Assembling spatially explicit landscape models of pollen and spore dispersal by wind for risk assessment

Models of windblown pollen or spore movement are required to predict gene flow from genetically modified (GM) crops and the spread of fungal diseases. We suggest a simple form for a function describing the distance moved by a pollen grain or fungal spore, for use in generic models of dispersal. The function has power-law behaviour over sub-continental distances. We show that air-borne dispersal of rapeseed pollen in two experiments was inconsistent with an exponential model, but was fitted by power-law models, implying a large contribution from distant fields to the catches observed. After allowance for this 'background' by applying Fourier transforms to deconvolve the mixture of distant and local sources, the data were best fit by power-laws with exponents between 1.5 and 2. We also demonstrate that for a simple model of area sources, the median dispersal distance is a function of field radius and that measurement from the source edge can be misleading. Using an inverse-square dispersal distribution deduced from the experimental data and the distribution of rapeseed fields deduced by remote sensing, we successfully predict observed rapeseed pollen density in the city centres of Derby and Leicester (UK).

GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms. (c) 2005 Elsevier Ltd. All rights reserved.

Towards a unifying framework for pattern transformation in swarm systems

This paper identifies the major challenges in the area of pattern formation. The work is also motivated by the need for development of a single framework to surmount these challenges. A framework based on the control of macroscopic parameters is proposed. The issue of transformation of patterns is specifically considered. A definition for transformation and four special cases, namely elementary and geometrical transformations by repositioning all or some robots in the pattern are provided. Two feasible tools for pattern transformation namely, a macroscopic parameter method and a mathematical tool - Moebius transformation also known as the linear fractional transformation are introduced. The realization of the unifying framework considering planning and communication is reported.

Perspex machine VII: The universal perspex machine

The perspex machine arose from the unification of projective geometry with the Turing machine. It uses a total arithmetic, called transreal arithmetic, that contains real arithmetic and allows division by zero. Transreal arithmetic is redefined here. The new arithmetic has both a positive and a negative infinity which lie at the extremes of the number line, and a number nullity that lies off the number line. We prove that nullity, 0/0, is a number. Hence a number may have one of four signs: negative, zero, positive, or nullity. It is, therefore, impossible to encode the sign of a number in one bit, as floating-, point arithmetic attempts to do, resulting in the difficulty of having both positive and negative zeros and NaNs. Transrational arithmetic is consistent with Cantor arithmetic. In an extension to real arithmetic, the product of zero, an infinity, or nullity with its reciprocal is nullity, not unity. This avoids the usual contradictions that follow from allowing division by zero. Transreal arithmetic has a fixed algebraic structure and does not admit options as IEEE, floating-point arithmetic does. Most significantly, nullity has a simple semantics that is related to zero. Zero means "no value" and nullity means "no information." We argue that nullity is as useful to a manufactured computer as zero is to a human computer. The perspex machine is intended to offer one solution to the mind-body problem by showing how the computable aspects of mind and. perhaps, the whole of mind relates to the geometrical aspects of body and, perhaps, the whole of body. We review some of Turing's writings and show that he held the view that his machine has spatial properties. In particular, that it has the property of being a 7D lattice of compact spaces. Thus, we read Turing as believing that his machine relates computation to geometrical bodies. We simplify the perspex machine by substituting an augmented Euclidean geometry for projective geometry. This leads to a general-linear perspex-machine which is very much easier to pro-ram than the original perspex-machine. We then show how to map the whole of perspex space into a unit cube. This allows us to construct a fractal of perspex machines with the cardinality of a real-numbered line or space. This fractal is the universal perspex machine. It can solve, in unit time, the halting problem for itself and for all perspex machines instantiated in real-numbered space, including all Turing machines. We cite an experiment that has been proposed to test the physical reality of the perspex machine's model of time, but we make no claim that the physical universe works this way or that it has the cardinality of the perspex machine. We leave it that the perspex machine provides an upper bound on the computational properties of physical things, including manufactured computers and biological organisms, that have a cardinality no greater than the real-number line.

Predictive control using feedback linearization based on dynamic neural models

This paper presents a hybrid control strategy integrating dynamic neural networks and feedback linearization into a predictive control scheme. Feedback linearization is an important nonlinear control technique which transforms a nonlinear system into a linear system using nonlinear transformations and a model of the plant. In this work, empirical models based on dynamic neural networks have been employed. Dynamic neural networks are mathematical structures described by differential equations, which can be trained to approximate general nonlinear systems. A case study based on a mixing process is presented.

Application of auto regressive models of wavelet sub-bands for classifying Terahertz pulse measurements

This paper presents an approach for automatic classification of pulsed Terahertz (THz), or T-ray, signals highlighting their potential in biomedical, pharmaceutical and security applications. T-ray classification systems supply a wealth of information about test samples and make possible the discrimination of heterogeneous layers within an object. In this paper, a novel technique involving the use of Auto Regressive (AR) and Auto Regressive Moving Average (ARMA) models on the wavelet transforms of measured T-ray pulse data is presented. Two example applications are examined - the classi. cation of normal human bone (NHB) osteoblasts against human osteosarcoma (HOS) cells and the identification of six different powder samples. A variety of model types and orders are used to generate descriptive features for subsequent classification. Wavelet-based de-noising with soft threshold shrinkage is applied to the measured T-ray signals prior to modeling. For classi. cation, a simple Mahalanobis distance classi. er is used. After feature extraction, classi. cation accuracy for cancerous and normal cell types is 93%, whereas for powders, it is 98%.

Implementing innovation: designers, users and actor-networks

The role of users is an often-overlooked aspect of studies of innovation and diffusion. Using an actor-network theory (ANT) approach, four case studies examine the processes of implementing a piece of CAD (computer aided design) software, BSLink, in different organisations and describe the tailoring done by users to embed the software into working practices. This not only results in different practices of use at different locations, but also transforms BSLink itself into a proliferation of BSLinks-in-use. A focus group for BSLink users further reveals the gaps between different users' expectations and ways of using the software, and between different BSLinks-in-use. It also demonstrates the contradictory demands this places on its further development. The ANT-informed approach used treats both innovation and diffusion as processes of translation within networks. It also emphasises the political nature of innovation and implementation, and the efforts of various actors to delegate manoeuvres for increased influence onto technological artefacts.

Space partitioning for scalable K-means

K-Means is a popular clustering algorithm which adopts an iterative refinement procedure to determine data partitions and to compute their associated centres of mass, called centroids. The straightforward implementation of the algorithm is often referred to as `brute force' since it computes a proximity measure from each data point to each centroid at every iteration of the K-Means process. Efficient implementations of the K-Means algorithm have been predominantly based on multi-dimensional binary search trees (KD-Trees). A combination of an efficient data structure and geometrical constraints allow to reduce the number of distance computations required at each iteration. In this work we present a general space partitioning approach for improving the efficiency and the scalability of the K-Means algorithm. We propose to adopt approximate hierarchical clustering methods to generate binary space partitioning trees in contrast to KD-Trees. In the experimental analysis, we have tested the performance of the proposed Binary Space Partitioning K-Means (BSP-KM) when a divisive clustering algorithm is used. We have carried out extensive experimental tests to compare the proposed approach to the one based on KD-Trees (KD-KM) in a wide range of the parameters space. BSP-KM is more scalable than KDKM, while keeping the deterministic nature of the `brute force' algorithm. In particular, the proposed space partitioning approach has shown to overcome the well-known limitation of KD-Trees in high-dimensional spaces and can also be adopted to improve the efficiency of other algorithms in which KD-Trees have been used.

A CAD-based computer vision system

A vision system for recognizing rigid and articulated three-dimensional objects in two-dimensional images is described. Geometrical models are extracted from a commercial computer aided design package. The models are then augmented with appearance and functional information which improves the system's hypothesis generation, hypothesis verification, and pose refinement. Significant advantages over existing CAD-based vision systems, which utilize only information available in the CAD system, are realized. Examples show the system recognizing, locating, and tracking a variety of objects in a robot work-cell and in natural scenes.

Visual surveillance using deformable models of vehicles

This paper presents recent developments to a vision-based traffic surveillance system which relies extensively on the use of geometrical and scene context. Firstly, a highly parametrised 3-D model is reported, able to adopt the shape of a wide variety of different classes of vehicle (e.g. cars, vans, buses etc.), and its subsequent specialisation to a generic car class which accounts for commonly encountered types of car (including saloon, batchback and estate cars). Sample data collected from video images, by means of an interactive tool, have been subjected to principal component analysis (PCA) to define a deformable model having 6 degrees of freedom. Secondly, a new pose refinement technique using “active” models is described, able to recover both the pose of a rigid object, and the structure of a deformable model; an assessment of its performance is examined in comparison with previously reported “passive” model-based techniques in the context of traffic surveillance. The new method is more stable, and requires fewer iterations, especially when the number of free parameters increases, but shows somewhat poorer convergence. Typical applications for this work include robot surveillance and navigation tasks.

A virtual head-stick rehabilitation robot system

For individuals with upper-extremity motor disabilities, the head-stick is a simple and intuitive means of performing manipulations because it provides direct proprioceptive information to the user. Through practice and use of inherent proprioceptive cues, users may become quite adept at using the head-stick for a number of different tasks. The traditional head-stick is limited, however, to the user's achievable range of head motion and force generation, which may be insufficient for many tasks. The authors describe an interface to a robot system which emulates the proprioceptive qualities of a traditional head-stick while also allowing for augmented end-effector ranges of force and motion. The design and implementation of the system in terms of coordinate transforms, bilateral telemanipulator architecture, safety systems, and system identification of the master is described, in addition to preliminary evaluation results.

Robot free will

We introduce the perspex machine which unifies projective geometry and Turing computation and results in a supra-Turing machine. We show two ways in which the perspex machine unifies symbolic and non-symbolic AI. Firstly, we describe concrete geometrical models that map perspexes onto neural networks, some of which perform only symbolic operations. Secondly, we describe an abstract continuum of perspex logics that includes both symbolic logics and a new class of continuous logics. We argue that an axiom in symbolic logic can be the conclusion of a perspex theorem. That is, the atoms of symbolic logic can be the conclusions of sub-atomic theorems. We argue that perspex space can be mapped onto the spacetime of the universe we inhabit. This allows us to discuss how a robot might be conscious, feel, and have free will in a deterministic, or semi-deterministic, universe. We ground the reality of our universe in existence. On a theistic point, we argue that preordination and free will are compatible. On a theological point, we argue that it is not heretical for us to give robots free will. Finally, we give a pragmatic warning as to the double-edged risks of creating robots that do, or alternatively do not, have free will.

Perspex machine X: software development

The Perspex Machine arose from the unification of computation with geometry. We now report significant redevelopment of both a partial C compiler that generates perspex programs and of a Graphical User Interface (GUI). The compiler is constructed with standard compiler-generator tools and produces both an explicit parse tree for C and an Abstract Syntax Tree (AST) that is better suited to code generation. The GUI uses a hash table and a simpler software architecture to achieve an order of magnitude speed up in processing and, consequently, an order of magnitude increase in the number of perspexes that can be manipulated in real time (now 6,000). Two perspex-machine simulators are provided, one using trans-floating-point arithmetic and the other using transrational arithmetic. All of the software described here is available on the world wide web. The compiler generates code in the neural model of the perspex. At each branch point it uses a jumper to return control to the main fibre. This has the effect of pruning out an exponentially increasing number of branching fibres, thereby greatly increasing the efficiency of perspex programs as measured by the number of neurons required to implement an algorithm. The jumpers are placed at unit distance from the main fibre and form a geometrical structure analogous to a myelin sheath in a biological neuron. Both the perspex jumper-sheath and the biological myelin-sheath share the computational function of preventing cross-over of signals to neurons that lie close to an axon. This is an example of convergence driven by similar geometrical and computational constraints in perspex and biological neurons.

Evolution of coronal mass ejection morphology with increasing heliocentric distance. II. In Situ observations

Interplanetary coronal mass ejections (ICMEs) are often observed to travel much faster than the ambient solar wind. If the relative speed between the two exceeds the fast magnetosonic velocity, then a shock wave will form. The Mach number and the shock standoff distance ahead of the ICME leading edge is measured to infer the vertical size of an ICME in a direction that is perpendicular to the solar wind flow. We analyze the shock standoff distance for 45 events varying between 0.5 AU and 5.5 AU in order to infer their physical dimensions. We find that the average ratio of the inferred vertical size to measured radial width, referred to as the aspect ratio, of an ICME is 2.8 ± 0.5. We also compare these results to the geometrical predictions from Paper I that forecast an aspect ratio between 3 and 6. The geometrical solution varies with heliocentric distance and appears to provide a theoretical maximum for the aspect ratio of ICMEs. The minimum aspect ratio appears to remain constant at 1 (i.e., a circular cross section) for all distances. These results suggest that possible distortions to the leading edge of ICMEs are frequent. But, these results may also indicate that the constants calculated in the empirical relationship correlating the different shock front need to be modified; or perhaps both distortions and a change in the empirical formulae are required.

Land re-use, complexity and actor-networks: a framework for research

This paper will present a conceptual framework for the examination of land redevelopment based on a complex systems/networks approach. As Alvin Toffler insightfully noted, modern scientific enquiry has become exceptionally good at splitting problems into pieces but has forgotten how to put the pieces back together. Twenty-five years after his remarks, governments and corporations faced with the requirements of sustainability are struggling to promote an ‘integrated’ or ‘holistic’ approach to tackling problems. Despite the talk, both practice and research provide few platforms that allow for ‘joined up’ thinking and action. With socio-economic phenomena, such as land redevelopment, promising prospects open up when we assume that their constituents can make up complex systems whose emergent properties are more than the sum of the parts and whose behaviour is inherently difficult to predict. A review of previous research shows that it has mainly focused on idealised, ‘mechanical’ views of property development processes that fail to recognise in full the relationships between actors, the structures created and their emergent qualities. When reality failed to live up to the expectations of these theoretical constructs then somebody had to be blamed for it: planners, developers, politicians. However, from a ‘synthetic’ point of view the agents and networks involved in property development can be seen as constituents of structures that perform complex processes. These structures interact, forming new more complex structures and networks. Redevelopment then can be conceptualised as a process of transformation: a complex system, a ‘dissipative’ structure involving developers, planners, landowners, state agencies etc., unlocks the potential of previously used sites, transforms space towards a higher order of complexity and ‘consumes’ but also ‘creates’ different forms of capital in the process. Analysis of network relations point toward the ‘dualism’ of structure and agency in these processes of system transformation and change. Insights from actor network theory can be conjoined with notions of complexity and chaos to build an understanding of the ways in which actors actively seek to shape these structures and systems, whilst at the same time are recursively shaped by them in their strategies and actions. This approach transcends the blame game and allows for inter-disciplinary inputs to be placed within a broader explanatory framework that does away with many past dichotomies. Better understanding of the interactions between actors and the emergent qualities of the networks they form can improve our comprehension of the complex socio-spatial phenomena that redevelopment comprises. The insights that this framework provides when applied in UK institutional investment into redevelopment are considered to be significant.