Sparse PCA via Covariance Thresholding
Yash Deshpande, Andrea Montanari
Introduction
The standard method of principal component analysis involves computing the sample covariance matrix and estimates by its principal eigenvector . It is a well-known fact that, in the high dimensional regime, this yields an inconsistent estimate (see [JL09]). Namely unless . Even worse, [BBAP05] and [Pau07] demonstrate the following phase transition phenomenon. Assuming that , if the estimate is asymptotically orthogonal to the signal, i.e. . On the other hand, for , remains bounded away from zero as . This phase transition phenomenon has attracted considerable attention recently within random matrix theory [FP07, CDMF09, BGN11, KY13].
These inconsistency results motivated several efforts to exploit additional structural information on the signal . In two influential papers, [JL04, JL09] considered the case of a signal that is sparse in a suitable basis, e.g. in the wavelet domain. Without loss of generality, we will assume here that is sparse in the canonical basis , …. In a nutshell, [JL09] propose the following:
Order the diagonal entries of the Gram matrix , and let be the set of indices corresponding to the largest entries.
Set to zero all the entries of unless , and estimate with the principal eigenvector of the resulting matrix.
At the same time, this result is not as strong as might have been expected. By searching exhaustively over all possible supports of size (a method that has complexity of order ) the correct support can be identified with high probability as soon as . No method can succeed for much smaller , because of information theoretic obstructions. We refer the reader to [AW09] for more details.
Over the last ten years, a significant effort has been devoted to developing practical algorithms that outperform diagonal thresholding, see e.g. [MWA05, ZHT06, dEGJL07, dBG08, WTH09]. In particular, [dEGJL07] developed a promising M-estimator based on a semidefinite programming (SDP) relaxation. [AW09] also carried out an analysis of this method and proved that, ifThroughout the paper, we denote by constants that can depend on problem parameters and . We denote by upper case (lower case ) generic absolute constants that are bigger (resp. smaller) than 1, but which might change from line to line. (i) , and (ii) the SDP solution has rank one, then the SDP relaxation provides a consistent estimator of the support of .
At first sight, this appears as a satisfactory solution of the original problem. No procedure can estimate the support of from less than samples, and the SDP relaxation succeeds in doing it from –at most– a constant factor more samples. This picture was upset by a recent, remarkable result by [KNV13] who showed that the rank-one condition assumed by Amini and Wainwright does not hold for . This result is consistent with recent work of [BR13] demonstrating that sparse PCA cannot be performed in polynomial time in the regime , under a certain computational complexity conjecture for the so-called planted clique problem.
In summary, the sparse PCA problem demonstrates a fascinating interplay between computational and statistical barriers.
and disregarding computational considerations, the support of can be estimated consistently if and only if . This can be done, for instance, by exhaustive search over all the possible supports of . We refer to [VL12, CMW+13] for a minimax analysis.
the problem appears to be much more difficult. There is rigorous evidence [BR13, MW+15b, MW15a, WBS14] that no polynomial algorithm can reconstruct the support unless . On the positive side, a very simple algorithm (Johnstone and Lu’s diagonal thresholding) succeeds for .
Of course, several elements are still missing in this emerging picture. In the present paper we address one of them, providing an answer to the following question:
Is there a polynomial time algorithm that is guaranteed to solve the sparse PCA problem with high probability for ?
We answer this question positively by analyzing a covariance thresholding algorithm that proceeds, briefly, as follows. (A precise, general definition, with some technical changes is given in the next section.)
Form the empirical covariance matrix and set to zero all its entries that are in modulus smaller than , for a suitably chosen constant.
Compute the principal eigenvector of this thresholded matrix.
Estimate the support of by thresholding .
Such a covariance thresholding approach was proposed in [KNV13], and is in turn related to earlier work by [BL08b, CZZ+10]. The formulation discussed in the next section presents some technical differences that have been introduced to simplify the analysis. Notice that, to simplify proofs, we assume to be known: this issue is discussed in the next two sections.
The rest of the paper is organized as follows. In the next section we provide a detailed description of the algorithm and state our main results. The proof strategy for our results is explained in Section 3. Our theoretical results assume full knowledge of problem parameters for ease of proof. In light of this, in Section 4 we discuss a practical implementation of the same idea that does not require prior knowledge of problem parameters, and is data-driven. We also illustrate the method through simulations. The complete proofs are in Sections 5, 7 and 6 respectively.
A preliminary version of this paper appeared in [DM14]. This paper extends significantly the results in [DM14]. In particular, by following an analogous strategy, we improve greatly the bounds obtained by [DM14]. This significantly improves the regimes of on which we can obtain non-trivial results. The proofs follow a similar strategy but are, correspondingly, more careful.
Algorithm and main results
We provide a detailed description of the covariance thresholding algorithm for the general model (1) in Table 1. For notational convenience, we shall assume that sample vectors are given (instead of ): .
We start by splitting the data into two halves: and and compute the respective sample covariance matrices and respectively. Define to be the population covariance minus identity, i.e.
Throughout, we let and denote the support of and its size respectively, for . We further let and . The matrix is used, in steps to to obtain a good estimate for the low rank part of the population covariance . The algorithm first computes , a centered version of the empirical covariance as follows:
where is the sample covariance matrix.
In step of the algorithm, this estimate is used to construct good estimates of the eigenvectors . Finally, in step , these estimates are combined with the (independent) second half of the data to construct estimators for the support of the individual eigenvectors . In the first two subsections we will focus on the estimation of and the individual principal components. Our results on support recovery are provided in the final subsection.
Our first result bounds the estimation error of the soft thresholding procedure in operator norm.
There exist numerical constants such that the following happens. Assume , and let . We keep the thresholding level according to
[BL08a, BL08b, Kar08, CZZ+10, CL11] considered the operator norm error of thresholding estimators for structured covariance matrices. Specializing to our case of exact sparsity, the result of [BL08a] implies that, with high probability:
Theorem 1 ensures consistency under a weaker sparsity condition, viz. is sufficient. Also, the resulting rate depends on instead of . In other words, in order to achieve for a fixed , it is sufficient as opposed to .
Crucially, in this regime for , Theorem 1 suggests a threshold of order as opposed to which is used in [BL08a, CZ+12]. As we will see in Section 3, this regime mathematically more challenging than the one of [BL08a, CZ+12]. By setting for a large enough constant , all the entries of outside the support of are set to . In contrast, a large part of our proof is devoted to control the operator norm of the noise part of .
2 Estimating the principal components
We next turn to the question of estimating the principal components . Of course, these are not identifiable if there are degeneracies in the population eigenvalues . We thus introduce the following identifiability condition.
The spike strengths are all distinct. We denote by and . Namely, is the largest signal strength and is the minimum gap.
Notice the minimization over the sign . This is required because the principal components are only identifiable up to a sign. Analogous results can obtained for alternate loss functions such as the projection distance:
The theorem below is an immediate consequence of Theorem 1. In particular, it uses the guarantee of Theorem 1 to show that the corresponding principal components of provide good estimates of the principal components .
There exists a numerical constant such that the following holds. Suppose that Assumption A1 holds in addition to the conditions , , and . Set as according to Theorem 1, and let denote the principal eigenvectors of . Then, with probability
Let . By Davis-Kahn sin-theta theorem [DK70], we have, for ,
For , the claim follows by using Theorem 1. If , the claim is obviously true since always. ∎
3 Support recovery
Finally, we consider the question of support recovery of the principal components . The second phase of our algorithm aims at estimating union of the supports from the estimated principal components . Note that, although is not even expected to be sparse, it is easy to see that the largest entries of should have significant overlap with . Step 6 of the algorithm exploit this property to construct a consistent estimator of the support of the spike .
We will require the following assumption to ensure support recovery.
There exist constants such that the following holds. The non-zero entries of the spikes satisfy for all . Further, for any for every . Without loss of generality, we will assume .
Assume the spiked covariance model of Eq. (1) satisfying assumptions A1 and A2, and further , , and for a large enough numerical constant. Consider the Covariance Thresholding algorithm of Table 1, with as in Theorem 1 .
Then there exists such that, if
then the algorithm recovers the union of supports of with probability (i.e. we have ).
The proof in Section 7 also provides an explicit expression for the constant .
In Assumption A2, the requirement on the minimum size of is standard in support recovery literature [Wai09, MB06]. Additionally, however, we require that when the supports of overlap, they are of the same order, quantified by the parameter . Relaxing this condition is a potential direction for future work.
Recovering the signed supports and , up to a sign flip, is possible using the same technique as recovering the supports above, and poses no additional difficulty.
Algorithm intuition and proof strategy
Recall that . For , the principal eigenvector of , and hence of is positively correlated with , i.e. is bounded away from zero. However, for , the noise component in dominates and the two vectors become asymptotically orthogonal, i.e. for instance . In order to reduce the noise level, we must exploit the sparsity of the spike .
Now, letting , and , we can rewrite as
Consider again the decomposition (16). Since the soft thresholding function is affine when , we would expect that the following decomposition holds approximately (for instance, in operator norm):
Since and each entry of has magnitude at least , the first term is still approximately rank one, with
This is straightforward to see since soft thresholding introduces a maximum bias of per entry of the matrix, while the factor comes due to the support size of (see Proposition 6.2 below for a rigorous argument).
The main technical challenge now is to control the operator norm of the perturbation . We know that has entries of variance , for . If entries were independent with mild tail conditions, this would imply –with high probability–
for some constant . Combining the bias bound from Eq. (18) and the heuristic decomposition of Eq. (19) with the decomposition (17) results in the bound
Our analysis formalizes this argument and shows that such a bound is essentially correct when . A modified bound is proved for (see Theorem 4 for a general statement).
The key technical challenge in our proof is the analysis of the operator norm of such matrices, when is the soft-thresholding function, with threshold of order . Earlier results are not general enough to cover this case. [EK10a, EK10b] provide conditions under which the spectrum of is close to a rescaling of the spectrum of . We are interested instead in a different regime in which the spectrum of is very different from the one of . [CS13] consider -dependent kernels, but their results are asymptotic and concern the weak limit of the empirical spectral distribution of . This does not yield an upper bound on the spectral norm of . Finally, [FM15] consider the spectral norm of kernel random matrices for smooth kernels , only in the proportional regime .
Our approach to proving Theorem 1 follows instead the -net method: we develop high probability bounds on the maximum Rayleigh quotient:
Unfortunately, this turns out not to be true over the whole space of , i.e. the Rayleigh quotient is not Lipschitz continuous in the underlying Gaussian variables . Our approach, instead, shows that for typical values of , we can control the gradient of with respect to , and extract the required concentration only from such local information of the function. This is formalized in our concentration lemma 5.4, which we apply extensively while proving Theorem 1. This lemma is a significantly improved version of the analogous result in [DM14].
Practical aspects and empirical results
Specializing to the rank one case, Theorems 2 and 3 show that Covariance Thresholding succeeds with high probability for a number of samples , while Diagonal Thresholding requires . The reader might wonder whether eliminating the factor has any practical relevance or is a purely conceptual improvement. Figure 1 presents simulations on synthetic data under the strictly sparse model, and the Covariance Thresholding algorithm of Table 1, used in the proof of Theorem 3. The objective is to check whether the factor has an impact at moderate . We compare this with Diagonal Thresholding.
We plot the empirical success probability as a function of for several values of , with . The empirical success probability was computed by using independent instances of the problem. A few observations are of interest: Covariance Thresholding appears to have a significantly larger success probability in the ‘difficult’ regime where Diagonal Thresholding starts to fail; The curves for Diagonal Thresholding appear to decrease monotonically with indicating that proportional to is not the right scaling for this algorithm (as is known from theory); In contrast, the curves for Covariance Thresholding become steeper for larger , and, in particular, the success probability increases with for . This indicates a sharp threshold for , as suggested by our theory.
In terms of practical applicability, our algorithm in Table 1 has the shortcomings of requiring knowledge of problem parameters . Furthermore, the thresholds suggested by theory need not be optimal. We next describe a principled approach to estimating (where possible) the parameters of interest and running the algorithm in a purely data-dependent manner. Assume the following model, for
We let be the empirical mean estimate for . Further letting we see that entries of are mean and variance . We let where denotes the median absolute deviation of the entries of the matrix in the argument, and is a constant scale factor. Guided by the Gaussian case, we take .
We define and soft threshold it to get using as above. Our proof of Theorem 2 relies on the fact that has eigenvalues that are separated from the bulk of the spectrum. Hence, we estimate using : the number of eigenvalues separated from the bulk in . The edge of the spectrum can be computed numerically using the Stieltjes transform method as in [CS13].
Let denote the eigenvector of . Our theoretical analysis indicates that is expected to be close to . In order to denoise , we assume , where is additive random noise (perhaps with some sparse corruptions). We then threshold ‘at the noise level’ to recover a better estimate of . To do this, we estimate the standard deviation of the “noise” by . Here we set –again guided by the Gaussian heuristic– . Since is sparse, this procedure returns a good estimate for the size of the noise deviation. We let denote the vector obtained by hard thresholding : set and We then let and return as our estimate for .
Note that –while different in several respects– this empirical approach shares the same philosophy of the algorithm in Table 1. On the other hand, the data-driven algorithm presented in this section is less straightforward to analyze, a task that we defer to future work.
Figure 1 also shows results of a support recovery experiment using the ‘data-driven’ version of this section. Covariance thresholding in this form also appears to work for supports of size . Figure 2 shows the performance of vanilla PCA, Diagonal Thresholding and Covariance Thresholding on the “Three Peak” example of [JL04]. This signal is sparse in the wavelet domain and the simulations employ the data-driven version of covariance thresholding. A similar experiment with the “box” example of Johnstone and Lu is provided in Figure 3. These experiments demonstrate that, while for large values of both Diagonal Thresholding and Covariance Thresholding perform well, the latter appears superior for smaller values of .
Proof preliminaries
In this section we review some notation and preliminary facts that we will use throughout the paper.
We let denotes the support of the spike . Also, we denote the union of the supports of by . The complement of a set is denoted by .
We write for the soft-thresholding function. By we denote the derivative of with respect to the first argument, which exists Lebesgue almost everywhere. To simplify the notation, we omit the second argument when it is understood from context.
In the statements of our results, consider the limit of large and large with certain conditions on (as in Theorem 1). This limit will be referred to either as “ large enough” or “ large enough” where the phrase “large enough” indicates dependence of (and thereby ) on specific problem parameters.
The Gaussian distribution function will be denoted by .
2 Preliminary facts
A subset is called an -net of if every point in may be approximated by one in with error at most . More precisely:
The minimum cardinality of an -net of , if finite, is called its covering number.
The following two facts are useful while using -nets to bound the spectral norm of a matrix. For proofs, we refer the reader to [Ver12, Lemmas 5.2, 5.4].
Let be the unit sphere in dimensions. Then there exists an -net of , satisfying:
The lemma then follows as . ∎
We now state a general concentration lemma. This will be our basic tool to establish Theorem 2, and thereby Theorem 3.
Here is an independent copy of .
We first implement the symmetrization. Note that:
Here we use Jensen’s inequality with the monotonicity of to obtain and with the convexity of to obtain .
Now we choose , for .
Here is Markov’s inequality, and is the symmetrization bound Eq. (33), where we use the fact that is non-decreasing and convex in .
Define the set . Then:
Here follows as . Equality follows from noting that is measurable with respect to and, hence, first integrating with respect to , a Gaussian random variable that is independent of . The final inequality follows by using the fact that on the set .
Since this bound is uniform over , we can use it in (41):
We can now set , to obtain the exponent above as . The prefactor is bounded by when . Therefore, as required, we obtain:
Combining this with Eq. (38) and the fact that gives Eq. (28) and, consequently, the lemma. ∎
By a simple application of Cauchy-Schwarz, this lemma implies the following.
The following two lemmas are well-known concentration of measure results. The forms below can be found in [Ver12, Corollary 5.35], [LM00, Lemma 1] respectively.
Let . Then
Proof of Theorem 1
Since , we have:
We let be the diagonal entries not included in any support. (Recall that denote the union of the supports.) Further let , , and , or, equivalently . Since these are disjoint we have:
The first term corresponds to the ‘signal’ component, while the last three terms correspond to the ‘noise’ component.
Theorem 1 is a direct consequence of the next five propositions. The first demonstrates that, even for a low level of thresholding, viz. , the term has small operator norm. The second demonstrates that the soft thresholding operation preserves the signal in the term . The next two propositions show that the cross and diagonal terms and are negligible as well. Finally, in the last proposition, we demonstrate that, for the regime of thresholding far above the noise level, i.e. , the noise terms and vanish entirely.
Let denote the second term of Eq. (54). Since ,
Then, there exists an absolute constant such that the following happens. Assuming that and , then with probability
Let denote the first term in Eq. (54):
Assume that and : Then with probability :
Let denote the matrix corresponding to the third term of Eq. (54):
Assuming the conditions of Proposition 6.1 and, additionally, that , there exist constants such that with probability
Let denote the matrix corresponding to the third term of Eq. (54):
With probability we have that .
For some absolute constant , we have for that, with probability :
Therefore, and .
At this point we remark that the probability can be made quantitative, for e.g. of the form , for every large enough. For simplicity of exposition we do not pursue this in the paper.
We defer the proofs of Propositions 6.1, 6.2, 6.3, 6.4 and 6.5 to Sections 6.1, 6.2, 6.3, 6.4 and 6.5 respectively. By combining them for , we immediately obtain the following bound.
There exist numerical constants such that the following happens. Assume , and . Then with probability :
The proof is obtained by adding the error terms from Propositions 6.1, 6.2, 6.3 and 6.4, and noting that is bounded. ∎
Using Propositions 6.1, 6.2, 6.3 and 6.4, together with a suitable choice of , we obtain the proof of Theorem 1.
Note that in the case there is no thresholding and hence the result follows from the fact that [Ver12, Remark 5.40].
We assume now that and the case that . In that case we set . Below we will keep a large enough constant, and check that each of the error terms in Propositions 6.1, 6.2, 6.3 and 6.4 is upper bounded by (a constant times) the right-hand side of Eq. (7). Throughout will denote a generic constant that can be made as large as we want, and can change from line to line.
where in the last step we used .
From Proposition 6.3, we get, using the same argument as in Eq. (65)
Finally, the term of Proposition 6.4 is also bounded as desired using (dividing both sides by and using the fact that is increasing).
The case of is easier. In that case, we can keep with large enough so that for of Proposition 6.5. Then, by Proposition 6.5, we know that and . Therefore we only need consider the terms and . For these terms we can use Propositions 6.2 and 6.4 respectively and, arguing as in the earlier case , we obtain the desired result. ∎
Fix any . There exists an absolute constants such that:
Consider the good set given by:
which holds because of triangle inequality and the fact that . We can now apply Lemma 5.4 to bound the RHS of Eq. (71) and get:
We can simplify the terms on the right-hand side to obtain the result of the lemma. With , Stirling’s approximation and Lemma 5.2 we have:
Assume that . Given and a unit vector , let and denote the projections of onto supports respectively. We have:
whence, by triangle inequality and
We can use now Lemma 5.4, to get, for as defined above and any :
where the last line follows by Cauchy-Schwarz, as in the proof of Lemma 6.7, and the fact that using the upper bound .
By standard bounds and, as , , we have
Combining this with Eq. (101) we now get:
Under the condition of , the gradient also satisfies, when evaluated at :
The rest of the proof is then the same as before. ∎
Given these lemmas, we can now establish Proposition 6.1.
With , the first term is controlled by Lemma 6.7 while the final two are controlled by Lemma 6.8. We choose in Eq. (116), and
for large enough so that, using the bounds of Lemmas 6.7 and 6.8, we have:
This probability bound is provided is not too large: we choose which guarantees that the bound above is when for some large enough. This concludes the proposition. ∎
2 Proof of Proposition 6.2
We decompose the empirical covariance matrix (6) as
With a view to employing this inequality, we use Eq. (119) and the triangle inequality:
where the last line follows by noticing that the first term is supported on of size and then using bias bound Eq. (122) entry-wise. We next bound each of the three terns on the right hand side.
The last inequality follows from the Bai-Yin law on eigenvalues of Wishart matrices [Ver12, Corollary 5.35].
Consider the second term in Eq (125). By orthonormality of , the matrix is orthogonally equivalent to , where we recall that denotes the submatrix of formed by the columns in . Denoting by the orthogonal projector onto the column space of , we then have, with high probability,
Here the penultimate inequality follows by Lemma 5.6 noting that, by invariance under rotations (and since project onto a random subspace of dimensions independent of ), is distributed as the norm of a matrix with i.i.d. standard normal entries, with dimensions , .
Finally, for the third term of Eq. (125) we use the Bai-Yin law of Wishart matrices [Ver12, Corollary 5.35] to obtain, with high probability:
Finally, substituting the above bounds in Eq. (125), we get
3 Proof of Proposition 6.3
Fix an , and let . Then, there exists an absolute constant such that, for any :
Let, as before, denote the -net of unit vectors supported on of size at most and let . Then, by Lemma 5.3, with :
Therefore, arguing as in proof of Proposition 6.1 (see Lemma 6.7):
Consider the good set of pairs \big{(}{\mathbf{Z}},{\mathbf{Z}}^{\prime}\big{)} satisfying:
For \big{(}({\mathbf{Z}},{\mathbf{Z}}^{\prime}\big{)}\in\mathcal{G}_{4}, and , define . Now Using Eqs. (140) and (142, the gradient evaluated at satisfies:
Now applying Corollary 5.5, for :
Let , observing that , we have the bound (using Lemma 5.2 and Stirling’s approximation):
Now we prove a similar lemma when has entries that are “spread out”.
where .
For simplicity of notation, it is convenient to introduce the vector . Throughout the proof, we will use that and . We compute the gradients as follows:
Combining the bounds in Eqs.(153), (156), we obtain
With , we define the good set of pairs satisfying
Define with . By Eq. (158) the gradient evaluated at is bounded by
Hence on the good set , we have:
Therefore the gradient satisfies, on the good set:
where the last equality holds since and by tail bounds on chi-squared random variables. Further
By the above argument, the first term is at most and we turn to the second term. By the Chernoff bound
As before, we will let . The first term is controlled via Lemma 6.9, while the second is controlled by Lemma 6.10. We keep where
so that, via the bounds of Lemmas 6.9, 6.10 and that :
We now set A=\big{(}(\tau^{2}/K)\exp(\tau^{2}/K)\big{)}^{1/2} with for a suitable constant and, since , we get that . Furthermore, it is straightforward to see that , and this implies that
With this setting of , we get the form of below, as required for the proposition.
4 Proof of Proposition 6.4
Since is a diagonal matrix, its spectral norm is bounded by the maximum of its entries. This is easily done as, for every :
By the Chernoff bound for -squared random variables as in Lemma 5.7 followed by the union bound, with probability :
for some absolute . Here we used the fact that .
5 Proof of Proposition 6.5
It suffices to show that with probability
This is a standard argument [BL08b, Lemma A.3] where (following the dependence on ) it suffices to take for a sufficiently large absolute constant. We note here that the same can also be proved via the conditioning technique applied in the proofs of Propositions 6.1 and 6.3.
Proof of Theorems 3
We then have, for and ,
We next bound, with high probability, for . Throughout we let .
where in the last inequality we used .
Consider next the second term. Since , it follows that , for a Gaussian random variable with variance
By union bound over , we obtain
Finally, consider the last term. By rotational invariance of , the distribution of only depends on the angle between and . Calling this angle , we have
Both of these terms have Bernstein-type tail bonds, whence
By putting together Eqs. (194), (199), (203), and using assumption A2, we get
Let . We claim that the above implies that, with high probability, for all .
where the last inequality follows from Eq. (14).
On the other hand, By Theorem 2 and using the assumption (14), we can guarantee
Hence for , and considering –to be definite– , we get
where, in the first inequality, we used .
This concludes the proof. Keeping track of the dependence on , , , , we get that the following conditions are sufficient for the theorem’s conclusion to hold (with a suitable numerical constant):
All of these conditions are implied by the assumptions of Theorem 3, namely Eq. (14). In particular, this is shown by using the fact that for .
Acknowledgements
We are grateful to David Donoho for his feedback on this manuscript. This work was partially supported by the NSF CAREER award CCF-0743978, the NSF grant CCF-1319979, and the grants AFOSR/DARPA FA9550-12-1-0411 and FA9550-13-1-0036.