scholarly journals GTM: The Generative Topographic Mapping

1998 ◽  
Vol 10 (1) ◽  
pp. 215-234 ◽  
Author(s):  
Christopher M. Bishop ◽  
Markus Svensén ◽  
Christopher K. I. Williams

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 transformation between the latent space and the data space. In this article, we introduce a form of nonlinear latent variable model called the generative topographic mapping, for which the parameters of the model can be determined using the expectation-maximization 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 multiphase oil pipeline.

Author(s):  
Nobuhiko Yamaguchi ◽  

Generative Topographic Mapping (GTM) is a nonlinear latent variable model introduced as a data visualization technique by Bishop et al. In this paper, we focus on variational Bayesian inference in GTM. Variational Bayesian GTM, first proposed by Olier et al., uses a single regularization term and regularization parameter to avoid overfitting and therefore cannot be used to control the degree of regularization locally. To overcome this problem, we propose variational Bayesian inference with Automatic Relevance Determination (ARD) hierarchical prior for use with GTM. The proposed model uses multiple regularization parameters and therefore can be used to control the degree of regularization in local areas of data space individually. Several experiments show that GTM that we propose provides better visualization than conventional GTM approaches.


2020 ◽  
Author(s):  
Archit Verma ◽  
Barbara Engelhardt

Joint analysis of multiple single cell RNA-sequencing (scRNA-seq) data is confounded by technical batch effects across experiments, biological or environmental variability across cells, and different capture processes across sequencing platforms. Manifold alignment is a principled, effective tool for integrating multiple data sets and controlling for confounding factors. We demonstrate that the semi-supervised t-distributed Gaussian process latent variable model (sstGPLVM), which projects the data onto a mixture of fixed and latent dimensions, can learn a unified low-dimensional embedding for multiple single cell experiments with minimal assumptions. We show the efficacy of the model as compared with state-of-the-art methods for single cell data integration on simulated data, pancreas cells from four sequencing technologies, induced pluripotent stem cells from male and female donors, and mouse brain cells from both spatial seqFISH+ and traditional scRNA-seq.Code and data is available at https://github.com/architverma1/sc-manifold-alignment


2021 ◽  
Author(s):  
◽  
Rajbir Singh Nirwan

Machine Learning (ML) is so pervasive in our todays life that we don't even realise that, more often than expected, we are using systems based on it. It is also evolving faster than ever before. When deploying ML systems that make decisions on their own, we need to think about their ignorance of our uncertain world. The uncertainty might arise due to scarcity of the data, the bias of the data or even a mismatch between the real world and the ML-model. Given all these uncertainties, we need to think about how to build systems that are not totally ignorant thereof. Bayesian ML can to some extent deal with these problems. The specification of the model using probabilities provides a convenient way to quantify uncertainties, which can then be included in the decision making process. In this thesis, we introduce the Bayesian ansatz to modeling and apply Bayesian ML models in finance and economics. Especially, we will dig deeper into Gaussian processes (GP) and Gaussian process latent variable model (GPLVM). Applied to the returns of several assets, GPLVM provides the covariance structure and also a latent space embedding thereof. Several financial applications can be build upon the output of the GPLVM. To demonstrate this, we build an automated asset allocation system, a predictor for missing asset prices and identify other structure in financial data. It turns out that the GPLVM exhibits a rotational symmetry in the latent space, which makes it harder to fit. Our second publication reports, how to deal with that symmetry. We propose another parameterization of the model using Householder transformations, by which the symmetry is broken. Bayesian models are changed by reparameterization, if the prior is not changed accordingly. We provide the correct prior distribution of the new parameters, such that the model, i.e. the data density, is not changed under the reparameterization. After applying the reparametrization on Bayesian PCA, we show that the symmetry of nonlinear models can also be broken in the same way. In our last project, we propose a new method for matching quantile observations, which uses order statistics. The use of order statistics as the likelihood, instead of a Gaussian likelihood, has several advantages. We compare these two models and highlight their advantages and disadvantages. To demonstrate our method, we fit quantiled salary data of several European countries. Given several candidate models for the fit, our method also provides a metric to choose the best option. We hope that this thesis illustrates some benefits of Bayesian modeling (especially Gaussian processes) in finance and economics and its usage when uncertainties are to be quantified.


Author(s):  
Wei Xu ◽  
Alan Ritter ◽  
Chris Callison-Burch ◽  
William B. Dolan ◽  
Yangfeng Ji

We present MultiP (Multi-instance Learning Paraphrase Model), a new model suited to identify paraphrases within the short messages on Twitter. We jointly model paraphrase relations between word and sentence pairs and assume only sentence-level annotations during learning. Using this principled latent variable model alone, we achieve the performance competitive with a state-of-the-art method which combines a latent space model with a feature-based supervised classifier. Our model also captures lexically divergent paraphrases that differ from yet complement previous methods; combining our model with previous work significantly outperforms the state-of-the-art. In addition, we present a novel annotation methodology that has allowed us to crowdsource a paraphrase corpus from Twitter. We make this new dataset available to the research community.


2013 ◽  
Vol 21 (4) ◽  
pp. 468-491 ◽  
Author(s):  
Thomas König ◽  
Moritz Marbach ◽  
Moritz Osnabrügge

This article presents a new method for estimating positions of political parties across country- and time-specific contexts by introducing a latent variable model for manifesto data. We estimate latent positions and exploit bridge observations to make the scales comparable. We also incorporate expert survey data as prior information in the estimation process to avoid ex post facto interpretation of the latent space. To illustrate the empirical contribution of our method, we estimate the left-right positions of 388 parties competing in 238 elections across twenty-five countries and over sixty years. Compared to the puzzling volatility of existing estimates, we find that parties more modestly change their left-right positions over time. We also show that estimates without country- and time-specific bias parameters risk serious, systematic bias in about two-thirds of our data. This suggests that researchers should carefully consider the comparability of party positions across countries and/or time.


2020 ◽  
Author(s):  
Jonathan Rush ◽  
Philippe Rast ◽  
Scott Michael Hofer

Intensive repeated measurement designs are frequently used to investigate within-person variation over relatively brief intervals of time. The majority of research utilizing these designs rely on unit-weighted scale scores, which assume that the constructs are measured without error. An alternative approach makes use of multilevel structural equation models (MSEM), which permit the specification of latent variables at both within-person and between-person levels. These models disaggregate measurement error from systematic variance, which should result in less biased within-person estimates and larger effect sizes. Differences in power, precision, and bias between multilevel unit-weighted and MSEM models were compared through a series of Monte Carlo simulations. Results based on simulated data revealed that precision was consistently poorer in the MSEM models than the unit-weighted models, particularly when reliability was low. However, the degree of bias was considerably greater in the unit-weighted model than the latent variable model. Although the unit-weighted model consistently underestimated the effect of a covariate, it generally had similar power relative to the MSEM model due to the greater precision. Considerations for scale development and the impact of within-person reliability are highlighted.


2014 ◽  
Vol 38 (5) ◽  
pp. 411-422 ◽  
Author(s):  
Mauricio Garnier-Villarreal ◽  
Mijke Rhemtulla ◽  
Todd D. Little

We examine longitudinal extensions of the two-method measurement design, which uses planned missingness to optimize cost-efficiency and validity of hard-to-measure constructs. These designs use a combination of two measures: a “gold standard” that is highly valid but expensive to administer, and an inexpensive (e.g., survey-based) measure that contains systematic measurement bias (e.g., response bias). Using simulated data on four measurement occasions, we compared the cost-efficiency and validity of longitudinal designs where the gold standard is measured at one or more measurement occasions. We manipulated the nature of the response bias over time (constant, increasing, fluctuating), the factorial structure of the response bias over time, and the constraints placed on the latent variable model. Our results showed that parameter bias is lowest when the gold standard is measured on at least two occasions. When a multifactorial structure was used to model response bias over time, it is necessary to have the “gold standard” measures included at every time point, in which case most of the parameters showed low bias. Almost all parameters in all conditions displayed high relative efficiency, suggesting that the 2-method design is an effective way to reduce costs and improve both power and accuracy in longitudinal research.


1999 ◽  
Vol 11 (2) ◽  
pp. 443-482 ◽  
Author(s):  
Michael E. Tipping ◽  
Christopher M. Bishop

Principal component analysis (PCA) is one of the most popular techniques for processing, compressing, and visualizing data, although its effectiveness is limited by its global linearity. While nonlinear variants of PCA have been proposed, an alternative paradigm is to capture data complexity by a combination of local linear PCA projections. However, conventional PCA does not correspond to a probability density, and so there is no unique way to combine PCA models. Therefore, previous attempts to formulate mixture models for PCA have been ad hoc to some extent. In this article, PCA is formulated within a maximum likelihood framework, based on a specific form of gaussian latent variable model. This leads to a well-defined mixture model for probabilistic principal component analyzers, whose parameters can be determined using an expectation-maximization algorithm. We discuss the advantages of this model in the context of clustering, density modeling, and local dimensionality reduction, and we demonstrate its application to image compression and handwritten digit recognition.


2019 ◽  
Vol 20 (1) ◽  
pp. 71-95
Author(s):  
Zhihua Ma ◽  
Guanghui Chen

Multiple responses of mixed types are naturally encountered in a variety of data analysis problems, which should be jointly analysed to achieve higher efficiency gains. As an efficient approach for joint modelling, the latent variable model induces dependence among the mixed outcomes through a shared latent variable. Generally, the latent variable is assumed to be normal, which is not that flexible and realistic in practice. This tutorial article demonstrates how to jointly analyse mixed continuous and ordinal responses using a semiparametric latent variable model by allowing the latent variable to follow a Dirichlet process (DP) prior, and illustrates how to implement Bayesian inference through a powerful R package nimble. Two model comparison criteria, deviance information criterion (DIC) and logarithm of the pseudo-marginal likelihood (LPML), are employed for model selection. Simulated data and data from a social survey study are used for illustrating the proposed method with nimble. An extension of DP prior to DP mixtures prior is introduced as well.


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