"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

Capturing Regular Human Activity through a Learning Context Memory

A learning context memory consisting of two main parts is presented. The first part performs lossy data compression, keeping the amount of stored data at a minimum by combining similar context attributes — the compression rate for the presented GPS data is 150:1 on average. The resulting data is stored in an appropriate data structure highlighting the level of compression. Elements with a high level of compression are used in the second part to form the start and end points of episodes capturing common activity consisting of consecutive events. The context memory is used to investigate how little context data can be stored containing still enough information to capture regular human activity

A new paradigm for SpeckNets:inspiration from fungal colonies

In this position paper, we propose the development of a new biologically inspired paradigm based on fungal colonies, for the application to pervasive adaptive systems. Fungal colonies have a number of properties that make them an excellent candidate for inspiration for engineered systems. Here we propose the application of such inspiration to a speckled computing platform. We argue that properties from fungal colonies map well to properties and requirements for controlling SpeckNets and suggest that an existing mathematical model of a fungal colony can developed into a new computational paradigm

A Hormone-Inspired Arbitration System For Self Identifying Abilities Amongst A Heterogeneous Robot Swarm

Current exploration of adaptation in robot swarms requires the swarm or individuals within that swarm to have knowledge of their own capabilities. Across long term use a swarms understanding of its capabilities may become inaccurate due to wear or faults in the system. In addition to this, systems capable of self designing morphologies are becoming increasingly feasible. In these self designing examples it would be impossible to have accurate knowledge of capability before executing a task for the first time. We propose an arbitration system that requires no explicit knowledge of capability but instead uses hormone-inspired values to decide on an environmental preference. The robots in the swarm differ by wheel type and thus how quickly they are able to move across terrain. The goal of this system is to allow robots to identify their strengths within a swarm and allocate themselves to areas of an environment with a floor type that suits their ability. This work shows that the use of a hormone-inspired arbitration system can extrapolate robot capability and adapt the systems preference of terrain to suit said capability.</p

Immune-Inspired Error Detection for Multiple Faulty Robots in Swarm Robotics

Error detection and recovery are important issues in swarm robotics research, as they are a means by which fault tolerance can be achieved. Our previous work has looked at error detection for single failures in a swarm robotics scenario with the Receptor Density Algorithm. Three modes of failure to the wheels of individual robots was investigated and comparable performance to other statistical methods was achieved. In this paper, we investigate the potential of extending this approach to a robot swarm with multiple faulty robots. Two experiements have been conducted: A swarm of ten robots with 1 to 8 faulty robots, and a swarm of 10 to 20 robots with varying number of faulty robots. Results from the experiments showed that the proposed approach is able to detect errors in multiple faulty robots. The results also suggest the need to further investigate other aspects of the robot swarm that can potentially affect the performance of detection such as the communication range.</p

The rise in computational systems biology approaches for understanding NF-κB signaling dynamics

A study by Cheng et al. in this issue of Science Signaling highlights the distinct single-cell signaling characteristics conferred by pathways mediated by the adaptor proteins MyD88 and TRIF in the TLR4-dependent activation of the transcription factor nuclear factor κB (NF-κB)

Computational models of the NF-κB signalling pathway

In this review article, we discuss the current state of computational modelling of the nuclear factor-kappa B (NF-κB) signalling pathway. NF-κB is a transcription factor, which is ubiquitous within cells and controls a number of immune responses, including inflammation and apoptosis. The NF-κB signalling pathway is tightly regulated, commencing with activation at the cell membrane, signal transduction through various components within the cytoplasm, translocation of NF-κB into the nucleus and, finally, the transcription of various genes relating to the innate and adaptive immune responses. There have been a number of computational (mathematical) models developed of the signalling pathway over the past decade. This review describes how these approaches have helped advance our understanding of NF-κB control

Run-time detection of faults in autonomous mobile robots based on the comparison of simulated and real robot behaviour

© 2014 IEEE. This paper presents a novel approach to the run-time detection of faults in autonomous mobile robots, based on simulated predictions of real robot behaviour. We show that although simulation can be used to predict real robot behaviour, drift between simulation and reality occurs over time due to the reality gap. This necessitates periodic reinitialisation of the simulation to reduce false positives. Using a simple obstacle avoidance controller afflicted with partial motor failure, we show that selecting the length of this reinitialisation time period is non-trivial, and that there exists a trade-off between minimising drift and the ability to detect the presence of faults

A Fractal Immune Network

Abstract. Proteins are the driving force in development (embryogenesis) and the immune system. Here we describe how a model of proteins designed for evolutionary development in computers can be combined with a model of immune systems. Full details of a prototype system are provided, and preliminary experiments presented. Results show that evolution is able to adjust the mapping between input data and antigens and cause useful changes to the subnetworks formed by the immune algorithm