Covariance matrix preparation for quantum principal component analysis
Instituto de Física Teórica, UAM/CSIC（UAM/CSIC理论物理研究所）；Universidad Autónoma de Madrid（马德里自治大学）；Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）；Quantum Science Center（量子科学中心）
Max Hunter Gordon, M. Cerezo, Lukasz Cincio, Patrick J. Coles
Principal component analysis (PCA) is a dimensionality reduction method in data analysis that involves diagonalizing the covariance matrix of the dataset. Recently, quantum algorithms have been formulated for PCA based on diagonalizing a density matrix. These algorithms assume that the covariance matrix can be encoded in a density matrix, but a concrete protocol for this encoding has been lacking. Our work aims to address this gap. Assuming amplitude encoding of the data, with the data given by the ensemble $\{p_i,| ψ_i \rangle\}$, then one can easily prepare the ensemble average density matrix $\overlineρ = \sum_i p_i |ψ_i\rangle \langle ψ_i |$. We first show that $\overlineρ$ is precisely the covariance matrix whenever the dataset is centered. For quantum datasets, we exploit global phase symmetry to argue that there always exists a centered dataset consistent with $\overlineρ$, and hence $\overlineρ$ can always be interpreted as a covariance matrix. This provides a simple means for preparing the covariance matrix for arbitrary quantum datasets or centered classical datasets. For uncentered classical datasets, our method is so-called "PCA without centering", which we interpret as PCA on a symmetrized dataset. We argue that this closely corresponds to standard PCA, and we derive equations and inequalities that bound the deviation of the spectrum obtained with our method from that of standard PCA. We numerically illustrate our method for the MNIST handwritten digit dataset. We also argue that PCA on quantum datasets is natural and meaningful, and we numerically implement our method for molecular ground-state datasets.
A central roadblock to analyzing quantum algorithms on quantum states is the lack of a comparable input model for classical algorithms. Inspired by recent work of the author [E. Tang, STOC'19], we introduce such a model, where we assume we can efficiently perform $\ell^2$-norm samples of input data, a natural analogue to quantum algorithms that assume efficient state preparation of classical data. Though this model produces less practical algorithms than the (stronger) standard model of classical computation, it captures versions of many of the features and nuances of quantum linear algebra al…
This paper deals with the estimation of a high-dimensional covariance with a conditional sparsity structure and fast-diverging eigenvalues. By assuming sparse error covariance matrix in an approximate factor model, we allow for the presence of some cross-sectional correlation even after taking out common but unobservable factors. We introduce the Principal Orthogonal complEment Thresholding (POET) method to explore such an approximate factor structure with sparsity. The POET estimator includes the sample covariance matrix, the factor-based covariance matrix (Fan, Fan, and Lv, 2008), the thresh…
University of Pennsylvania（宾夕法尼亚大学）；University of Rochester（罗切斯特大学）
Graph neural networks (GNN) are an effective framework that exploit inter-relationships within graph-structured data for learning. Principal component analysis (PCA) involves the projection of data on the eigenspace of the covariance matrix and draws similarities with the graph convolutional filters in GNNs. Motivated by this observation, we study a GNN architecture, called coVariance neural network (VNN), that operates on sample covariance matrices as graphs. We theoretically establish the stability of VNNs to perturbations in the covariance matrix, thus, implying an advantage over standard P…
We present a new straightforward principal component analysis (PCA) method based on the diagonalization of the weighted variance-covariance matrix through two spectral decomposition methods: power iteration and Rayleigh quotient iteration. This method allows one to retrieve a given number of orthogonal principal components amongst the most meaningful ones for the case of problems with weighted and/or missing data. Principal coefficients are then retrieved by fitting principal components to the data while providing the final decomposition. Tests performed on real and simulated cases show that o…
Covariances from categorical variables are defined using a regular simplex expression for categories. The method follows the variance definition by Gini, and it gives the covariance as a solution of simultaneous equations. The calculated results give reasonable values for test data. A method of principal component analysis (RS-PCA) is also proposed using regular simplex expressions, which allows easy interpretation of the principal components. The proposed methods apply to variable selection problem of categorical data USCensus1990 data. The proposed methods give appropriate criterion for the …
This paper presents new algorithms to solve the feature-sparsity constrained PCA problem (FSPCA), which performs feature selection and PCA simultaneously. Existing optimization methods for FSPCA require data distribution assumptions and are lack of global convergence guarantee. Though the general FSPCA problem is NP-hard, we show that, for a low-rank covariance, FSPCA can be solved globally (Algorithm 1). Then, we propose another strategy (Algorithm 2) to solve FSPCA for the general covariance by iteratively building a carefully designed proxy. We prove theoretical guarantees on approximation …
This paper considers sparse spiked covariance matrix models in the high-dimensional setting and studies the minimax estimation of the covariance matrix and the principal subspace as well as the minimax rank detection. The optimal rate of convergence for estimating the spiked covariance matrix under the spectral norm is established, which requires significantly different techniques from those for estimating other structured covariance matrices such as bandable or sparse covariance matrices. We also establish the minimax rate under the spectral norm for estimating the principal subspace, the pri…
Dimension reduction for high-dimensional compositional data plays an important role in many fields, where the principal component analysis of the basis covariance matrix is of scientific interest. In practice, however, the basis variables are latent and rarely observed, and standard techniques of principal component analysis are inadequate for compositional data because of the simplex constraint. To address the challenging problem, we relate the principal subspace of the centered log-ratio compositional covariance to that of the basis covariance, and prove that the latter is approximately iden…
While a set of covariance matrices corresponding to different populations are unlikely to be exactly equal they can still exhibit a high degree of similarity. For example, some pairs of variables may be positively correlated across most groups, while the correlation between other pairs may be consistently negative. In such cases much of the similarity across covariance matrices can be described by similarities in their principal axes, the axes defined by the eigenvectors of the covariance matrices. Estimating the degree of across-population eigenvector heterogeneity can be helpful for a variet…
Based on some new robust estimators of the covariance matrix, we propose stable versions of Principal Component Analysis (PCA) and we qualify it independently of the dimension of the ambient space. We first provide a robust estimator of the orthogonal projector on the largest eigenvectors of the covariance matrix. The behavior of such an estimator is related to the size of the gap in the spectrum of the covariance matrix and in particular a large gap is needed in order to get a good approximation. To avoid the assumption of a large eigengap in the spectrum of the covariance matrix we propose a…
Fan et al. [$\mathit{Annals}$ $\mathit{of}$ $\mathit{Statistics}$ $\textbf{47}$(6) (2019) 3009-3031] constructed a distributed principal component analysis (PCA) algorithm to reduce the communication cost between multiple servers significantly. However, their algorithm's guarantee is only for sub-Gaussian data. Spurred by this deficiency, this paper enhances the effectiveness of their distributed PCA algorithm by utilizing robust covariance matrix estimators of Minsker [$\mathit{Annals}$ $\mathit{of}$ $\mathit{Statistics}$ $\textbf{46}$(6A) (2018) 2871-2903] and Ke et al. [$\mathit{Statistical…
Covariance operators of random functions are crucial tools to study the way random elements concentrate over their support. The principal component analysis of a random function X is well-known from a theoretical viewpoint and extensively used in practical situations. In this work we focus on local covariance operators. They provide some pieces of information about the distribution of X around a fixed point of the space x₀. A description of the asymptotic behaviour of the theoretical and empirical counterparts is carried out. Asymptotic developments are given under assumptions on the loc…
Principal component analysis is an important pattern recognition and dimensionality reduction tool in many applications. Principal components are computed as eigenvectors of a maximum likelihood covariance $\widehatΣ$ that approximates a population covariance $Σ$, and these eigenvectors are often used to extract structural information about the variables (or attributes) of the studied population. Since PCA is based on the eigendecomposition of the proxy covariance $\widehatΣ$ rather than the ground-truth $Σ$, it is important to understand the approximation error in each individual eigenvector …
We propose a stable version of Principal Component Analysis (PCA) in the general framework of a separable Hilbert space. It consists in interpreting the projection on the first eigenvectors as a step function applied to the spectrum of the covariance operator and in replacing it with a smooth cut-off of the eigenvalues. We study the problem from a statistical point of view, so that we assume that we do not have direct access to the covariance operator but we have to estimate it from an i.i.d. sample. We provide some results on the quality of the approximation of our spectral cut-off in terms o…
This paper develops nonasymptotic information inequalities for the estimation of the eigenspaces of a covariance operator. These results generalize previous lower bounds for the spiked covariance model, and they show that recent upper bounds for models with decaying eigenvalues are sharp. The proof relies on lower bound techniques based on group invariance arguments which can also deal with a variety of other statistical models.
Highly robust factored principal component analysis for matrix-valued outlier accommodation and explainable detection via matrix minimum covariance determinant
We consider the problem of decomposing a large covariance matrix into the sum of a low-rank matrix and a diagonally dominant matrix, and we call this problem the "Diagonally-Dominant Principal Component Analysis (DD-PCA)". DD-PCA is an effective tool for designing statistical methods for strongly correlated data. We showcase the use of DD-PCA in two statistical problems: covariance matrix estimation, and global detection in multiple testing. Using the output of DD-PCA, we propose a new estimator for estimating a large covariance matrix with factor structure. Thanks to a nice property of diagon…
We study the meta-learning for support (i.e. the set of non-zero entries) recovery in high-dimensional Principal Component Analysis. We reduce the sufficient sample complexity in a novel task with the information that is learned from auxiliary tasks. We assume each task to be a different random Principal Component (PC) matrix with a possibly different support and that the support union of the PC matrices is small. We then pool the data from all the tasks to execute an improper estimation of a single PC matrix by maximising the $l_1$-regularised predictive covariance to establish that with high…
This work aims to give non-asymptotic results for estimating the first principal component of a multivariate random process. We first define the covariance function and the covariance operator in the multivariate case. We then define a projection operator. This operator can be seen as a reconstruction step from the raw data in the functional data analysis context. Next, we show that the eigenelements can be expressed as the solution to an optimization problem, and we introduce the LASSO variant of this optimization problem and the associated plugin estimator. Finally, we assess the estimator's…
Principal components analysis (PCA) is a widely used dimension reduction technique with an extensive range of applications. In this paper, an online distributed algorithm is proposed for recovering the principal eigenspaces. We further establish its rate of convergence and show how it relates to the number of nodes employed in the distributed computation, the effective rank of the data matrix under consideration, and the gap in the spectrum of the underlying population covariance matrix. The proposed algorithm is illustrated on low-rank approximation and $\boldsymbol{k}$-means clustering tasks…
Outliers contaminating data sets are a challenge to statistical estimators. Even a small fraction of outlying observations can heavily influence most classical statistical methods. In this paper we propose generalized spherical principal component analysis, a new robust version of principal component analysis that is based on the generalized spatial sign covariance matrix. Supporting theoretical properties of the proposed method including influence functions, breakdown values and asymptotic efficiencies are studied, and a simulation study is conducted to compare our new method to existing meth…
In the era of big data, reducing data dimensionality is critical in many areas of science. Widely used Principal Component Analysis (PCA) addresses this problem by computing a low dimensional data embedding that maximally explain variance of the data. However, PCA has two major weaknesses. Firstly, it only considers linear correlations among variables (features), and secondly it is not suitable for categorical data. We resolve these issues by proposing Maximally Correlated Principal Component Analysis (MCPCA). MCPCA computes transformations of variables whose covariance matrix has the largest …
The model implied by factor score predictors does not reproduce the non-diagonal elements of the observed covariance matrix as well as the factor loadings. It is therefore investigated whether it is possible to estimate factor loadings for which the model implied by the factor score predictors optimally reproduces the non-diagonal elements of the observed covariance matrix. Accordingly, loading estimates are proposed for which the model implied by the factor score predictors allows for a least-squares approximation of the non-diagonal elements of the observed covariance matrix. This estimation…
We consider a family of vector dot products that can be implemented using sign changes and addition operations only. The dot products are energy-efficient as they avoid the multiplication operation entirely. Moreover, the dot products induce the $\ell_1$-norm, thus providing robustness to impulsive noise. First, we analytically prove that the dot products yield symmetric, positive semi-definite generalized covariance matrices, thus enabling principal component analysis (PCA). Moreover, the generalized covariance matrices can be constructed in an Energy Efficient (EEF) manner due to the multipl…
Principal component analysis (PCA) is a classical dimension reduction method which projects data onto the principal subspace spanned by the leading eigenvectors of the covariance matrix. However, it behaves poorly when the number of features p is comparable to, or even much larger than, the sample size n. In this paper, we propose a new iterative thresholding approach for estimating principal subspaces in the setting where the leading eigenvectors are sparse. Under a spiked covariance model, we find that the new approach recovers the principal subspace and leading eigenvectors consistently, an…
We consider spatially dependent functional data collected under a geostatistics setting, where locations are sampled from a spatial point process. The functional response is the sum of a spatially dependent functional effect and a spatially independent functional nugget effect. Observations on each function are made on discrete time points and contaminated with measurement errors. Under the assumption of spatial stationarity and isotropy, we propose a tensor product spline estimator for the spatio-temporal covariance function. When a coregionalization covariance structure is further assumed, w…
Massachusetts Institute of Technology（麻省理工学院）；Peking University（北京大学）；California Institute of Technology（加州理工学院）
Principal component analysis (PCA) has achieved great success in unsupervised learning by identifying covariance correlations among features. If the data collection fails to capture the covariance information, PCA will not be able to discover meaningful modes. In particular, PCA will fail the spatial Gaussian Process (GP) model in the undersampling regime, i.e. the averaged distance of neighboring anchor points (spatial features) is greater than the correlation length of GP. Counterintuitively, by drawing the connection between PCA and Schrödinger equation, we can not only attack the undersamp…
Anomalies and outliers are common in real-world data, and they can arise from many sources, such as sensor faults. Accordingly, anomaly detection is important both for analyzing the anomalies themselves and for cleaning the data for further analysis of its ambient structure. Nonetheless, a precise definition of anomalies is important for automated detection and herein we approach such problems from the perspective of detecting sparse latent effects embedded in large collections of noisy data. Standard Graphical Lasso-based techniques can identify the conditional dependency structure of a colle…
We develop two methods for the following fundamental statistical task: given an $ε$-corrupted set of $n$ samples from a $d$-dimensional sub-Gaussian distribution, return an approximate top eigenvector of the covariance matrix. Our first robust PCA algorithm runs in polynomial time, returns a $1 - O(ε\logε^{-1})$-approximate top eigenvector, and is based on a simple iterative filtering approach. Our second, which attains a slightly worse approximation factor, runs in nearly-linear time and sample complexity under a mild spectral gap assumption. These are the first polynomial-time algorithms yie…
The Stein paradox has played an influential role in the field of high dimensional statistics. This result warns that the sample mean, classically regarded as the "usual estimator", may be suboptimal in high dimensions. The development of the James-Stein estimator, that addresses this paradox, has by now inspired a large literature on the theme of "shrinkage" in statistics. In this direction, we develop a James-Stein type estimator for the first principal component of a high dimension and low sample size data set. This estimator shrinks the usual estimator, an eigenvector of a sample covariance…
We derive the asymptotic distributions of the spiked eigenvalues and eigenvectors under a generalized and unified asymptotic regime, which takes into account the spike magnitude of leading eigenvalues, sample size, and dimensionality. This new regime allows high dimensionality and diverging eigenvalue spikes and provides new insights into the roles the leading eigenvalues, sample size, and dimensionality play in principal component analysis. The results are proven by a technical device, which swaps the role of rows and columns and converts the high-dimensional problems into low-dimensional one…
In recent years, samples of time-varying object data such as time-varying networks that are not in a vector space have been increasingly collected. These data can be viewed as elements of a general metric space that lacks local or global linear structure and therefore common approaches that have been used with great success for the analysis of functional data, such as functional principal component analysis, cannot be applied. In this paper we propose metric covariance, a novel association measure for paired object data lying in a metric space $(Ω,d)$ that we use to define a metric auto-covari…
We proposed a general Principal Orthogonal complEment Thresholding (POET) framework for large-scale covariance matrix estimation based on an approximate factor model. A set of high level sufficient conditions for the procedure to achieve optimal rates of convergence under different matrix norms were brought up to better understand how POET works. Such a framework allows us to recover the results for sub-Gaussian in a more transparent way that only depends on the concentration properties of the sample covariance matrix. As a new theoretical contribution, for the first time, such a framework all…
Principal component analysis (PCA) is a widespread technique for data analysis that relies on the covariance-correlation matrix of the analyzed data. However to properly work with high-dimensional data, PCA poses severe mathematical constraints on the minimum number of different replicates or samples that must be included in the analysis. Here we show that a modified algorithm works not only on well dimensioned datasets, but also on degenerated ones.
In sparse principal component analysis we are given noisy observations of a low-rank matrix of dimension $n\times p$ and seek to reconstruct it under additional sparsity assumptions. In particular, we assume here each of the principal components $\mathbf{v}_1,\dots,\mathbf{v}_r$ has at most $s_0$ non-zero entries. We are particularly interested in the high dimensional regime wherein $p$ is comparable to, or even much larger than $n$. In an influential paper, \cite{johnstone2004sparse} introduced a simple algorithm that estimates the support of the principal vectors $\mathbf{v}_1,\dots,\mathbf{…
We consider principal component analysis (PCA) in decomposable Gaussian graphical models. We exploit the prior information in these models in order to distribute its computation. For this purpose, we reformulate the problem in the sparse inverse covariance (concentration) domain and solve the global eigenvalue problem using a sequence of local eigenvalue problems in each of the cliques of the decomposable graph. We demonstrate the application of our methodology in the context of decentralized anomaly detection in the Abilene backbone network. Based on the topology of the network, we propose an…
Fully symmetric learning rules for principal component analysis can be derived from a novel objective function suggested in our previous work. We observed that these learning rules suffer from slow convergence for covariance matrices where some principal eigenvalues are close to each other. Here we describe a modified objective function with an additional term which mitigates this convergence problem. We show that the learning rule derived from the modified objective function inherits all fixed points from the original learning rule (but may introduce additional ones). Also the stability of th…
Principal Component Analysis is a novel way of of dimensionality reduction. This problem essentially boils down to finding the top k eigen vectors of the data covariance matrix. A considerable amount of literature is found on algorithms meant to do so such as an online method be Warmuth and Kuzmin, Matrix Stochastic Gradient by Arora, Oja's method and many others. In this paper we see some of these stochastic approaches to the PCA optimization problem and comment on their convergence and runtime to obtain an epsilon sub-optimal solution. We revisit convex relaxation based methods for stochasti…
Functional Principal Component Analysis (FPCA) has become a widely-used dimension reduction tool for functional data analysis. When additional covariates are available, existing FPCA models integrate them either in the mean function or in both the mean function and the covariance function. However, methods of the first kind are not suitable for data that display second-order variation, while those of the second kind are time-consuming and make it difficult to perform subsequent statistical analyses on the dimension-reduced representations. To tackle these issues, we introduce an eigen-adjusted…
In this paper we analyze different ways of performing principal component analysis throughout three different approaches: robust covariance and correlation matrix estimation, projection pursuit approach and non-parametric maximum entropy algorithm. The objective of these approaches is the correction of the well known sensitivity to outliers of the classical method for principal component analysis. Due to their robustness, they perform very well in contaminated data, while the classical approach fails to preserve the characteristics of the core information.
In this article, we consider the problem of recovering the underlying trajectory when the longitudinal data are sparsely and irregularly observed and noise-contaminated. Such data are popularly analyzed with functional principal component analysis via the Principal Analysis by Conditional Estimation (PACE) method. The PACE method may sometimes be numerically unstable because it involves the inverse of the covariance matrix. We propose a sparse orthonormal approximation (SOAP) method as an alternative. It estimates the optimal empirical basis functions in the best approximation framework rather…
