short) are strongly simplified models of gene regulatory networks (GRNs), which have also been widely studied as abstract models of complex systems and have been used to simulate different phenomena. We define the “common sea” (CS) as the set of nodes that take the same value in all the attractors of a given network realization, and the “specific part” (SP) as the set of all the other nodes, and we study their properties in different ensembles, generated with different parameter values. Both the CS and of the SP can be composed of one or more weakly connected components, which are emergent intermediate-level structures. We show that the study of these sets provides very important information about the behavior of the model. The distribution of distances between attractors is also examined. Moreover, we show how the notion of a “common sea” of genes can be used to analyze data from single-cell experiments

Bio-inspired Dynamic Control Systems with Time Delays

The world around us exhibits a rich and ever changing environment of startling, bewildering and fascinating complexity. Almost everything is never as simple as it seems, but through the chaos we may catch fleeting glimpses of the mechanisms within. Throughout the history of human endeavour we have mimicked nature to harness it for our own ends. Our attempts to develop truly autonomous and intelligent machines have however struggled with the limitations of our human ability. This has encouraged some to shirk this responsibility and instead model biological processes and systems to do it for us. This Thesis explores the introduction of continuous time delays into biologically inspired dynamic control systems. We seek to exploit rich temporal dynamics found in physical and biological systems for modelling complex or adaptive behaviour through the artificial evolution of networks to control robots. Throughout, arguments have been presented for the modelling of delays not only to better represent key facets of physical and biological systems, but to increase the computational potential of such systems for the synthesis of control. The thorough investigation of the dynamics of small delayed networks with a wide range of time delays has been undertaken, with a detailed mathematical description of the fixed points of the system and possible oscillatory modes developed to fully describe the behaviour of a single node. Exploration of the behaviour for even small delayed networks illustrates the range of complex behaviour possible and guides the development of interesting solutions. To further exploit the potential of the rich dynamics in such systems, a novel approach to the 3D simulation of locomotory robots has been developed focussing on minimising the computational cost. To verify this simulation tool a simple quadruped robot was developed and the motion of the robot when undergoing a manually designed gait evaluated. The results displayed a high degree of agreement between the simulation and laser tracker data, verifying the accuracy of the model developed. A new model of a dynamic system which includes continuous time delays has been introduced, and its utility demonstrated in the evolution of networks for the solution of simple learning behaviours. A range of methods has been developed for determining the time delays, including the novel concept of representing the time delays as related to the distance between nodes in a spatial representation of the network. The application of these tools to a range of examples has been explored, from Gene Regulatory Networks (GRNs) to robot control and neural networks. The performance of these systems has been compared and contrasted with the efficacy of evolutionary runs for the same task over the whole range of network and delay types. It has been shown that delayed dynamic neural systems are at least as capable as traditional Continuous Time Recurrent Neural Networks (CTRNNs) and show significant performance improvements in the control of robot gaits. Experiments in adaptive behaviour, where there is not such a direct link between the enhanced system dynamics and performance, showed no such discernible improvement. Whilst we hypothesise that the ability of such delayed networks to generate switched pattern generating nodes may be useful in Evolutionary Robotics (ER) this was not borne out here. The spatial representation of delays was shown to be more efficient for larger networks, however these techniques restricted the search to lower complexity solutions or led to a significant falloff as the network structure becomes more complex. This would suggest that for anything other than a simple genotype, the direct method for encoding delays is likely most appropriate. With proven benefits for robot locomotion and the open potential for adaptive behaviour delayed dynamic systems for evolved control remain an interesting and promising field in complex systems research

Engineering behavioural differentiation in robots controlled by Boolean networks

The design of control software for robots that are required to face different and unpredictable environmental conditions is of paramount importance in current robotic research. A viable solution to attain such a control software consists in exploiting the rich dynamics of biological cell models; indeed, cells are capable of differentiating into specific types, each characterized by peculiar behavioural traits suited to the particular environmental condition in which the cell acts. Moreover, if properly triggered, cells can also undergo type changes. Inspired by this phenomenon, in this work we have devised a method to support the automatic design of robots controlled by Boolean networks (BNs), which are a notable model of genetic regulatory networks. The initial behaviour of the robot is not specific, i.e. its BN is in an undifferentiated state. When specific environmental conditions appear, the BN changes its dynamics that in turn induces a specific behaviour in the robot. If, subsequently, the environmental signals change, the robot is able to return to the initial, undifferentiated behaviour and then differentiate again into a different behaviour, according to the external signals. This method is shown in detail, along with a thorough experimental analysis, in a case study involving taxis behaviours

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u