jmlr jmlr2012 jmlr2012-9 knowledge-graph by maker-knowledge-mining

9 jmlr-2012-A Topic Modeling Toolbox Using Belief Propagation


Source: pdf

Author: Jia Zeng

Abstract: Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interests and touches on many important applications in text mining, computer vision and computational biology. This paper introduces a topic modeling toolbox (TMBP) based on the belief propagation (BP) algorithms. TMBP toolbox is implemented by MEX C++/Matlab/Octave for either Windows 7 or Linux. Compared with existing topic modeling packages, the novelty of this toolbox lies in the BP algorithms for learning LDA-based topic models. The current version includes BP algorithms for latent Dirichlet allocation (LDA), authortopic models (ATM), relational topic models (RTM), and labeled LDA (LaLDA). This toolbox is an ongoing project and more BP-based algorithms for various topic models will be added in the near future. Interested users may also extend BP algorithms for learning more complicated topic models. The source codes are freely available under the GNU General Public Licence, Version 1.0 at https://mloss.org/software/view/399/. Keywords: topic models, belief propagation, variational Bayes, Gibbs sampling

Reference: text


Summary: the most important sentenses genereted by tfidf model

sentIndex sentText sentNum sentScore

1 This paper introduces a topic modeling toolbox (TMBP) based on the belief propagation (BP) algorithms. [sent-4, score-0.82]

2 TMBP toolbox is implemented by MEX C++/Matlab/Octave for either Windows 7 or Linux. [sent-5, score-0.124]

3 Compared with existing topic modeling packages, the novelty of this toolbox lies in the BP algorithms for learning LDA-based topic models. [sent-6, score-1.124]

4 The current version includes BP algorithms for latent Dirichlet allocation (LDA), authortopic models (ATM), relational topic models (RTM), and labeled LDA (LaLDA). [sent-7, score-0.68]

5 This toolbox is an ongoing project and more BP-based algorithms for various topic models will be added in the near future. [sent-8, score-0.606]

6 Interested users may also extend BP algorithms for learning more complicated topic models. [sent-9, score-0.451]

7 The source codes are freely available under the GNU General Public Licence, Version 1. [sent-10, score-0.032]

8 Keywords: topic models, belief propagation, variational Bayes, Gibbs sampling 1. [sent-13, score-0.56]

9 Introduction The past decade has seen rapid development of latent Dirichlet allocation (LDA) (Blei et al. [sent-14, score-0.109]

10 , 2003) for solving topic modeling problems because of its elegant three-layer graphical representation as well as two efficient approximate inference methods such as Variational Bayes (VB) (Blei et al. [sent-15, score-0.566]

11 , 2003) and collapsed Gibbs Sampling (GS) (Griffiths and Steyvers, 2004). [sent-16, score-0.087]

12 Both VB and GS have been widely used to learn variants of LDA-based topic models until our recent work (Zeng et al. [sent-17, score-0.462]

13 , 2011) reveals that there is yet another learning algorithm for LDA based on loopy belief propagation (BP). [sent-18, score-0.19]

14 The basic idea of BP is inspired by the collapsed GS algorithm, in which the three-layer LDA can be interpreted as being collapsed into a two-layer factor graph (Kschischang et al. [sent-19, score-0.192]

15 The sum-product BP algorithm operates on the factor graph (Bishop, 2006). [sent-21, score-0.018]

16 Extensive experiments confirm that BP is faster and more accurate than both VB and GS, and thus is a strong candidate for becoming the standard topic modeling algorithm. [sent-22, score-0.529]

17 For example, we show how to learn three typical variants of LDA-based topic models, such as author-topic models (ATM) (Rosen-Zvi et al. [sent-23, score-0.462]

18 , 2004), relational topic models (RTM) (Chang and Blei, 2010), and labeled LDA (LaLDA) (Ramage et al. [sent-24, score-0.559]

19 , 2009) using BP based on the novel factor graph representations (Zeng et al. [sent-25, score-0.018]

20 We have implemented the topic modeling toolbox called TMBP by MEX C++ in the Matlab/Octave interface based on VB, GS and BP algorithms. [sent-27, score-0.635]

21 Compared with other topic modeling c 2012 Jia Zeng. [sent-28, score-0.511]

22 Z ENG packages,1234567 the novelty of this toolbox lies in the BP algorithms for topic modeling. [sent-29, score-0.613]

23 This paper introduces how to use this toolbox for basic topic modeling tasks. [sent-30, score-0.652]

24 Co-occurrence: the different word indices w in the same document d tend to have the same topic label. [sent-33, score-0.672]

25 Smoothness: the same word indices w in the different documents d tend to have the same topic label. [sent-35, score-0.631]

26 Clustering: all word indices w do not tend to be associated with the same topic label. [sent-37, score-0.631]

27 Based on the above rules, recent approximate inference methods compute the marginal distribution of topic label µw,d (k) = p(zk = 1) called message, and estimate parameters using the iterative EM w,d (Bishop, 2006) algorithm according to the maximum-likelihood criterion. [sent-38, score-0.471]

28 The major difference among these inference methods lies in the message update equation. [sent-39, score-0.211]

29 VB updates messages by complicated digamma functions, which cause bias and slow down message updating (Zeng et al. [sent-40, score-0.263]

30 GS updates messages by topic labels randomly sampled from the message in the previous iteration. [sent-42, score-0.603]

31 The sampling process does not keep all uncertainty encoded in the previous message. [sent-43, score-0.023]

32 In contrast, BP directly uses the previous message to update the current message without sampling. [sent-44, score-0.273]

33 Similar ideas have also been proposed within the approximate mean-field framework (Asuncion, 2010) as the zero-order approximation of the collapsed VB (CVB0) algorithm (Asuncion et al. [sent-45, score-0.087]

34 While proper settings of hyperparameters can make the topic modeling performance comparable among different inference methods (Asuncion et al. [sent-47, score-0.58]

35 , 2009), we still advocate the BP algorithms because of their ease of use and fast speed. [sent-48, score-0.02]

36 Table 1 compares the message update equations among VB, GS and BP. [sent-49, score-0.152]

37 Compared with BP, VB uses the digamma function Ψ in message update, and GS uses the discrete count of sampled topic labels n−i based on word tokens rather than word index in mesw,d sage update. [sent-50, score-0.972]

38 The Dirichlet hyperparameters α and β can be viewed as the pseudo-messages. [sent-51, score-0.031]

39 The notations −w and −d denote all word indices except w and all document indices except d, and −i denotes all word tokens except the current word token i. [sent-52, score-0.575]

40 Because VB and GS have been widely used for learning different LDA-based topic models, it is easy to develop the corresponding BP algorithms for learning these LDA-based topic models by 1. [sent-55, score-0.895]

41 either removing the digamma function in the VB or without sampling from the posterior probability in the GS algorithm. [sent-91, score-0.115]

42 For example, we show how to develop the corresponding BP algorithms for two typical LDA-based topic models such as ATM and RTM (Zeng et al. [sent-92, score-0.462]

43 An Example of Using TMBP TMBP toolbox contains source codes for learning LDA based on VB, GS, and BP (Zeng et al. [sent-95, score-0.156]

44 , 2011, 2012a,b,c), learning author-topic models (ATM) (Rosen-Zvi et al. [sent-96, score-0.029]

45 , 2004) based on GS and BP, learning relational topic models (RTM) (Chang and Blei, 2010) and labeled LDA (Ramage et al. [sent-97, score-0.559]

46 Here, we present a demo for the synchronous BP algorithm. [sent-101, score-0.045]

47 The results (the training perplexity at every 10 iterations and the top five words in each of ten topics) are printed on the screen: ∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗ The sBP A l g o r i t h m ∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗∗ I t e r a t i o n 10 o f 5 0 0 : 1041. [sent-104, score-0.026]

48 Labeled LDA: A supervised topic model for credit attribution in multi-labeled corpora. [sent-180, score-0.483]


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Keywords: high-dimensional undirected graph estimation, glasso, huge, semiparametric graph estimation, data-dependent model selection, lossless screening, lossy screening 1. Overview Undirected graphs is a natural approach to describe the conditional independence among many variables. Each node of the graph represents a single variable and no edge between two variables implies that they are conditional independent given all other variables. In the past decade, significant progress has been made on designing efficient algorithms to learn undirected graphs from high-dimensional observational data sets. Most of these methods are based on either the penalized maximum-likelihood estimation (Friedman et al., 2007) or penalized regression methods (Meinshausen and B¨ hlmann, 2006). Existing packages include glasso, Covpath and CLIME. In particuu ∗. Also in the Department of Biostatistics. †. Also in the Department of Machine Learning. c 2012 Zhao, Liu, Roeder, Lafferty and Wasserman. Z HAO , L IU , ROEDER , L AFFERTY AND WASSERMAN lar, the glasso package has been widely adopted by statisticians and computer scientists due to its friendly user-inference and efficiency. In this paper1 we describe a newly developed R package named huge (High-dimensional Undirected Graph Estimation) coded in C. The package includes a wide range of functional modules and addresses some drawbacks of the graphical lasso algorithm. To gain more scalability, the package supports two modes of screening, lossless (Witten et al., 2011) and lossy screening. When using lossy screening, the user can select the desired screening level to scale up for high-dimensional problems, but this introduces some estimation bias. 2. Software Design and Implementation The package huge aims to provide a general framework for high-dimensional undirected graph estimation. The package includes Six functional modules (M1-M6) facilitate a flexible pipeline for analysis (Figure 1). M1. Data Generator: The function huge.generator() can simulate multivariate Gaussian data with different undirected graphs, including hub, cluster, band, scale-free, and Erd¨ s-R´ nyi o e random graphs. The sparsity level of the obtained graph and signal-to-noise ratio can also be set up by users. M2. Semiparametric Transformation: The function huge.npn() implements the nonparanormal method (Liu et al., 2009, 2012) for estimating a semiparametric Gaussian copula model.The nonparanormal family extends the Gaussian distribution by marginally transforming the variables. Computationally, the nonparanormal transformation only requires one pass through the data matrix. M3. Graph Screening: The scr argument in the main function huge() controls the use of largescale correlation screening before graph estimation. The function supports the lossless screening (Witten et al., 2011) and the lossy screening. Such screening procedures can greatly reduce the computational cost and achieve equal or even better estimation by reducing the variance at the expense of increased bias. Figure 1: The graph estimation pipeline. M4. Graph Estimation: Similar to the glasso package, the method argument in the huge() function supports two estimation methods: (i) the neighborhood pursuit algorithm (Meinshausen and B¨ hlmann, 2006) and (ii) the graphical lasso algorithm (Friedman et al., 2007). We apply u the coordinate descent with active set and covariance update, as well as other tricks suggested in Friedman et al. (2010). We modified the warm start trick to address the potential divergence problem of the graphical lasso algorithm (Mazumder and Hastie, 2011). The code is also memory-optimized using the sparse matrix data structure when estimating and storing full regularization paths for large 1. This paper is only a summary of the package huge. For more details please refer to the online vignette. 1060 H IGH - DIMENSIONAL U NDIRECTED G RAPH E STIMATION data sets. we also provide a complementary graph estimation method based on thresholding the sample correlation matrix, which is computationally efficient and widely applied in biomedical research. M5. Model Selection: The function huge.select() provides two regularization parameter selection methods: the stability approach for regularization selection (StARS) (Liu et al., 2010); and rotation information criterion (RIC). We also provide a likelihood-based extended Bayesian information criterion. M6. Graph Visualization: The plotting functions huge.plot() and plot() provide visualizations of the simulated data sets, estimated graphs and paths. The implementation is based on the igraph package. 3. User Interface by Example We illustrate the user interface by analyzing a stock market data which we contribute to the huge package. We acquired closing prices from all stocks in the S&P; 500 for all the days that the market was open between Jan 1, 2003 and Jan 1, 2008. This gave us 1258 samples for the 452 stocks that remained in the S&P; 500 during the entire time period. > > > > > library(huge) data(stockdata) # Load the data x = log(stockdata$data[2:1258,]/stockdata$data[1:1257,]) # Preprocessing x.npn = huge.npn(x, npn.func=

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