Andrew J. Greensted

RISA: A Hardware Platform for Evolutionary Design

Reconfigurable integrated system array is a new form of field programmable digital device incorporating both hardware and software reconfigurable elements. RISA was developed specifically for implementing biologically inspired electronic systems. The architecture is particularly suited for investigating evolvable hardware due to the flexibility of RISAs configuration system. Fine grained partial reconfiguration is supported and random configuration bitstreams will not cause device damage. This paper describes the new RISA chip and the features that make it suitable for bio-inspired applications.

T Cell Receptor Signalling Inspired Kernel Density Estimation and Anomaly Detection

The T cell is able to perform fine-grained anomaly detection via its T Cell Receptor and intracellular signalling networks. We abstract from models of T Cell signalling to develop a new Artificial Immune System concepts involving the internal components of the TCR. We show that the concepts of receptor signalling have a natural interpretation as Parzen Window Kernel Density Estimation applied to anomaly detection. We then demonstrate how the dynamic nature of the receptors allows anomaly detection when probability distributions vary in time.

Implementation results for a fault-tolerant multicellular architecture inspired by endocrine communication

The hybrid redundancy structure found at the cellular level of higher animals provides complex organism with the three key features of a reliability-engineered system: fault tolerance, detection and recovery. For this reason, both the operation and organisation of this redundancy scheme provide an attractive source of inspiration for an electronic fault tolerant system. The electronic architecture documented within this paper models the cooperative operation and consequent fault masking of the multiple cells that form biological organs. A communication-system, inspired by endocrinology, is then used to network together these cells, coordinating their activity as organs, and controlling the operation of data processing tasks on a data stream. The bioNode hardware platform is used to implement and test the presented endocrinology inspired architecture. Results of the systems operation are provided to demonstrate the architectures ability to maintain correct computation on. a data stream whilst being subjected to multiple and varied hardware faults.

An endocrinologic-inspired hardware implementation of a multicellular system

Within higher animals there operates an inter-cell communication system that is responsible for regulating the physiological balance of its host. The endocrine system uses hormone mediated messages to control the function of remote cell groups, invoking reactions to maintain chemical and physical equilibrium. The operation and structure of the endocrine system exhibits robustness and fault tolerance that has inspired the creation of reliability engineered electronic architecture. Previous work established a software model of such a system. The model was able to simulate arbitrary processing of a data stream whilst demonstrating tolerance to faults and repair. Following from this work, this paper outlines improvements to this model and the initial steps of its conversion into a hardware electronic system. The Bionode System contains thirty individual nodes connected in a loosely coupled network. Each Bionode contains a microcontroller and FPGA that can be configured to model the functionality of a cell; specifically the underlying endocrine based communication system and the top-level functions that perform useful data processing operations.

Modelling the Tunability of Early T Cell Signalling Events

The Tunable Activation Threshold hypothesis of T Cells is investigated through computational modelling of T cell signalling pathways. Modelling techniques involving the i¾?-calculus and the PRISM model checker are presented, and are applied to produce a stochastic model of T cell signalling. Initial results which demonstrate tuning of T cells are presented.

Extrinsic evolvable hardware on the RISA architecture

The RISA Architecture is a novel reconfigurable hardware platform containing both hardware and software reconfigurable elements. This paper describes the architecture and the features that make it suitable for implementing biologically inspired systems such as the evolution of digital circuits. Some of the architectures capabilities are demonstrated with the results of evolving a simple combinatorial circuit using one of the fabricated RISA devices.

On immune inspired homeostasis for electronic systems

Many electronic systems would benefit from the inclusion of self-regulatory mechanisms. We strive to build systems that can predict, or be aware of, imminent threats upon their specified operation. Then, based on this prediction, the system can alter its operation or configuration to circumvent the effects of the threat. In this position paper, we discuss the role of the immune system can play in serving as inspiration for the development of homeostatic engineered systems, through the development of an immune inspired extensible architecture. We outline the major requirements for such an architecture, and discuss issues that arise as a result and propose possible solutions: things are never as simple as they first appear.

Elucidation of T cell signalling models

A potential mechanism that allows T cells to reliably discriminate pMHC ligands involves an interplay between kinetic proofreading, negative feedback and a destruction of this negative feedback. We analyse a detailed model of these mechanisms which involves the TCR, SHP1 and ERK. We discover that the behaviour of pSHP1 negative feedback is of primary importance, and particularly the influence of a kinetic proofreading base negative feedback state on pSHP1 dynamics. The CD8 co-receptor is shown to benefit from a kinetic proofreading locking mechanism and is able to overcome pSHP1 negative influences to sensitise a T cell.

Fault tolerance via endocrinologic based communication for multiprocessor systems

The communication mechanism used by the biological cells of higher animals is an integral part of an organisms ability to tolerate cell deficiency or loss. The massive redundancy found at the cellular level is fully taken advantage of by the biological endocrinologic processes. Endocrinology, the study of intercellular communication, involves the mediation of chemical messengers called hormones to stimulate or inhibit intracellular processes. This paper presents a software model of a multiprocessor system design that uses an interprocessor communication system similar to the endocrine system. The feedback mechanisms that govern the concentration of hormones are mimicked to control data and control packets between processors. The system is able to perform arbitrary dataflow processing. Each processing stage within the system is undertaken by a separate group of microprocessors. The flow of data, and the activation of the next stage within the process is undertaken using the bioinspired communication technique. The desired result is a system capable of maintained operation despite processor loss. The feasibility of the multiprocessor system is demonstrated by using the model to perform a simple mathematical calculation on a stream of input data.

Fitness functions for the unconstrained evolution of digital circuits

This work is part of a project that aims to develop and operate integrated evolvable hardware systems using unconstrained evolution. Experiments are carried out on an evolvable hardware platform featuring both combinatorial and registered logic as well as sequential feedback loops. In order to be able to accurately assess the transient output of the system and at the same time speed up evolution, new fitness evaluation methods are introduced. These bitwise and hierarchical fitness evaluation methods are adapted and further developed specifically for hardware implementation. It is shown that the newly developed approaches are particularly powerful in coping with two important issues: computational ambiguities, which generally occur when evaluating binary strings, and transient effects resulting from measuring hardware output. On two combinatorial problems it is shown that the new fitness functions improve the performance of evolution and allow stable solutions to be found more reliably. The experiments are carried out with a recently developed hardware platform called reconfigurable integrated system array (RISA).