Sparse inverse covariance estimation with the graphical lasso

Abstract

We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm—the graphical lasso—that is remarkably fast: It solves a 1000-node problem (∼500000 parameters) in at most a minute and is 30–4000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinshausen and Bühlmann (2006). We illustrate the method on some cell-signaling data from proteomics.

1. INTRODUCTION

In recent years a number of authors have proposed the estimation of sparse undirected graphical models through the use of L₁ (lasso) regularization. The basic model for continuous data assumes that the observations have a multivariate Gaussian distribution with mean μ and covariance matrix Σ. If the ijth component of Σ⁻¹ is zero, then variables i and j are conditionally independent, given the other variables. Thus, it makes sense to impose an L₁ penalty for the estimation of Σ⁻¹ to increase its sparsity.

Meinshausen and Bühlmann (2006) take a simple approach to this problem; they estimate a sparse graphical model by fitting a lasso model to each variable, using the others as predictors. The component is then estimated to be nonzero if either the estimated coefficient of variable i on j or the estimated coefficient of variable j on i is nonzero (alternatively, they use an AND rule). They show that asymptotically, this consistently estimates the set of nonzero elements of Σ⁻¹.

Other authors have proposed algorithms for the exact maximization of the L₁-penalized log-likelihood; Yuan and Lin (2007), Banerjee and others (2007), and Dahl and others (2007) adapt interior-point optimization methods for the solution to this problem. Both papers also establish that the simpler approach of Meinshausen and Bühlmann (2006) can be viewed as an approximation to the exact problem.

We use the blockwise coordinate descent approach in Banerjee and others (2007) as a launching point and propose a new algorithm for the exact problem. This new procedure is extremely simple and is substantially faster competing approaches in our tests. It also bridges the “conceptual gap” between the (Meinshausen and Bühlmann, 2006) proposal and the exact problem.

2. THE PROPOSED METHOD

Suppose, we have N multivariate normal observations of dimension p, with mean μ and covariance Σ. Following Banerjee and others (2007), let Θ = Σ ⁻¹, and let S be the empirical covariance matrix, the problem is to maximize the penalized log-likelihood

(2.1)

over nonnegative definite matrices Θ. † Here, tr denotes the trace and ‖Θ‖₁ is the L₁ norm—the sum of the absolute values of the elements of Σ ⁻¹. Expression (2.1) is the Gaussian log-likelihood of the data, partially maximized with respect to the mean parameter μ. Yuan and Lin (2007) solve this problem using the interior-point method for the “maxdet” problem, proposed by Vandenberghe and others (1998). Banerjee and others (2007) develop a different framework for the optimization, which was the impetus for our work.

Banerjee and others (2007) show that the problem (2.1) is convex and consider estimation of Σ (rather than Σ ⁻¹) as follows. Let W be the estimate of Σ. They show that one can solve the problem by optimizing over each row and corresponding column of W in a block coordinate descent fashion. Partitioning W and S

(2.2)

they show that the solution for

(2.3)

This is a box-constrained quadratic program (QP), which they solve using an interior-point procedure. Permuting the rows and columns so the target column is always the last, they solve a problem like (2.3) for each column, updating their estimate of W after each stage. This is repeated until convergence. If this procedure is initialized with a positive definite matrix, they show that the iterates from this procedure remains positive definite and invertible, even if p > N.

Using convex duality, Banerjee and others (2007) go on to show that solving (2.3) is equivalent to solving the dual problem

(2.4)

where b = W₁₁^−1/2s₁₂‡; if β solves (2.4), then w₁₂ =W₁₁ β solves (2.3). Expression (2.4) resembles a lasso regression and is the basis for our approach.

First we verify the equivalence between the solutions (2.1) and (2.4) directly. Expanding the relation W Θ = I gives an expression that will be useful below:

(2.5)

Now the subgradient equation for maximization of the log-likelihood (2.1) is

(2.6)

using the fact that the derivative of log det Θ equals Θ ⁻¹ = W, given in, for example, Boyd and Vandenberghe (2004, p 641). Here Γ_ij ∈ sign (Θ_ij); that is Γ_ij = sign(Θ_ij) if Θ_ij ≠0, else Γ_ij ∈[−1,1] if Θ_ij = 0.

Now the upper right block of (2.6) is

(2.7)

On the other hand, the subgradient equation from (2.4) works out to be

(2.8)

where ν ∈ sign(β) elementwise. Now suppose (W, Γ) solves (2.6), and hence, (w₁₂, γ₁₂) solves (2.7). Then β =W₁₁⁻¹w₁2 and ν = −γ12 solves (2.8). The equivalence of the first 2 terms is obvious. For the sign terms, since W₁₁θ₁₂ + w₁₂ θ₂₂ = 0 from (2.5), we have that θ₁₂ = −θ₂₂W₁₁⁻¹w₁₂. Since θ₂₂ > 0, it follows that sign(θ₁₂) = −sign(W₁₁⁻¹w₁₂) = −sign(β). This proves the equivalence. We note that the solution β to the lasso problem (2.4) gives us (up to a negative constant) the corresponding part of Θ: θ₁₂ = −θ₂₂β.

Now to the main point of this paper. Problem (2.4) looks like a lasso (L₁-regularized) least-squares problem. In fact if W₁₁ = S₁₁, then the solutions are easily seen to equal the lasso estimates for the pth variable on the others and hence related to the Meinshausen and Bühlmann (2006) proposal. As pointed out by Banerjee and others (2007), W₁₁ ≠ S₁₁ in general, and hence, the Meinshausen and Bühlmann (2006) approach does not yield the maximum likelihood estimator. They point out that their blockwise interior point procedure is equivalent to recursively solving and updating the lasso problem (2.4), but do not pursue this approach. We do, to great advantage, because fast coordinate descent algorithms (Friedman and others, 2007) make solution of the lasso problem very attractive.

In terms of inner products, the usual lasso estimates for the pth variable on the others take as input the data S₁₁ and s₁₂. To solve (2.4), we instead use W₁₁ and s₁₂, where W₁₁ is our current estimate of the upper block of W. We then update w and cycle through all of the variables until convergence.

Note that from (2.6), the solution w_ii = s_ii + ρ for all i, since θ_ii > 0, and hence, Γ_ii = 1. For convenience we call this algorithm the graphical lasso. Here is the algorithm in detail:

     Graphical lasso algorithm

1. Start with W = S + ρI. The diagonal of W remains unchanged in what follows.

2. For each j = 1,2,… p,1,2,…p,…, solve the lasso problem (2.4), which takes as input the inner products W₁₁ and s₁₂. This gives a p− 1 vector solution . Fill in the corresponding row and column of W using w₁₂ = W₁₁.

3. Continue until convergence.

There is a simple, conceptually appealing way to view this procedure. Given a data matrix X and outcome vector Y, we can think of the linear least-squares regression estimates (X^TX) ⁻¹ X_Ty as functions not of the raw data, but instead the inner products X^TX and X^Ty. Similarly, one can show that the lasso estimates are functions of these inner products as well. Hence, in the current problem, we can think of the lasso estimates for the pth variable on the others as having the functional form

(2.9)

But application of the lasso to each variable does not solve problem (2.1); to solve this via the graphical lasso we instead use the inner products W₁₁ and s₁₂. That is, we replace (2.9) by

(2.10)

The point is that problem (2.1) is not equivalent to p separate regularized regression problems, but to p coupled lasso problems that share the same W and Θ =W⁻¹. The use of in place of W¹¹ S₁₁ shares the information between the problems in an appropriate fashion.

Note that each iteration in step (2.2) implies a permutation of the rows and columns to make the target column the last. The lasso problem in step (2.2) above can be efficiently solved by coordinate descent (Friedman and others, 2007), (Wu and Lange, 2007). Here are the details. Letting V =W₁₁ and u = s₁₂, then the update has the form

(2.11)

for j =1,2,…,p,1,2,…p,…, where S is the soft-threshold operator:

(2.12)

We cycle through the predictors until convergence. In our implementation, the procedure stops when the average absolute change in W is less than t · ave |S^−diag|, where S^−diag are the off-diagonal elements of the empirical covariance matrix S, and t is a fixed threshold, set by default at 0.001.

Note that will typically be sparse, and so the computation w₁₂ =W₁₁ will be fast; if there are r nonzero elements, it takes rp operations.

Although our algorithm has estimated =W, we can recover =W⁻¹ relatively cheaply. Note that from the partitioning in (2.5), we have

from which we derive the standard partitioned inverse expressions

(2.13)

(2.14)

But since =W₁₁⁻¹w₁₂, we have that ₂₂ = 1/(w₂₂ −w₁₂^T and ₁₂ = −₂₂. Thus, ₁₂ is a simple rescaling of by −₂₂, which is easily computed. Although these calculations could be included in step 2.2 of the graphical lasso algorithm, they are not needed till the end; hence, we store all the coefficients β for each of the p problems in a p × p matrix and compute after convergence.

Interestingly, if W = S, these are just the formulas for obtaining the inverse of a partitioned matrix. That is, if we set W = S and ρ = 0 in the above algorithm, then one sweep through the predictors computes S⁻¹, using a linear regression at each stage.

REMARK 2.1 In some situations it might make sense to specify different amounts of regularization for each variable, or even allow each inverse covariance element to be penalized differently. Thus, we maximize the log-likelihood

(2.15)

where P ={ρjk} with ρjk = ρkj, and * indicates componentwise multiplication. It is easy to show that (2.15) is maximized by the preceding algorithm, with ρ replaced by ρjk in the soft-thresholding step (2.11). Typically, one might take for some values ρ1,ρ2,…ρp, to allow different amounts of regularization for each variable.

REMARK 2.2 If the diagonal elements are left out of the penalty in (2.1), the solution for w_iiis simply s_ii, and otherwise the algorithm is the same as before.

3. TIMING COMPARISONS

We simulated Gaussian data from both sparse and dense scenarios, for a range of problem sizes p. The sparse scenario is the AR(1) model taken from Yuan and Lin (2007): ${({\Sigma }^{-1})}_{ii}=1$, ${({\Sigma }^{-1})}_{i,i-1}={({\Sigma }^{-1})}_{i-1,i}=0.5$, and zero otherwise. In the dense scenario, ${({\Sigma }^{-1})}_{ii}=2$, ${({\Sigma }^{-1})}_{ii}=1$ otherwise. We chose the penalty parameter so that the solution had about the actual number of nonzero elements in the sparse setting and about half of total number of elements in the dense setting. The graphical lasso procedure was coded in Fortran, linked to an R language function. All timings were carried out on a Intel Xeon 2.80 GHz processor.

We compared the graphical lasso to the COVSEL program provided by Banerjee and others (2007). This is a Matlab program, with a loop that calls a C language code to do the box-constrained QP for each column of the solution matrix. To be as fair as possible to COVSEL, we only counted the CPU time spent in the C program. We set the maximum number of outer iterations to 30 and, following the authors code, set the the duality gap for convergence to 0.1.

The number of CPU seconds for each trial is shown in Table 1. The algorithm took between 2 and 8 iterations of the outer loop. In the dense scenarios for p = 200 and 400, COVSEL had not converged by 30 iterations. We see that the graphical lasso is 30–4000 times faster than COVSEL and only about 2–10 times slower than the approximate method.

Table 1.

Timings (seconds) for graphical lasso, Meinhausen–Buhlmann approximation, and COVSEL procedures

p	Problem type	(1) Graphical lasso	(2) Approximation	(3) COVSEL	Ratio of (3) to (1)
100	Sparse	0.014	0.007	34.7	2476.4
100	Dense	0.053	0.018	2.2	40.9
200	Sparse	0.050	0.027	> 205.35	> 4107
200	Dense	0.497	0.146	16.9	33.9
400	Sparse	1.23	0.193	> 1616.7	> 1314.3
400	Dense	6.2	0.752	313.0	50.5

Figure 1 shows the number of CPU seconds required for the graphical lasso procedure, for problem sizes up to 1000. The computation time is $O(p^3)$ for dense problems and considerably less than that for sparse problems. Even in the dense scenario, it solves a 1000-node problem (∼ 500 000 parameters) in about a minute. However, the computation time depends strongly on the value of ρ, as illustrated in Table 2. Number of CPU seconds required for the graphical lasso procedure.

Fig. 1.

Number of CPU seconds required for the graphical lasso procedure.

Table 2.

Timing results for dense scenario, p = 400, for different values of the regularization parameter ρ. The middle column is the number of nonzero coefficients

ρ	Fraction nonzero	CPU time (s)
0.01	0.96	26.7
0.03	0.62	8.5
0.06	0.36	4.1
0.60	0.00	0.4

4. ANALYSIS OF CELL-SIGNALLING DATA

For illustration, we analyze a flow cytometry data set on p = 11 proteins and n = 7466 cells, from Sachs and others (2003). These authors fit a directed acyclic graph (DAG) to the data, producing the network in Figure 2.

Fig. 2.

Directed acylic graph from cell-signaling data, from Sachs and others (2003).

The result of applying the graphical lasso to these data is shown in Figure 3, for 12 different values of the penalty parameter ρ. There is moderate agreement between, for example, the graph for L₁ norm = 0. 00496 and the DAG:The former has about half of the edges and nonedges that appear in the DAG. Figure 4 shows the lasso coefficients as a function of total L₁ norm of the coefficient vector.

Fig. 3.

Cell-signaling data: Undirected graphs from graphical lasso with different values of the penalty parameter ρ.

Fig. 4.

Cell-signaling data: Profile of coefficients as the total L₁norm of the coefficient vector increases, that is as ρdecreases. Profiles for the largest coefficients are labeled with the corresponding pair of proteins.

In the left panel of Figure 5, we tried 2 different kinds of 10-fold cross-validation for estimation of the parameter ρ. In the “regression” approach, we fit the graphical lasso to nine-tenths of the data and used the penalized regression model for each protein to predict the value of that protein in the validation set. We then averaged the squared prediction errors over all 11 proteins. In the “likelihood” approach, we again applied the graphical lasso to nine-tenths of the data and then evaluated the log-likelihood (2.1) over the validation set. The 2 cross-validation curves indicate that the unregularized model is the best, not surprising given the large number of observations and relatively small number of parameters. However, we also see that the likelihood approach is far less variable than the regression method.

Fig. 5.

Cell-signaling data. Left panel shows 10-fold cross-validation using both regression and likelihood approaches (details in text). Right panel compares the regression sum of squares of the exact graphical lasso approach to the Meinhausen–Buhlmann approximation.

The right panel compares the cross-validated sum of squares of the exact graphical lasso approach to the Meinhausen–Buhlmann approximation. For lightly regularized models, the exact approach has a clear advantage.

5. DISCUSSION

We have presented a simple and fast algorithm for estimation of a sparse inverse covariance matrix using an L₁ penalty. It cycles through the variables, fitting a modified lasso regression to each variable in turn. The individual lasso problems are solved by coordinate descent.

The speed of this new procedure should facilitate the application of sparse inverse covariance procedures to large data sets involving thousands of parameters.

An R language package glasso is available on the third author's Web site.

FUNDING

National Science Foundation (DMS-97-64431 to J.F., DMS-0505676 to T. H., DMS-9971405 to R.T.); National Institutes of Health (2R01 CA 72028-07 to T. H.); National Institutes of Health Contract (N01-HV-28183 to R.T.).