172513
Comparing networks with differing neural-node functions using transputer-based genetic algorithms
Different neural net node computational functions are compared using feedforward backpropagation networks. Three node types are examined: the standard model, ellipsoidal nodes and quadratic nodes. After preliminary experiments on simple small problems, in which quadratic nodes performed very well, networks of differing nodes types are applied to the speech recognition 104 speaker E-task using a fixed architecture. Ellipsoidal nodes were found to work well, but not as well as the standard model. Quadratic nodes did not perform well on the larger task. To facilitate an architecture independent comparison a transputer-based genetic algorithm is then used to compare ellipsoidal and mixed ellipsoidal and standard networks with the standard model. These experiments confirmed the earlier conclusion that ellipsoidal networks could not compare favourably with the standard model on the 104 speaker E-task. In an evolutionary search in which layer node types were free to adjust ellipsoidal nodes had a tendency to become extinct or barely survive. If the presence of ellipsoidal nodes was enforced then the resulting networks again performed poorly when compared with the standard model.
14169547
Non-linear modelling and chaotic neural networks
Proposes a simple methodology to construct an iterative neural network which mimics a given chaotic time series. The methodology uses the Gamma test to identify a suitable (possibly irregular) embedding of the chaotic time series from which a one step predictive model may be constructed. This model is then iterated to produce a close approximation to the original chaotic dynamics. Having constructed such networks we show how the chaotic dynamics may be stabilised using time-delayed feedback, which is a plausible method for stabilisation in biological neural systems. Using delayed feedback control, which is activated in the presence of a stimulus, such networks can behave as an associative memory, in which the act of recognition corresponds to stabilisation onto an unstable periodic orbit. We briefly illustrate how two identical dynamically independent copies of such a chaotic iterative network may be synchronised using the delayed feedback method. Although less biologically plausible, these techniques may have interesting applications in secure communications.
11348191
A note on the Gamma test
This note describes a simple technique, the Gamma (or Near Neighbour) test, which in many cases can be used to considerably simplify the design process of constructing a smooth data model such as a neural network. The Gamma test is a data analysis routine, that (in an optimal implementation) runs in time O(MlogM)as M→∞,where Mis the number of sample data points, and which aims to estimate the best Mean Squared Error (MSError) that can be achieved by any continuous or smooth (bounded first partial derivatives) data model constructed using the data.
9554976
Evolutionary Divide and Conquer (I): A Novel Genetic Approach to the TSP
Experiments with genetic algorithms using permutation operators applied to the traveling salesman problem (TSP) tend to suggest that these algorithms fail in two respects when applied to very large problems: they scale rather poorly as the number of cities n increases, and the solution quality degrades rapidly. We propose an alternative approach for genetic algorithms applied to hard combinatoric search which we call Evolutionary Divide and Conquer (EDAC). This method has potential for any search problem in which knowledge of good solutions for subproblems can be exploited to improve the solution of the problem itself. The idea is to use the genetic algorithm to explore the space of problem subdivisions rather than the space of solutions themselves. We give some preliminary results of this method applied to the geometric TSP.
3022268
Feature selection for genetic sequence classification
MOTIVATION
Most of the existing methods for genetic sequence classification are based on a computer search for homologies in nucleotide or amino acid sequences. The standard sequence alignment programs scale very poorly as the number of sequences increases or the degree of sequence identity is <30%. Some new computationally inexpensive methods based on nucleotide or amino acid compositional analysis have been proposed, but prediction results are still unsatisfactory and depend on the features chosen to represent the sequences.


RESULTS
In this paper, a feature selection method based on the Gamma (or near-neighbour) test is proposed. If there is a continuous or smooth map from feature space to the classification target values, the Gamma test gives an estimate for the mean-squared error of the classification, despite the fact that one has no a priori knowledge of the smooth mapping. We can search a large space of possible feature combinations for a combination which gives a smallest estimated mean-squared error using a genetic algorithm. The method was used for feature selection and classification of the large subunits of rRNA according to RDP (Ribosomal Database Project) phylogenetic classes. The sequences were represented by dinucleotide frequency distribution. The nearest-neighbour criterion has been used to estimate the predictive accuracy of the classification based on the selected features. For examples discussed, we found that the classification according to the first nearest neighbour is correct for 80% of the test samples. If we consider the set of the 10 nearest neighbours, then 94% of the test samples are classified correctly.


AVAILABILITY
The principal novel component of this method is the Gamma test and this can be downloaded compiled for Unix Sun 4, Windows 95 and MS-DOS from http://www.cs.cf.ac.uk/ec/


CONTACT
s.margetts@cs.cf.ac.uk
20473212
Towards a formal theory of defeasible deontic conditionals
The paper outlines the approach to the analysis of deontic conditionals taken in earlier work of Jones and Pörn, comparing it briefly with two main trends within dyadic deontic logic, and discussing problems associated with the augmentation principle and the factual detachment principle. A modification of the Jones and Pörn system is then presented, using a classical but not normal (in the sense of Chellas) deontic modality, to provide the basis for an alternative analysis of deontic conditionals. This new analysis validates neither the factual detachment nor the augmentation principles. However, influenced by the approach of Delgrande to default reasoning, it is shown how a restricted form of factual detachment might be accommodated within the revised system.
47276
A multi-processing software infrastructure for robotic systems
Robotic systems and their software design are based on the same principles found in other computer applications. However, while many computer systems to date are deeply rooted in concepts such as multi-processing, multi-threads, modularity, etc., robotic systems are still limited by mono-processing, centralized designs. The paper addresses these limitations by proposing a new philosophy for robotic system software design - software infrastructure $that allows for the design of an efficient, modular, fault-tolerant, and distributed software architecture. Two examples of this infrastructure applied to mobile robot navigation are also discussed.
3048144
An analysis of extensible modelling for functional genomics data
BackgroundSeveral data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types. Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time.ResultsIn this paper we review the data formats that exist in functional genomics, some of which have become de facto or de jure standards, with a particular focus on how each domain has been modelled, and how each format allows extensions. We describe the tasks that are frequently performed over data formats and analyse how well each task is supported by a particular modelling structure.ConclusionFrom our analysis, we make recommendations as to the types of modelling structure that are most suitable for particular types of experimental annotation. There are several standards currently under development that we believe could benefit from systematically following a set of guidelines.
4157117
Data Access and Integration in the ISPIDER Proteomics Grid
Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources.
16685816
An object model and database for functional genomics
MOTIVATION
Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development of public data repositories and to improve data sharing. There is an established data format for microarrays (microarray gene expression markup language, MAGE-ML) and a draft standard for proteomics (PEDRo). We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics.


RESULTS
We have created a functional genomics experiment object model (FGE-OM), developed from the microarray model, MAGE-OM and two models for proteomics, PEDRo and our own model (Gla-PSI-Glasgow Proposal for the Proteomics Standards Initiative). FGE-OM comprises three namespaces representing (i) the parts of the model common to all functional genomics experiments; (ii) microarray-specific components; and (iii) proteomics-specific components. We believe that FGE-OM should initiate discussion about the contents and structure of the next version of MAGE and the future of proteomics standards. A prototype database called RNA And Protein Abundance Database (RAPAD), based on FGE-OM, has been implemented and populated with data from microbial pathogenesis.


AVAILABILITY
FGE-OM and the RAPAD schema are available from http://www.gusdb.org/fge.html, along with a set of more detailed diagrams. RAPAD can be accessed by registration at the site.