Generative topographic mapping applied to clustering and visualization of motor unit action potentials

The identification and visualization of clusters formed by motor unit action potentials (MUAPs) is an essential step in investigations seeking to explain the control of the neuromuscular system. This work introduces the generative topographic mapping (GTM), a novel machine learning tool, for clustering of MUAPs, and also it extends the GTM technique to provide a way of visualizing MUAPs. The performance of GTM was compared to that of three other clustering methods: the self-organizing map (SOM), a Gaussian mixture model (GMM), and the neural-gas network (NGN). The results, based on the study of experimental MUAPs, showed that the rate of success of both GTM and SOM outperformed that of GMM and NGN, and also that GTM may in practice be used as a principled alternative to the SOM in the study of MUAPs. A visualization tool, which we called GTM grid, was devised for visualization of MUAPs lying in a high-dimensional space. The visualization provided by the GTM grid was compared to that obtained from principal component analysis (PCA). (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Die generative Herstellung von Dentalmodellen- eine Rapid Manufacturing Herausforderung

Heutzutage stehen zunehmend – z.B. durch den raschen Fortschritt bei den bildgebenden Verfahren – digitale Datensätze im Dentalbereich zur Verfügung. CAD/CAM-syteme gehören dabei in der Zahntechnik längst zum Stande der Technik. Für die Anwendung derartiger Systeme ist jedoch ein Gipsmodell nötig, welches zum Beginn der Prozesskette vom Zahntechniker mittels eines optischen Scanners digitalisiert wird. Die Weiterentwicklung intraoraler Scanner ermöglicht heutzutage außerdem die Digitalisierung ganzer Kiefer im Patientenmund durch den Zahnarzt. Insbesondere für z.B. die ästhetischen Restaurationen bildet hier das zahntechnische Modell nach wie vor die unersetzliche Arbeitsgrundlage für den Techniker. In der vorliegenden Arbeit wird dazu ein Rapid Manufacturing Verfahren zur Herstellung von Dentalmodellen auf Basis der Stereolithographie vorgestellt. Dabei wird auf die besonderen Anforderungen hinsichtlich Präzision, Robustheit und Wirtschaftlichkeit von generativen Fertigungsverfahren für dentale Applikationen eingegangen und eine neu entwickelte Baustrategie vorgestellt, mittels derer die o.g. Anforderungen erfüllt werden

A Hybrid Model for Multimodal Brain Tumor Segmentation

We present a fully automatic segmentation method for multi-modal brain tumor segmentation. The proposed generative-discriminative hybrid model generates initial tissue probabilities, which are used subsequently for enhancing the classi�cation and spatial regularization. The model has been evaluated on the BRATS2013 training set, which includes multimodal MRI images from patients with high- and low-grade gliomas. Our method is capable of segmenting the image into healthy (GM, WM, CSF) and pathological tissue (necrotic, enhancing and non-enhancing tumor, edema). We achieved state-of-the-art performance (Dice mean values of 0.69 and 0.8 for tumor subcompartments and complete tumor respectively) within a reasonable timeframe (4 to 15 minutes).

Generative acts: Family and community involvement of older Australians

The article adopts a developmental approach to successful human aging by exploring the concept of generativity in relation to a study of older Australians' lived experiences of involvement in the family and community. Qualitative data, collected through focus group interviews, were analyzed interpretively using recent developments in Erikson's theory of generativity as a framework. As a result, the present study contributes an in-depth understanding of the role of generative acts to the lives of older people. The data provide illustrative support for Erikson's contention of a generativity/stagnation crisis in later life. Involvement in the family and community is seen as a productive and generative activity, which promotes a positive experience of aging. Two further emergent themes are also explored. First, the experiences of study participants illustrate the reciprocal and cyclical nature of grand-generativity, and the importance of intergenerational relationships. Finally, the data contribute to our knowledge of cultural generativity, and in particular the passing on of cultural knowledge through narratives and modeling.

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.

Using generative models for handwritten digit recognition

We describe a method of recognizing handwritten digits by fitting generative models that are built from deformable B-splines with Gaussian ``ink generators'' spaced along the length of the spline. The splines are adjusted using a novel elastic matching procedure based on the Expectation Maximization (EM) algorithm that maximizes the likelihood of the model generating the data. This approach has many advantages. (1) After identifying the model most likely to have generated the data, the system not only produces a classification of the digit but also a rich description of the instantiation parameters which can yield information such as the writing style. (2) During the process of explaining the image, generative models can perform recognition driven segmentation. (3) The method involves a relatively small number of parameters and hence training is relatively easy and fast. (4) Unlike many other recognition schemes it does not rely on some form of pre-normalization of input images, but can handle arbitrary scalings, translations and a limited degree of image rotation. We have demonstrated our method of fitting models to images does not get trapped in poor local minima. The main disadvantage of the method is it requires much more computation than more standard OCR techniques.

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.

Developments of the generative topographic mapping

The generative topographic mapping (GTM) model was introduced by Bishop et al. (1998, Neural Comput. 10(1), 215-234) as a probabilistic re- formulation of the self-organizing map (SOM). It offers a number of advantages compared with the standard SOM, and has already been used in a variety of applications. In this paper we report on several extensions of the GTM, including an incremental version of the EM algorithm for estimating the model parameters, the use of local subspace models, extensions to mixed discrete and continuous data, semi-linear models which permit the use of high-dimensional manifolds whilst avoiding computational intractability, Bayesian inference applied to hyper-parameters, and an alternative framework for the GTM based on Gaussian processes. All of these developments directly exploit the probabilistic structure of the GTM, thereby allowing the underlying modelling assumptions to be made explicit. They also highlight the advantages of adopting a consistent probabilistic framework for the formulation of pattern recognition algorithms.

GTM: the generative topographic mapping

This thesis describes the Generative Topographic Mapping (GTM) --- a non-linear latent variable model, intended for modelling continuous, intrinsically low-dimensional probability distributions, embedded in high-dimensional spaces. It can be seen as a non-linear form of principal component analysis or factor analysis. It also provides a principled alternative to the self-organizing map --- a widely established neural network model for unsupervised learning --- resolving many of its associated theoretical problems. An important, potential application of the GTM is visualization of high-dimensional data. Since the GTM is non-linear, the relationship between data and its visual representation may be far from trivial, but a better understanding of this relationship can be gained by computing the so-called magnification factor. In essence, the magnification factor relates the distances between data points, as they appear when visualized, to the actual distances between those data points. There are two principal limitations of the basic GTM model. The computational effort required will grow exponentially with the intrinsic dimensionality of the density model. However, if the intended application is visualization, this will typically not be a problem. The other limitation is the inherent structure of the GTM, which makes it most suitable for modelling moderately curved probability distributions of approximately rectangular shape. When the target distribution is very different to that, theaim of maintaining an `interpretable' structure, suitable for visualizing data, may come in conflict with the aim of providing a good density model. The fact that the GTM is a probabilistic model means that results from probability theory and statistics can be used to address problems such as model complexity. Furthermore, this framework provides solid ground for extending the GTM to wider contexts than that of this thesis.

Constructing localized non-linear projection manifolds in a principled way:hierarchical generative topographic mapping

It has been argued that a single two-dimensional visualization plot may not be sufficient to capture all of the interesting aspects of complex data sets, and therefore a hierarchical visualization system is desirable. In this paper we extend an existing locally linear hierarchical visualization system PhiVis (Bishop98a) in several directions: 1. We allow for em non-linear projection manifolds. The basic building block is the Generative Topographic Mapping. 2. We introduce a general formulation of hierarchical probabilistic models consisting of local probabilistic models organized in a hierarchical tree. General training equations are derived, regardless of the position of the model in the tree. 3. Using tools from differential geometry we derive expressions for local directionalcurvatures of the projection manifold. Like PhiVis, our system is statistically principled and is built interactively in a top-down fashion using the EM algorithm. It enables the user to interactively highlight those data in the parent visualization plot which are captured by a child model.We also incorporate into our system a hierarchical, locally selective representation of magnification factors and directional curvatures of the projection manifolds. Such information is important for further refinement of the hierarchical visualization plot, as well as for controlling the amount of regularization imposed on the local models. We demonstrate the principle of the approach on a toy data set andapply our system to two more complex 12- and 19-dimensional data sets.

A hybrid generative/discriminative framework to train a semantic parser from an un-annotated corpus

We propose a hybrid generative/discriminative framework for semantic parsing which combines the hidden vector state (HVS) model and the hidden Markov support vector machines (HM-SVMs). The HVS model is an extension of the basic discrete Markov model in which context is encoded as a stack-oriented state vector. The HM-SVMs combine the advantages of the hidden Markov models and the support vector machines. By employing a modified K-means clustering method, a small set of most representative sentences can be automatically selected from an un-annotated corpus. These sentences together with their abstract annotations are used to train an HVS model which could be subsequently applied on the whole corpus to generate semantic parsing results. The most confident semantic parsing results are selected to generate a fully-annotated corpus which is used to train the HM-SVMs. The proposed framework has been tested on the DARPA Communicator Data. Experimental results show that an improvement over the baseline HVS parser has been observed using the hybrid framework. When compared with the HM-SVMs trained from the fully-annotated corpus, the hybrid framework gave a comparable performance with only a small set of lightly annotated sentences. © 2008. Licensed under the Creative Commons.

Feature LDA:a supervised topic model for automatic detection of web API documentations from the web

Web APIs have gained increasing popularity in recent Web service technology development owing to its simplicity of technology stack and the proliferation of mashups. However, efficiently discovering Web APIs and the relevant documentations on the Web is still a challenging task even with the best resources available on the Web. In this paper we cast the problem of detecting the Web API documentations as a text classification problem of classifying a given Web page as Web API associated or not. We propose a supervised generative topic model called feature latent Dirichlet allocation (feaLDA) which offers a generic probabilistic framework for automatic detection of Web APIs. feaLDA not only captures the correspondence between data and the associated class labels, but also provides a mechanism for incorporating side information such as labelled features automatically learned from data that can effectively help improving classification performance. Extensive experiments on our Web APIs documentation dataset shows that the feaLDA model outperforms three strong supervised baselines including naive Bayes, support vector machines, and the maximum entropy model, by over 3% in classification accuracy. In addition, feaLDA also gives superior performance when compared against other existing supervised topic models.

Visualisation of heterogeneous data with the generalised generative topographic mapping

Heterogeneous and incomplete datasets are common in many real-world visualisation applications. The probabilistic nature of the Generative Topographic Mapping (GTM), which was originally developed for complete continuous data, can be extended to model heterogeneous (i.e. containing both continuous and discrete values) and missing data. This paper describes and assesses the resulting model on both synthetic and real-world heterogeneous data with missing values.

Visualisation of heterogeneous data with simultaneous feature saliency using Generalised Generative Topographic Mapping

Most machine-learning algorithms are designed for datasets with features of a single type whereas very little attention has been given to datasets with mixed-type features. We recently proposed a model to handle mixed types with a probabilistic latent variable formalism. This proposed model describes the data by type-specific distributions that are conditionally independent given the latent space and is called generalised generative topographic mapping (GGTM). It has often been observed that visualisations of high-dimensional datasets can be poor in the presence of noisy features. In this paper we therefore propose to extend the GGTM to estimate feature saliency values (GGTMFS) as an integrated part of the parameter learning process with an expectation-maximisation (EM) algorithm. The efficacy of the proposed GGTMFS model is demonstrated both for synthetic and real datasets.

Of Marx and Makers: an Historical Perspective on Generative Justice

In Marxist frameworks “distributive justice” depends on extracting value through a centralized state. Many new social movements—peer to peer economy, maker activism, community agriculture, queer ecology, etc.—take the opposite approach, keeping value in its unalienated form and allowing it to freely circulate from the bottom up. Unlike Marxism, there is no general theory for bottom-up, unalienated value circulation. This paper examines the concept of “generative justice” through an historical contrast between Marx’s writings and the indigenous cultures that he drew upon. Marx erroneously concluded that while indigenous cultures had unalienated forms of production, only centralized value extraction could allow the productivity needed for a high quality of life. To the contrary, indigenous cultures now provide a robust model for the “gift economy” that underpins open source technological production, agroecology, and restorative approaches to civil rights. Expanding Marx’s concept of unalienated labor value to include unalienated ecological (nonhuman) value, as well as the domain of freedom in speech, sexual orientation, spirituality and other forms of “expressive” value, we arrive at an historically informed perspective for generative justice.