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Non-Standard Computation Group

Group seminars list of speakers and abstracts: 2009-10


These seminars are run jointly between the Non-Standard Computation Group in Computer Science and the Intelligent Systems Group in Electronics.

Speaker Title and Abstract Date and Location
Peter Hines (CS) Information-theoretic classification: from cognitive science to communication channels: This talk is about the problem of classification in situations without a metric distance function. It describes an information-theoretic approach motivated by notoriously difficult datasets in cognitive science, but applicable in a significantly wider range of settings. Theoretical and practical results are given.
1315-1415 23rd Oct, 2009 PT/005
Casper Macindoe 1315-1415 6th Nov, 2009 Wentworth Common Room (TRANSIT seminar)
Viv Kendon (Leeds) Analogue computation with microwaves: I will motivate and describe preliminary studies of a microwave-based analogue computer. We are developing an alternative set of basic components closer to those required for quantum analogue computation (CVQC), instead of the usual set based on Shannon's general purpose analogue computer (GPAC). We demonstrate the basic behaviour of the experimental devices in two frequency regimes, 10 MHz propagating in co-axial cable, and 20 GHz propagating in rectangular waveguides.
1315-1415 20th Nov, 2009 PT/005
Cristina Costa Santini(Elec) Molecular Software and Hardware for Programmed Chemical Synthesis:This project is an EPSRC funded project and involves 4 UK universities. In this talk I will first explain the project's aim: programmed chemical synthesis mediated by DNA based systems. Then I will give an introduction about DNA based systems, together with some examples. Finally, I will talk about York's role on this interdisciplinary project, which is the autonomous control of the programmed chemical synthesis. A few ideas that are currently being considered will be discussed. Theoretically, both conventional and unconventional ideas are acceptable. In practice, the developed idea will be tested on a 'wet lab' experiment, therefore molecular issues, such as crosstalk and yield, have to be carefully considered. Comments and suggestions from the audience will be very welcome.
1315-1415 4th Dec, 2009 CS103
Christmas Break
Simon Hickenbotham (CS) Everything exists underneath: bioinspired computing at the enzyme level: The majority of bioinspired computing fields emulate biological systems that have appeared comparatively recently in evolutionary history. By contrast, work in the Plazzmid project is attempting to build evolutionary systems more akin to bacteria and their precursors in the early earth. The bacteria have efficiently organised genomes that are capable of rapid adaptation to new stimuli, but the mechanisms of genomic organisation require rich simulations of the molecular classes involved. In order to make an evolvable system that captures this richness, we have devised an artificial chemistry that emulates the properties of the enzymes that curate the genome. This talk gives an overview of this evolvable artificial chemistry, and presents some initial results for evolution in an RNA-world analogue. 1315-1415 22nd Jan, 2010 CS103
Mark Read (CS) Simulation to Inform Immunology: The Tale of a Programmable Lab Rat: Agent based modelling and simulation techniques are frequently touted as being useful tools that can inform the experimental Biologist: integrating, organizing and exploring data; prompting insightful questions; permitting the investigation or derivation of hypotheses concerning system behaviour; and more. Though these arguments hold great promise, the discipline itself is still immature. There are few techniques informing and guiding the development of such tools, and there exists as yet few examples where this promise is fully delivered. In this talk I present my work to date in developing an agent based simulation of EAE (a murine proxy for multiple sclerosis) in a principled manner; a case study that purposes to demonstrate the value of agent based techniques to immunological research. I will discuss the challenges and solutions encountered in developing the tool, and in its use in conducting in silico experimentation that really can inform immunology. 1315-1415 5th Feb, 2010 CS103
Luca Albergante : Uni. Milan, Italy Granuloma formation in leishmaniasis: a complex immunological response: Granuloma is a mechanism employed by the immune system to contain and overcome the infection caused by some parasites, such as leishmania. The seminar will present a mathematical model (stochastic petri net) of hepatic granulomas, discussing some of the challenges posed by the modelling process and addressing the main immunological problems that the model will study. 1315-1415 19th Feb, 2010 CS103
Dr Gerald Schaefer, Department of Computer Science, Loughborough. Rule-based classification: techniques and biomedical applications: Classification is an important step in many medical applications and a variety of classification algorithms have been introduced in the literature. In my talk I will focus on rule-based classifier which have the advatange of interpretability and on the use of computational intelligence techniques for deriving rule bases. In particular, I will present a fuzzy rule-based classification system and show its usefulness to various medical applications including the diagnosis of breast cancer and the classification of gene expression data. Through a simple extension the presented classifier can be modified into a cost-sensitive one allowing to put more emphasis on the correct identification of certain classes. Furthermore I will present a genetic algorithm (GA)-based optimisation of the fuzzy rule base in order to arrive at a compact and effective classifier. I will conclude my talk by looking at ant colony optimsation (ACO) based classification. 1315-1415 5th March, 2010 CS103
Dr Fiona Polack, Department of Computer Science. Reflections on the Simulation of Complex Systems for Science: In studying complex systems, agent-based simulations offer the possibility of directly modelling components in an environment. However, the scientific value of agent-based simulations has been limited by inadequate scientific rigour. The paper focuses on agent-based simulations that are used in biological and bio-medical research. Starting from a review of best practice in simulation engineering, the paper identifies some of the key activities in developing complex systems simulations that support scientific research, and how these contribute to the essential development of mutual trust among developers and scientists. Examples from the authors' own experience illustrate how a range of studies have manifested these key activities, and identifies some successes and problems encountered. 1315-1415 19th March, 2010 B/B/103
Easter Break
Dr Ravi Vaidyanathan, Bristol Robotics Laboratory Biologically Inspired Robotic Architectures: Coupling, Complexity and Control : Complex behavior may be viewed as an emergent phenomenon resulting from the interaction of an entity with its environment through sensory-motor activity. From a systems perspective, the dynamic morphology of a structure plays a critical computational role in this process; in effect subsuming portions of the control architecture. In animals, for example, intrinsic properties of the musculoskeletal system augment the neural stabilization of the organism for an array of critical of functions. Invertebrates, in particular, have been able to exploit a wide range of behavioral niches because they utilize a body plan that can be modified to create functional adaptations optimized for a particular role. The talk will review basic methodologies for the enhancement of engineering (robotic) design based upon biological studies of animal behavior from a hierarchical systems perspective with emphasis on coupling between mechanics and control systems. Architectures founded upon biological inspiration will be summarized with specific examples from the speaker’s work, including recent research that has been featured in New Scientist, Flight Global Magazine, The Engineer, and on television specials produced by the Discovery Channel and Tokyo Broadcasting Systems. Applications highlighted will include medical and mobile robotic systems including the Morphing Micro Air-Land Vehicle and the Cockroach-Inspired Hexapod Robot. 1315-1415 7th May 2010 CS103
Dr Ed Clark The grey model of immunology: The adaptive immune system is orchestrated by the sorting of cells in the Thymus. T-cells with randomly generated receptors are either initiate programmed cell death in the Thymus or allowed to enter the rest of the body and co-ordinate attacks on anything carrying the molecular pattern(s) to which they bind. We introduce a mathematical framework to describe the properties of the chemistry which binds members of one set (epitopes), to members of a second set (paratopes). Within this framework we present a classical lock and key immunology theory of how paratopes bind to epitopes and what constraints the theory puts on the properties of the chemistry. We also introduce a competing theory, the ''grey model'', and analyse the constraints that the grey model puts on the properties of the chemistry. The theories are discussed in the context of experimental results and we present illustrative calculations to demonstrate the consequences of the theories in terms of coverage of the “non-self” epitopic space. We have developed clear and mathematically meaningful definitions of degeneracy and redundancy. There are also some interesting lessons about mathematical modelling across disciplines: two competing models that are physically distinct, produce the same mathematical results (up to a point), and many of the equations derived in this model appear in seemingly unrelated fields. The grey model itself finds direct application in characterising Artificial Chemistries. This work has been carried out in collaboration with Professor Melvin Cohn of the conceptual immunology group at the salk institute. 1315-1415 21st May, 2010 CS103
Dr David White Computing with Time using Genetic Programming: In this talk, I will regale you with stories from my PhD: long winter evenings spent fighting with software simulators that I couldn't understand, and endless hours watching experiments whilst wondering if I would finish before retirement age. Along the way, I came across the idea of using Genetic Programming to attack a problem I was actually trying to solve in order to use Genetic Programming. This peculiarity led me to some unusual ideas about the non-functional properties of software, and the discovery that evolutionary search can produce software that has quite strange timing behaviour. The results may find application in cryptography, and they also blur the boundaries between the functional and non-functional behaviour of software. 1315-1415 4th June, 2010 CS103
TBA 1315-1415 18th June, 2010 CS103

Previous seminars can be found here: 2008-09, 2007-08, 2006-07 and 2005-06
Seminar Organiser Jon Timmis