Dynamics and topographic organization of recursive self-organizing maps

Recently there has been an outburst of interest in extending topographic maps of vectorial data to more general data structures, such as sequences or trees. However, there is no general consensus as to how best to process sequences using topographicmaps, and this topic remains an active focus of neurocomputational research. The representational capabilities and internal representations of the models are not well understood. Here, we rigorously analyze a generalization of the self-organizingmap (SOM) for processing sequential data, recursive SOM (RecSOM) (Voegtlin, 2002), as a nonautonomous dynamical system consisting of a set of fixed input maps. We argue that contractive fixed-input maps are likely to produce Markovian organizations of receptive fields on the RecSOM map. We derive bounds on parameter β (weighting the importance of importing past information when processing sequences) under which contractiveness of the fixed-input maps is guaranteed. Some generalizations of SOM contain a dynamic module responsible for processing temporal contexts as an integral part of the model. We show that Markovian topographic maps of sequential data can be produced using a simple fixed (nonadaptable) dynamic module externally feeding a standard topographic model designed to process static vectorial data of fixed dimensionality (e.g., SOM). However, by allowing trainable feedback connections, one can obtain Markovian maps with superior memory depth and topography preservation. We elaborate on the importance of non-Markovian organizations in topographic maps of sequential data. © 2006 Massachusetts Institute of Technology.

Recursive self-organizing map as a contractive iterative function system

Recently, there has been a considerable research activity in extending topographic maps of vectorial data to more general data structures, such as sequences or trees. However, the representational capabilities and internal representations of the models are not well understood. We rigorously analyze a generalization of the Self-Organizing Map (SOM) for processing sequential data, Recursive SOM (RecSOM [1]), as a non-autonomous dynamical system consisting off a set of fixed input maps. We show that contractive fixed input maps are likely to produce Markovian organizations of receptive fields o the RecSOM map. We derive bounds on parameter $\beta$ (weighting the importance of importing past information when processing sequences) under which contractiveness of the fixed input maps is guaranteed.

GTM: A principled alternative to the self-organizing map

The Self-Organizing Map (SOM) algorithm has been extensively studied and has been applied with considerable success to a wide variety of problems. However, the algorithm is derived from heuristic ideas and this leads to a number of significant limitations. In this paper, we consider the problem of modelling the probability density of data in a space of several dimensions in terms of a smaller number of latent, or hidden, variables. We introduce a novel form of latent variable model, which we call the GTM algorithm (for Generative Topographic Mapping), which allows general non-linear transformations from latent space to data space, and which is trained using the EM (expectation-maximization) algorithm. Our approach overcomes the limitations of the SOM, while introducing no significant disadvantages. We demonstrate the performance of the GTM algorithm on simulated data from flow diagnostics for a multi-phase oil pipeline.

Understanding policy implementation processes as self-organizing systems

Implementation studies and related research in organizational theory can be enhanced by drawing on the field of complex systems to understand better and, as a consequence, more successfully manage change. This article reinterprets data previously published in the British Journal of Management to reveal a new contribution, that policy implementation processes should be understood as a self-organizing system in which adaptive abilities are extremely important for stakeholders. In other words, national policy is reinterpreted at the local level, with each local organization uniquely mixing elements of national policy with their own requirements making policy implementation unpredictable and more sketchy. The original article explained different paces and directions of change in terms of traditional management processes: leadership, politics, implementation and vision. By reinterpreting the data, it is possible to reveal that deeper level processes, which are more emergent, are also at work influencing change, which the authors label possibility space. Implications for theory, policy and practice are identified.

Data visualization with simultaneous feature selection

Data visualization algorithms and feature selection techniques are both widely used in bioinformatics but as distinct analytical approaches. Until now there has been no method of measuring feature saliency while training a data visualization model. We derive a generative topographic mapping (GTM) based data visualization approach which estimates feature saliency simultaneously with the training of the visualization model. The approach not only provides a better projection by modeling irrelevant features with a separate noise model but also gives feature saliency values which help the user to assess the significance of each feature. We compare the quality of projection obtained using the new approach with the projections from traditional GTM and self-organizing maps (SOM) algorithms. The results obtained on a synthetic and a real-life chemoinformatics dataset demonstrate that the proposed approach successfully identifies feature significance and provides coherent (compact) projections. © 2006 IEEE.

Magnification factors for the SOM and GTM algorithms

Magnification factors specify the extent to which the area of a small patch of the latent (or `feature') space of a topographic mapping is magnified on projection to the data space, and are of considerable interest in both neuro-biological and data analysis contexts. Previous attempts to consider magnification factors for the self-organizing map (SOM) algorithm have been hindered because the mapping is only defined at discrete points (given by the reference vectors). In this paper we consider the batch version of SOM, for which a continuous mapping can be defined, as well as the Generative Topographic Mapping (GTM) algorithm of Bishop et al. (1997) which has been introduced as a probabilistic formulation of the SOM. We show how the techniques of differential geometry can be used to determine magnification factors as continuous functions of the latent space coordinates. The results are illustrated here using a problem involving the identification of crab species from morphological data.

Self-adaptive probabilistic roadmap generation for intelligent virtual agents

Agents inhabiting large scale environments are faced with the problem of generating maps by which they can navigate. One solution to this problem is to use probabilistic roadmaps which rely on selecting and connecting a set of points that describe the interconnectivity of free space. However, the time required to generate these maps can be prohibitive, and agents do not typically know the environment in advance. In this paper we show that the optimal combination of different point selection methods used to create the map is dependent on the environment, no point selection method dominates. This motivates a novel self-adaptive approach for an agent to combine several point selection methods. The success rate of our approach is comparable to the state of the art and the generation cost is substantially reduced. Self-adaptation therefore enables a more efficient use of the agent's resources. Results are presented for both a set of archetypal scenarios and large scale virtual environments based in Second Life, representing real locations in London.

Data visualization during the early stages of drug discovery

Multidimensional compound optimization is a new paradigm in the drug discovery process, yielding efficiencies during early stages and reducing attrition in the later stages of drug development. The success of this strategy relies heavily on understanding this multidimensional data and extracting useful information from it. This paper demonstrates how principled visualization algorithms can be used to understand and explore a large data set created in the early stages of drug discovery. The experiments presented are performed on a real-world data set comprising biological activity data and some whole-molecular physicochemical properties. Data visualization is a popular way of presenting complex data in a simpler form. We have applied powerful principled visualization methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), to help the domain experts (screening scientists, chemists, biologists, etc.) understand and draw meaningful decisions. We also benchmark these principled methods against relatively better known visualization approaches, principal component analysis (PCA), Sammon's mapping, and self-organizing maps (SOMs), to demonstrate their enhanced power to help the user visualize the large multidimensional data sets one has to deal with during the early stages of the drug discovery process. The results reported clearly show that the GTM and HGTM algorithms allow the user to cluster active compounds for different targets and understand them better than the benchmarks. An interactive software tool supporting these visualization algorithms was provided to the domain experts. The tool facilitates the domain experts by exploration of the projection obtained from the visualization algorithms providing facilities such as parallel coordinate plots, magnification factors, directional curvatures, and integration with industry standard software. © 2006 American Chemical Society.

A modelling and simulation environment for self-aware and self-expressive systems

Self-awareness and self-expression are promising architectural concepts for embedded systems to be equipped with to match them with dedicated application scenarios and constraints in the avionic and space-flight industry. Typically, these systems operate in largely undefined environments and are not reachable after deployment for a long time or even never ever again. This paper introduces a reference architecture as well as a novel modelling and simulation environment for self-aware and self-expressive systems with transaction level modelling, simulation and detailed modelling capabilities for hardware aspects, precise process chronology execution as well as fine timing resolutions. Furthermore, industrial relevant system sizes with several self-aware and self-expressive nodes can be handled by the modelling and simulation environment.

A survey of self-awareness and its application in computing systems

Novel computing systems are increasingly being composed of large numbers of heterogeneous components, each with potentially different goals or local perspectives, and connected in networks which change over time. Management of such systems quickly becomes infeasible for humans. As such, future computing systems should be able to achieve advanced levels of autonomous behaviour. In this context, the system's ability to be self-aware and be able to self-express becomes important. This paper surveys definitions and current understanding of self-awareness and self-expression in biology and cognitive science. Subsequently, previous efforts to apply these concepts to computing systems are described. This has enabled the development of novel working definitions for self-awareness and self-expression within the context of computing systems.

Self-organising zooms for decentralised redundancy management in visual sensor networks

When visual sensor networks are composed of cameras which can adjust the zoom factor of their own lens, one must determine the optimal zoom levels for the cameras, for a given task. This gives rise to an important trade-off between the overlap of the different cameras’ fields of view, providing redundancy, and image quality. In an object tracking task, having multiple cameras observe the same area allows for quicker recovery, when a camera fails. In contrast having narrow zooms allow for a higher pixel count on regions of interest, leading to increased tracking confidence. In this paper we propose an approach for the self-organisation of redundancy in a distributed visual sensor network, based on decentralised multi-objective online learning using only local information to approximate the global state. We explore the impact of different zoom levels on these trade-offs, when tasking omnidirectional cameras, having perfect 360-degree view, with keeping track of a varying number of moving objects. We further show how employing decentralised reinforcement learning enables zoom configurations to be achieved dynamically at runtime according to an operator’s preference for maximising either the proportion of objects tracked, confidence associated with tracking, or redundancy in expectation of camera failure. We show that explicitly taking account of the level of overlap, even based only on local knowledge, improves resilience when cameras fail. Our results illustrate the trade-off between maintaining high confidence and object coverage, and maintaining redundancy, in anticipation of future failure. Our approach provides a fully tunable decentralised method for the self-organisation of redundancy in a changing environment, according to an operator’s preferences.

Self-aware and self-expressive camera networks

Smart cameras perform on-board image analysis, adapt their algorithms to changes in their environment, and collaborate with other networked cameras to analyze the dynamic behavior of objects. A proposed computational framework adopts the concepts of self-awareness and self-expression to more efficiently manage the complex tradeoffs among performance, flexibility, resources, and reliability. The Web extra at http://youtu.be/NKe31-OKLz4 is a video demonstrating CamSim, a smart camera simulation tool, enables users to test self-adaptive and self-organizing smart-camera techniques without deploying a smart-camera network.

GTM: the generative topographic mapping

Latent variable models represent the probability density of data in a space of several dimensions in terms of a smaller number of latent, or hidden, variables. A familiar example is factor analysis which is based on a linear transformations between the latent space and the data space. In this paper we introduce a form of non-linear latent variable model called the Generative Topographic Mapping, for which the parameters of the model can be determined using the EM algorithm. GTM provides a principled alternative to the widely used Self-Organizing Map (SOM) of Kohonen (1982), and overcomes most of the significant limitations of the SOM. We demonstrate the performance of the GTM algorithm on a toy problem and on simulated data from flow diagnostics for a multi-phase oil pipeline.

GTM: the generative topographic mapping

Latent variable models represent the probability density of data in a space of several dimensions in terms of a smaller number of latent, or hidden, variables. A familiar example is factor analysis which is based on a linear transformations between the latent space and the data space. In this paper we introduce a form of non-linear latent variable model called the Generative Topographic Mapping, for which the parameters of the model can be determined using the EM algorithm. GTM provides a principled alternative to the widely used Self-Organizing Map (SOM) of Kohonen (1982), and overcomes most of the significant limitations of the SOM. We demonstrate the performance of the GTM algorithm on a toy problem and on simulated data from flow diagnostics for a multi-phase oil pipeline.

Magnification factors for the GTM algorithm

The Generative Topographic Mapping (GTM) algorithm of Bishop et al. (1997) has been introduced as a principled alternative to the Self-Organizing Map (SOM). As well as avoiding a number of deficiencies in the SOM, the GTM algorithm has the key property that the smoothness properties of the model are decoupled from the reference vectors, and are described by a continuous mapping from a lower-dimensional latent space into the data space. Magnification factors, which are approximated by the difference between code-book vectors in SOMs, can therefore be evaluated for the GTM model as continuous functions of the latent variables using the techniques of differential geometry. They play an important role in data visualization by highlighting the boundaries between data clusters, and are illustrated here for both a toy data set, and a problem involving the identification of crab species from morphological data.