Biologically inspired, self organizing communication networks.

PhDThe problem of energy-efficient, reliable, accurate and self-organized target tracking in Wireless Sensor Networks (WSNs) is considered for sensor nodes with limited physical resources and abrupt manoeuvring mobile targets. A biologically inspired, adaptive multi-sensor scheme is proposed for collaborative Single Target Tracking (STT) and Multi-Target Tracking (MTT). Behavioural data obtained while tracking the targets including the targets’ previous locations is recorded as metadata to compute the target sampling interval, target importance and local monitoring interval so that tracking continuity and energy-efficiency are improved. The subsequent sensor groups that track the targets are selected proactively according to the information associated with the predicted target location probability such that the overall tracking performance is optimized or nearly-optimized. One sensor node from each of the selected groups is elected as a main node for management operations so that energy efficiency and load balancing are improved. A decision algorithm is proposed to allow the “conflict” nodes that are located in the sensing areas of more than one target at the same time to decide their preferred target according to the target importance and the distance to the target. A tracking recovery mechanism is developed to provide the tracking reliability in the event of target loss. The problem of task mapping and scheduling in WSNs is also considered. A Biological Independent Task Allocation (BITA) algorithm and a Biological Task Mapping and Scheduling (BTMS) algorithm are developed to execute an application using a group of sensor nodes. BITA, BTMS and the functional specialization of the sensor groups in target tracking are all inspired from biological behaviours of differentiation in zygote formation. Simulation results show that compared with other well-known schemes, the proposed tracking, task mapping and scheduling schemes can provide a significant improvement in energy-efficiency and computational time, whilst maintaining acceptable accuracy and seamless tracking, even with abrupt manoeuvring targets.Queen Mary university of London full Scholarshi

Degeneracy: a design principle for achieving robustness and evolvability

Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species. Increasing robustness, so is proposed, can lead to the emergence of evolvability if evolution proceeds over a neutral network that extends far throughout the fitness landscape. Here, we show that the design principles used to achieve robustness dramatically influence whether robustness leads to evolvability. In simulation experiments, we find that purely redundant systems have remarkably low evolvability while degenerate, i.e. partially redundant, systems tend to be orders of magnitude more evolvable. Surprisingly, the magnitude of observed variation in evolvability can neither be explained by differences in the size nor the topology of the neutral networks. This suggests that degeneracy, a ubiquitous characteristic in biological systems, may be an important enabler of natural evolution. More generally, our study provides valuable new clues about the origin of innovations in complex adaptive systems.Comment: Accepted in the Journal of Theoretical Biology (Nov 2009

Refining interaction search through signed iterative Random Forests

Advances in supervised learning have enabled accurate prediction in biological systems governed by complex interactions among biomolecules. However, state-of-the-art predictive algorithms are typically black-boxes, learning statistical interactions that are difficult to translate into testable hypotheses. The iterative Random Forest algorithm took a step towards bridging this gap by providing a computationally tractable procedure to identify the stable, high-order feature interactions that drive the predictive accuracy of Random Forests (RF). Here we refine the interactions identified by iRF to explicitly map responses as a function of interacting features. Our method, signed iRF, describes subsets of rules that frequently occur on RF decision paths. We refer to these rule subsets as signed interactions. Signed interactions share not only the same set of interacting features but also exhibit similar thresholding behavior, and thus describe a consistent functional relationship between interacting features and responses. We describe stable and predictive importance metrics to rank signed interactions. For each SPIM, we define null importance metrics that characterize its expected behavior under known structure. We evaluate our proposed approach in biologically inspired simulations and two case studies: predicting enhancer activity and spatial gene expression patterns. In the case of enhancer activity, s-iRF recovers one of the few experimentally validated high-order interactions and suggests novel enhancer elements where this interaction may be active. In the case of spatial gene expression patterns, s-iRF recovers all 11 reported links in the gap gene network. By refining the process of interaction recovery, our approach has the potential to guide mechanistic inquiry into systems whose scale and complexity is beyond human comprehension