jmlr jmlr2013 jmlr2013-59 knowledge-graph by maker-knowledge-mining

59 jmlr-2013-Large-scale SVD and Manifold Learning


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Author: Ameet Talwalkar, Sanjiv Kumar, Mehryar Mohri, Henry Rowley

Abstract: This paper examines the efficacy of sampling-based low-rank approximation techniques when applied to large dense kernel matrices. We analyze two common approximate singular value decomposition techniques, namely the Nystr¨ m and Column sampling methods. We present a theoretical o comparison between these two methods, provide novel insights regarding their suitability for various tasks and present experimental results that support our theory. Our results illustrate the relative strengths of each method. We next examine the performance of these two techniques on the largescale task of extracting low-dimensional manifold structure given millions of high-dimensional face images. We address the computational challenges of non-linear dimensionality reduction via Isomap and Laplacian Eigenmaps, using a graph containing about 18 million nodes and 65 million edges. We present extensive experiments on learning low-dimensional embeddings for two large face data sets: CMU-PIE (35 thousand faces) and a web data set (18 million faces). Our comparisons show that the Nystr¨ m approximation is superior to the Column sampling method for this o task. Furthermore, approximate Isomap tends to perform better than Laplacian Eigenmaps on both clustering and classification with the labeled CMU-PIE data set. Keywords: low-rank approximation, manifold learning, large-scale matrix factorization

Reference: text


Summary: the most important sentenses genereted by tfidf model

sentIndex sentText sentNum sentScore

1 We analyze two common approximate singular value decomposition techniques, namely the Nystr¨ m and Column sampling methods. [sent-8, score-0.278]

2 We next examine the performance of these two techniques on the largescale task of extracting low-dimensional manifold structure given millions of high-dimensional face images. [sent-11, score-0.217]

3 We present extensive experiments on learning low-dimensional embeddings for two large face data sets: CMU-PIE (35 thousand faces) and a web data set (18 million faces). [sent-13, score-0.245]

4 Keywords: low-rank approximation, manifold learning, large-scale matrix factorization 1. [sent-16, score-0.201]

5 3130 L ARGE - SCALE SVD AND M ANIFOLD L EARNING We then examine the performance of these two low-rank approximation techniques on the task of extracting low-dimensional manifold structure given millions of high-dimensional face images. [sent-52, score-0.25]

6 Good sampling of the underlying manifold is essential for this assumption to hold. [sent-57, score-0.241]

7 In fact, many manifold learning techniques provide guarantees that the accuracy of the recovered manifold increases as the number of data samples increases (Tenenbaum et al. [sent-58, score-0.352]

8 However, there is a trade-off between improved sampling of the manifold and the computational cost of manifold learning algorithms, and we explore these computational challenges in this work. [sent-60, score-0.397]

9 Hence, in this work we evaluate the efficacy of the Nystr¨ m method and the Column o sampling method on the task of large-scale manifold learning. [sent-64, score-0.241]

10 We also discuss our efficient implementation of a scalable manifold learning pipeline that leverages modern distributed computing architecture in order to construct neighborhood graphs, calculate shortest paths within these graphs and finally compute large-scale low-rank matrix approximations. [sent-65, score-0.306]

11 First, we show connections between two random sampling based singular value decomposition algorithms and provide the first direct comparison of their performances on a variety of approximation tasks. [sent-67, score-0.311]

12 In particular, we show that the Column sampling method is superior for approximating singular values, singular vectors and matrix projection approximations (defined in Section 3. [sent-68, score-0.644]

13 2), while the Nystr¨ m method is better for spectral o reconstruction approximations (also defined in Section 3. [sent-69, score-0.205]

14 Second, we apply these two algorithms to the task of large-scale manifold learning and present the largest scale study so far on manifold learning, using 18M data points. [sent-71, score-0.312]

15 To date, the largest manifold learning study involves the analysis of music data using 267K points (Platt, 2004). [sent-72, score-0.156]

16 Assuming that rank(T) = r, we can write the compact Singular Value Decomposition (SVD) of this matrix as T = UT ΣT V⊤ where ΣT is diagonal and contains the T singular values of T sorted in decreasing order and UT ∈ Ra×r and VT ∈ Rb×r are corresponding the left and right singular vectors of T. [sent-87, score-0.465]

17 Let C denote the n×l matrix formed by these columns and W the l ×l matrix consisting of the intersection of these l columns with the corresponding l rows of K. [sent-96, score-0.19]

18 More recently, it was presented in Williams o and Seeger (2000) to speed up kernel algorithms and has been used in applications ranging from manifold learning to image segmentation (Platt, 2004; Fowlkes et al. [sent-102, score-0.198]

19 Assuming a uniform sampling of o the columns, the Nystr¨ m method generates a rank-k approximation K of K for k < n defined by: o Knys = CW+ C⊤ ≈ K, k k (2) where Wk is the best k-rank approximation of W with respect to the spectral or Frobenius norm and ⊤ W+ denotes the pseudo-inverse of Wk . [sent-106, score-0.224]

20 3 If we write the SVD ⊤ of C as C = UC ΣC VC then the Column sampling method approximates the top k singular values (Σk ) and singular vectors (Uk ) of K as: Σcol = n ΣC,k l + and Ucol = UC = CVC,k ΣC,k . [sent-113, score-0.505]

21 Nystr¨ m Versus Column Sampling o Given that two sampling-based techniques exist to approximate the SVD of SPSD matrices, we pose a natural question: which method should one use to approximate singular values, singular vectors and low-rank approximations? [sent-117, score-0.469]

22 1 Singular Values and Singular Vectors As shown in (3) and (4), the singular values of K are approximated as the scaled singular values of W and C, respectively. [sent-121, score-0.386]

23 Formally, these scaling terms make the approximations in (3) and (4) unbiased estimators of the true singular values. [sent-123, score-0.253]

24 The Column sampling singular vectors (Ucol ) are orthonormal since they are the singular vectors of C. [sent-125, score-0.58]

25 In contrast, the Nystr¨ m singular vectors o (Unys ) are approximated by extrapolating the singular vectors of W as shown in (3), and are not orthonormal. [sent-126, score-0.454]

26 3, this adversely affects the accuracy of singular vector approximation from the Nystr¨ m method. [sent-128, score-0.266]

27 It is possible to orthonormalize the Nystr¨ m singular o o + vectors by using QR decomposition. [sent-129, score-0.227]

28 2 Low-rank Approximation Several studies have empirically shown that the accuracy of low-rank approximations of kernel matrices is tied to the performance of kernel-based learning algorithms (Williams and Seeger, 2000; Talwalkar and Rostamizadeh, 2010). [sent-136, score-0.165]

29 1, the optimal Kk is given by, Kk = Uk Σk U⊤ = Uk U⊤ K = KUk U⊤ k k k where the columns of Uk are the k singular vectors of K corresponding to the top k singular values of K. [sent-141, score-0.47]

30 We refer to Uk Σk U⊤ as Spectral Reconstruction, since it uses both the singular values and k vectors of K, and Uk U⊤ K as Matrix Projection, since it uses only singular vectors to compute the k projection of K onto the space spanned by vectors Uk . [sent-142, score-0.522]

31 These two low-rank approximations are equal only if Σk and Uk contain the true singular values and singular vectors of K. [sent-143, score-0.48]

32 1 M ATRIX P ROJECTION For Column sampling using (4), the low-rank approximation via matrix projection is ⊤ Kcol = Ucol,k U⊤ K = UC,k UC,k K = C((C⊤ C)k )+ C⊤ K, col,k k (5) 2 ⊤ where (C⊤ C)−1 = VC,k (ΣC,k )+ VC,k . [sent-148, score-0.197]

33 ⊤ Theorem 1 The Column sampling and Nystr¨ m matrix projections are of the form UC RUC K, where o l×l is SPSD. [sent-154, score-0.168]

34 Further, Column sampling gives the lowest reconstruction error (measured in R∈R · F ) among all such approximations if k = l. [sent-155, score-0.217]

35 Observation 1 For k = l, matrix projection for Column sampling reconstructs C exactly. [sent-156, score-0.188]

36 l Observation 2 For k = l, the span of the orthogonalized Nystr¨ m singular vectors equals the span o of Ucol , as discussed in Section 3. [sent-158, score-0.295]

37 Hence, matrix projection is identical for Column sampling and Orthonormal Nystr¨ m for k = l. [sent-160, score-0.164]

38 7K PIE-7K MNIST ESS ABN Data faces faces digits proteins abalones n 2731 7412 4000 4728 4177 d 2304 2304 784 16 8 Kernel linear linear linear RBF RBF Table 1: Description of the data sets used in our experiments comparing sampling-based matrix approximations (Sim et al. [sent-164, score-0.225]

39 The Column sampling spectral reconstruction has a similar form as (7): Kcol = Ucol,k Σcol,k U⊤ = col,k k 1 2 n/l C (C⊤ C)k + C⊤ . [sent-172, score-0.23]

40 Theorem 2 X shows that the optimal spectral reconstruction is data dependent and may differ from the Nystr¨ m o and Column sampling approximations. [sent-178, score-0.23]

41 o Theorem 2 Column sampling and Nystr¨ m spectral reconstructions of rank k are of the form o X⊤ UX ′ ,k ZU⊤′ ,k X, where Z ∈ Rk×k is SPSD. [sent-180, score-0.206]

42 Further, among all approximations of this form, neither X the Column sampling nor the Nystr¨ m approximation is optimal (in · F ). [sent-181, score-0.178]

43 3 Empirical Comparison To test the accuracy of singular values/vectors and low-rank approximations for different methods, we used several kernel matrices arising in different applications, as described in Table 3. [sent-186, score-0.358]

44 3135 TALWALKAR , K UMAR , M OHRI AND ROWLEY For singular values, we measured percentage accuracy of the approximate singular values with respect to the exact ones. [sent-190, score-0.448]

45 The empirical results show that the Column sampling method generates more accurate singular values than the Nystr¨ m method. [sent-193, score-0.278]

46 For singular vectors, the accuracy was measured by the dot product, that is, cosine of principal angles between the exact and the approximate singular vectors. [sent-195, score-0.426]

47 Figure 1(b) shows the difference in mean accuracy between Nystr¨ m and Column sampling methods, once again bucketed by groups of o singular vectors sorted in descending order based on their corresponding singular values. [sent-196, score-0.545]

48 The top 100 singular vectors were all better approximated by Column sampling for all data sets. [sent-197, score-0.312]

49 Furthermore, even when the Nystr¨ m singular vectors o are orthogonalized, the Column sampling approximations are superior, as shown in Figure 1(c). [sent-199, score-0.372]

50 4 1 2−5 Singular Vector Buckets 6−10 11−25 26−50 51−100 Singular Vector Buckets (b) (c) Figure 1: Comparison of singular values and vectors (values above zero indicate better performance of Nystr¨ m). [sent-218, score-0.227]

51 o Next we compared the low-rank approximations generated by the two methods using matrix projection and spectral reconstruction. [sent-222, score-0.212]

52 As motivated by Theorem 1, Column sampling generates better reconstructions via matrix projection (Figure 2(a)). [sent-224, score-0.186]

53 These results may appear somewhat surprising given the relatively poor quality of the singular values/vectors for the Nystr¨ m method, but they are o in agreement with the consequences of Theorem 3 and the fact that the kernel matrices we consider (aside from ‘DEXT’) are nearly low-rank. [sent-226, score-0.258]

54 (f) Percentage of columns (l/n) needed to achieve 75% relative accuracy for Nystr¨ m spectral reconstruction as a function of n. [sent-251, score-0.235]

55 o The non-orthonormality of the Nystr¨ m method’s singular vectors (Section 3. [sent-252, score-0.227]

56 Also, the accuracy of Orthonormal Nystr¨ m spectral reconstruction is worse relative to the standard Nystr¨ m o o approximation, as shown in Figure 2(d). [sent-255, score-0.185]

57 This result can be attributed to the fact that orthonormalization of the singular vectors leads to the loss of some of the unique properties described in Section 3. [sent-256, score-0.227]

58 k k We next tested the accuracy of spectral reconstruction for the two methods for varying values of k and a fixed l. [sent-260, score-0.185]

59 For each n, we performed grid search over l to find the minimal l for which the relative accuracy of Nystr¨ m spectral reconstruction was at least 75%. [sent-264, score-0.185]

60 Out-of-sample extension is often discussed in the context of manifold learning, in which case it involves efficiently deriving a low-dimensional embedding for an arbitrary test point given embeddings from a set of training points (rather than rerunning the entire manifold learning algorithm). [sent-267, score-0.512]

61 Moreover, it is possible to use Column sampling to learn embeddings on the initial sample, and then use the Nystr¨ m method for subsequent out-of-sample-extension. [sent-269, score-0.246]

62 Hence, o given a large set of samples, both the Nystr¨ m method and Column sampling are viable options to o enhance the scalability of manifold learning methods, as we will explore in Section 4. [sent-270, score-0.241]

63 Although we analyzed the effectiveness of these techniques for approximating singular values, singular vectors and low-rank matrix reconstruction, we have yet to discuss the effectiveness of these techniques in the context of actual machine learning tasks. [sent-273, score-0.465]

64 In this section, we will discuss how approximate embeddings can be used in the context of manifold learning, relying on the sampling based algorithms from the previous section to generate an approximate SVD. [sent-277, score-0.402]

65 We present the largest study to date for manifold learning, and provide a quantitative comparison of Isomap and Laplacian Eigenmaps for large scale face manifold construction on clustering and classification tasks. [sent-278, score-0.414]

66 1 I SOMAP Isomap aims to extract a low-dimensional data representation that best preserves all pairwise distances between input points, as measured by their geodesic distances along the manifold (Tenenbaum et al. [sent-290, score-0.287]

67 It approximates the geodesic distance assuming that input space distance provides good approximations for nearby points, and for faraway points it estimates distance as a series of hops between neighboring points. [sent-292, score-0.2]

68 4 It then minimizes an objective function that penalizes nearby inputs for being mapped to faraway outputs, with ‘nearness’ measured by the weight matrix W, and the solution to the objective is the bottom singular vectors of the symmetrized, normalized form of the graph Laplacian, L . [sent-299, score-0.297]

69 Using (3), the Nystr¨ m low-dimensional embeddings are: o k 1/2 + 1/2 Ynys = Σnys,k U⊤ = (ΣW )k nys,k ⊤ UW,k C⊤ . [sent-304, score-0.161]

70 Similarly, from (4) we can express the Column sampling low-dimensional embeddings as: 1/2 Ycol = Σcol,k U⊤ = col,k 4 n 1/2 (ΣC )k l + ⊤ VC,k C⊤ . [sent-305, score-0.246]

71 Further, notice that the optimal low-dimensional embeddings are in fact the square root of the optimal rank k approximation to the associated SPSD matrix, that is, Y⊤ Y = Kk , for Isomap. [sent-307, score-0.22]

72 As such, there is a connection between the task of approximating low-dimensional embeddings and the task of generating low-rank approximate spectral reconstructions, as discussed in Section 3. [sent-308, score-0.234]

73 5 −1 2 5 10 15 20 % of Columns Sampled (l / n ) Figure 3: Comparison of embeddings (values above zero indicate better performance of Nystr¨ m). [sent-319, score-0.161]

74 3 to measure the quality of the low-dimensional embeddings generated by the two techniques and see if the same trend exists. [sent-323, score-0.161]

75 We measured the quality of the low-dimensional embeddings by calculating the extent to which they preserve distances, which is the appropriate criterion in the context of manifold learning. [sent-324, score-0.317]

76 We then computed the approximate low-dimensional embeddings using the Nystr¨ m and Column sampling methods, and o then used these embeddings to compute the associated approximate squared distance matrix, D. [sent-326, score-0.432]

77 Surprisingly, we do not see the same trend in our empirical results for embeddings as we previously observed for spectral reconstruction, as the two techniques exhibit roughly similar behavior across data sets. [sent-331, score-0.234]

78 As a result, we decided to use both the Nystr¨ m and Column sampling methods for our subsequent manifold o learning study. [sent-332, score-0.241]

79 In addition to this visualization, comparison of exact neighbors and spill tree approximations for smaller subsets suggested good performance of spill trees. [sent-363, score-0.178]

80 These edges stem from inadequately sampled regions of the manifold and false positives introduced by the face detector. [sent-371, score-0.217]

81 3 A PPROXIMATING G EODESICS To construct the similarity matrix K in Isomap, one approximates geodesic distance by shortest-path lengths between every pair of nodes in the neighborhood graph. [sent-382, score-0.184]

82 (b) Number of components in the Webfaces-18M neighbor graph and the percentage of images within the largest connected component (‘% Largest’) for varying numbers of neighbors (t) with and without an upper limit on neighbor distances. [sent-401, score-0.194]

83 4 G ENERATING L OW- DIMENSIONAL E MBEDDINGS Before generating low-dimensional embeddings using Isomap, one needs to convert distances into similarities using a process called centering (Tenenbaum et al. [sent-405, score-0.221]

84 For the Nystr¨ m approximao tion, we computed W by double centering D, the l × l matrix of squared geodesic distances between 1 all landmark nodes, as W = − 2 HDH, where H = Il − 1 11⊤ is the centering matrix, Il is the l × l l identity matrix and 1 is a column vector of all ones. [sent-407, score-0.346]

85 Finally, we computed low-dimensional embeddings by multiplying the scaled singular vectors from approximate decomposition with C. [sent-411, score-0.388]

86 The PIE set contains faces in 13 poses, and such a fine sampling of the pose space makes clustering and classification tasks very challenging. [sent-465, score-0.235]

87 The 2D embeddings of PIE-35K (Figure 7 in Appendix E) reveal that Laplacian Eigenmaps projects data points into a small compact region. [sent-483, score-0.161]

88 When used for clustering, these compact embeddings lead to a few large clusters and several tiny clusters, thus explaining the high accuracy and low purity of the clusters. [sent-484, score-0.242]

89 Finally, the improved clustering results of Isomap over PCA for both data sets verify that the manifold of faces is not linear in the input space. [sent-487, score-0.257]

90 Moreover, we compared the performance of Laplacian Eigenmaps and Isomap embeddings on pose classification. [sent-531, score-0.21]

91 Hence, using KNN to compare lowlevel embeddings indirectly measures how well nearest neighbor information is preserved. [sent-535, score-0.224]

92 Thus, we used Nystr¨ m Isomap to generate embeddings o for Webfaces-18M. [sent-542, score-0.161]

93 After learning a face manifold from Webfaces-18M, we analyzed the results with various visualizations. [sent-543, score-0.217]

94 The top row of Figure 5 shows the 2D embeddings from Nystr¨ m Isomap. [sent-544, score-0.161]

95 It is interesting to see that embeddings tend to cluster the faces by pose. [sent-546, score-0.221]

96 In Figure 5, the top right figure shows the shortest paths on the manifold between different public figures. [sent-550, score-0.212]

97 Conclusion We have studied sampling based low-rank approximation algorithms, presenting an analysis of two techniques for approximating SVD on large dense SPSD matrices and providing a theoretical and empirical comparison. [sent-556, score-0.172]

98 Although the Column sampling method generates more accurate singular values, singular vectors and low-rank matrix projections, the Nystr¨ m method constructs better o low-rank approximations, which are of great practical interest as they do not use the full matrix. [sent-557, score-0.55]

99 Although several of the images above are not faces, some are actual faces, suggesting that certain areas of the face manifold are not adequately sampled by Webfaces-18M. [sent-579, score-0.254]

100 Thus the columns of X′ span the columns of X and UX ′ ,r is an orthonormal basis for X, that is, IN − UX ′ ,r U⊤′ ,r ∈ Null(X). [sent-597, score-0.163]


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Experiments were run on a Intel Xeon 5140 @ 2.33GHz processor with 8GB of RAM, and running Ubuntu 8.10 Server (64 bit). optdigit accuracy (%) GURLS (linear primal) GURLS (linear dual) LS-SVM linear GURLS (500 random features) GURLS (1000 random features) GURLS (Gaussian kernel) LS-SVM (Gaussian kernel) time (s) landsat accuracy (%) time (s) pendigit accuracy (%) time (s) 92.3 92.3 92.3 96.8 97.5 98.3 98.3 0.49 726 7190 25.6 207 13500 26100 63.68 66.3 64.6 63.5 63.5 90.4 90.51 0.22 1148 6526 28.0 187 20796 18430 82.24 82.46 82.3 96.7 95.8 98.4 98.36 0.23 5590 46240 31.6 199 100600 120170 Table 2: Comparison between GURLS and LS-SVM. 3203 TACCHETTI , M ALLAPRAGADA , S ANTORO AND ROSASCO Performance (%) 1 0.95 0.9 0.85 isolet(∇) letter(×) 0.8 pendigit(∆) 0.75 landsat(♦) optdigit(◦) 0.7 LIBSVM:rbf 0.65 GURLS++:rbf GURLS:randomfeatures-1000 0.6 GURLS:randomfeatures-500 0.55 0.5 0 10 GURLS:rbf 1 10 2 10 3 10 4 Time (s) 10 Figure 1: Prediction accuracy vs. computing time. The color represents the training method and the library used. In blue: the Matlab implementation of RLS with RBF kernel, in red: its C++ counterpart. In dark red: results of LIBSVM with RBF kernel. In yellow and green: results obtained using a linear kernel on 500 and 1000 random features respectively. We set up different pipelines and compared the performance to SVM, for which we used the python modular interface to LIBSVM (Chang and Lin, 2011). Automatic selection of the optimal regularization parameter is implemented identically in all experiments: (i) split the data; (ii) define a set of regularization parameter on a regular grid; (iii) perform hold-out validation. The variance of the Gaussian kernel has been fixed by looking at the statistics of the pairwise distances among training examples. The prediction accuracy of GURLS and GURLS++ is identical—as expected—but the implementation in C++ is significantly faster. The prediction accuracy of standard RLS-based methods is in many cases higher than SVM. Exploiting the primal formulation of RLS, we further ran experiments with the random features approximation (Rahimi and Recht, 2008). As show in Figure 1, the performance of this method is comparable to that of SVM at a much lower computational cost in the majority of the tested data sets. We further compared GURLS with another available least squares based toolbox: the LS-SVM toolbox (Suykens et al., 2001), which includes routines for parameter selection such as coupled simulated annealing and line/grid search. The goal of this experiment is to benchmark the performance of the parameter selection with random data splitting included in GURLS. For a fair comparison, we considered only the Matlab implementation of GURLS. Results are reported in Table 2. As expected, using the linear kernel with the primal formulation—not available in LS-SVM—is the fastest approach since it leverages the lower dimensionality of the input space. When the Gaussian kernel is used, GURLS and LS-SVM have comparable computing time and classification performance. Note, however, that in GURLS the number of parameter in the grid search is fixed to 400, while in LS-SVM it may vary and is limited to 70. The interesting results obtained with the random features implementation in GURLS, make it an interesting choice in many applications. Finally, all GURLS pipelines, in their Matlab implementation, are faster than LS-SVM and further improvements can be achieved with GURLS++ . Acknowledgments We thank Tomaso Poggio, Zak Stone, Nicolas Pinto, Hristo S. Paskov and CBCL for comments and insights. 3204 GURLS: A L EAST S QUARES L IBRARY FOR S UPERVISED L EARNING References C.-C. Chang and C.-J. Lin. LIBSVM: A library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2:27:1–27:27, 2011. Software available at http://www. csie.ntu.edu.tw/˜cjlin/libsvm. A. Rahimi and B. Recht. Weighted sums of random kitchen sinks: Replacing minimization with randomization in learning. In Advances in Neural Information Processing Systems, volume 21, pages 1313–1320, 2008. R. Rifkin, G. Yeo, and T. Poggio. Regularized least-squares classification. Nato Science Series Sub Series III Computer and Systems Sciences, 190:131–154, 2003. J. Suykens, T. V. Gestel, J. D. Brabanter, B. D. Moor, and J. Vandewalle. Least Squares Support Vector Machines. World Scientific, 2001. ISBN 981-238-151-1. 3205

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