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Dieyi Chen, Jiashun Jin, Zheng Tracy Ke

Subject clustering (i.e., the use of measured features to cluster subjects, such as patients or cells, into multiple groups) is a problem of great interest. In recent years, many approaches were proposed, among which unsupervised deep learning (UDL) has received a great deal of attention. Two interesting questions are (a) how to combine the strengths of UDL and other approaches, and (b) how these approaches compare to one other. We combine Variational Auto-Encoder (VAE), a popular UDL approach, with the recent idea of Influential Feature PCA (IF-PCA), and propose IF-VAE as a new method for subject clustering. We study IF-VAE and compare it with several other methods (including IF-PCA, VAE, Seurat, and SC3) on $10$ gene microarray data sets and $8$ single-cell RNA-seq data sets. We find that IF-VAE significantly improves over VAE, but still underperforms IF-PCA. We also find that IF-PCA is quite competitive, which slightly outperforms Seurat and SC3 over the $8$ single-cell data sets. IF-PCA is conceptually simple and permits delicate analysis. We demonstrate that IF-PCA is capable of achieving the phase transition in a Rare/Weak model. Comparatively, Seurat and SC3 are more complex and theoretically difficult to analyze (for these reasons, their optimality remains unclear).

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Jiashun Jin, Zheng Tracy Ke, Paxton Turner, Anru R. Zhang

How to detect a small community in a large network is an interesting problem, including clique detection as a special case, where a naive degree-based $\chi^2$-test was shown to be powerful in the presence of an Erd\H{o}s-Renyi background. Using Sinkhorn's theorem, we show that the signal captured by the $\chi^2$-test may be a modeling artifact, and it may disappear once we replace the Erd\H{o}s-Renyi model by a broader network model. We show that the recent SgnQ test is more appropriate for such a setting. The test is optimal in detecting communities with sizes comparable to the whole network, but has never been studied for our setting, which is substantially different and more challenging. Using a degree-corrected block model (DCBM), we establish phase transitions of this testing problem concerning the size of the small community and the edge densities in small and large communities. When the size of the small community is larger than $\sqrt{n}$, the SgnQ test is optimal for it attains the computational lower bound (CLB), the information lower bound for methods allowing polynomial computation time. When the size of the small community is smaller than $\sqrt{n}$, we establish the parameter regime where the SgnQ test has full power and make some conjectures of the CLB. We also study the classical information lower bound (LB) and show that there is always a gap between the CLB and LB in our range of interest.

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Jiashun Jin, Zheng Tracy Ke, Shengming Luo

SCORE is a recent approach to network community detection proposed by Jin (2015). In this note, we propose a simple improvement of SCORE, called SCORE+, and compare its performance with several other methods, using 10 different network data sets. For 7 of these data sets, the performances of SCORE and SCORE+ are similar, but for the other 3 data sets (Polbooks, Simmons, Caltech), SCORE+ provides a significant improvement.

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Jiashun Jin, Zheng Tracy Ke, Wanjie Wang

Consider a two-class clustering problem where we observe $X_i = \ell_i \mu + Z_i$, $Z_i \stackrel{iid}{\sim} N(0, I_p)$, $1 \leq i \leq n$. The feature vector $\mu\in R^p$ is unknown but is presumably sparse. The class labels $\ell_i\in\{-1, 1\}$ are also unknown and the main interest is to estimate them. We are interested in the statistical limits. In the two-dimensional phase space calibrating the rarity and strengths of useful features, we find the precise demarcation for the Region of Impossibility and Region of Possibility. In the former, useful features are too rare/weak for successful clustering. In the latter, useful features are strong enough to allow successful clustering. The results are extended to the case of colored noise using Le Cam's idea on comparison of experiments. We also extend the study on statistical limits for clustering to that for signal recovery and that for hypothesis testing. We compare the statistical limits for three problems and expose some interesting insight. We propose classical PCA and Important Features PCA (IF-PCA) for clustering. For a threshold $t > 0$, IF-PCA clusters by applying classical PCA to all columns of $X$ with an $L^2$-norm larger than $t$. We also propose two aggregation methods. For any parameter in the Region of Possibility, some of these methods yield successful clustering. We find an interesting phase transition for IF-PCA. Our results require delicate analysis, especially on post-selection Random Matrix Theory and on lower bound arguments.

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Jiashun Jin, Cun-Hui Zhang, Qi Zhang

Consider a linear regression model where the design matrix X has n rows and p columns. We assume (a) p is much large than n, (b) the coefficient vector beta is sparse in the sense that only a small fraction of its coordinates is nonzero, and (c) the Gram matrix G = X'X is sparse in the sense that each row has relatively few large coordinates (diagonals of G are normalized to 1). The sparsity in G naturally induces the sparsity of the so-called graph of strong dependence (GOSD). We find an interesting interplay between the signal sparsity and the graph sparsity, which ensures that in a broad context, the set of true signals decompose into many different small-size components of GOSD, where different components are disconnected. We propose Graphlet Screening (GS) as a new approach to variable selection, which is a two-stage Screen and Clean method. The key methodological innovation of GS is to use GOSD to guide both the screening and cleaning. Compared to m-variate brute-forth screening that has a computational cost of p^m, the GS only has a computational cost of p (up to some multi-log(p) factors) in screening. We measure the performance of any variable selection procedure by the minimax Hamming distance. We show that in a very broad class of situations, GS achieves the optimal rate of convergence in terms of the Hamming distance. Somewhat surprisingly, the well-known procedures subset selection and the lasso are rate non-optimal, even in very simple settings and even when their tuning parameters are ideally set.

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Yingying Fan, Jiashun Jin, Zhigang Yao

Consider a two-class classification problem where the number of features is much larger than the sample size. The features are masked by Gaussian noise with mean zero and covariance matrix $\Sigma$, where the precision matrix $\Omega=\Sigma^{-1}$ is unknown but is presumably sparse. The useful features, also unknown, are sparse and each contributes weakly (i.e., rare and weak) to the classification decision. By obtaining a reasonably good estimate of $\Omega$, we formulate the setting as a linear regression model. We propose a two-stage classification method where we first select features by the method of Innovated Thresholding (IT), and then use the retained features and Fisher's LDA for classification. In this approach, a crucial problem is how to set the threshold of IT. We approach this problem by adapting the recent innovation of Higher Criticism Thresholding (HCT). We find that when useful features are rare and weak, the limiting behavior of HCT is essentially just as good as the limiting behavior of ideal threshold, the threshold one would choose if the underlying distribution of the signals is known (if only). Somewhat surprisingly, when $\Omega$ is sufficiently sparse, its off-diagonal coordinates usually do not have a major influence over the classification decision. Compared to recent work in the case where $\Omega$ is the identity matrix [Proc. Natl. Acad. Sci. USA 105 (2008) 14790-14795; Philos. Trans. R. Soc. Lond. Ser. A Math. Phys. Eng. Sci. 367 (2009) 4449-4470], the current setting is much more general, which needs a new approach and much more sophisticated analysis. One key component of the analysis is the intimate relationship between HCT and Fisher's separation. Another key component is the tight large-deviation bounds for empirical processes for data with unconventional correlation structures, where graph theory on vertex coloring plays an important role.

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