Conditional Matrix Flows for Gaussian Graphical Models

Studying conditional independence among many variables with few observations is a challenging task. Gaussian Graphical Models (GGMs) tackle this problem by encouraging sparsity in the precision matrix through $l_q$ regularization with $q\leq1$. However, most GMMs rely on the $l_1$ norm because the objective is highly non-convex for sub-$l_1$ pseudo-norms. In the frequentist formulation, the $l_1$ norm relaxation provides the solution path as a function of the shrinkage parameter $\lambda$. In the Bayesian formulation, sparsity is instead encouraged through a Laplace prior, but posterior inference for different $\lambda$ requires repeated runs of expensive Gibbs samplers. Here we propose a general framework for variational inference with matrix-variate Normalizing Flow in GGMs, which unifies the benefits of frequentist and Bayesian frameworks. As a key improvement on previous work, we train with one flow a continuum of sparse regression models jointly for all regularization parameters $\lambda$ and all $l_q$ norms, including non-convex sub-$l_1$ pseudo-norms. Within one model we thus have access to (i) the evolution of the posterior for any $\lambda$ and any $l_q$ (pseudo-) norm, (ii) the marginal log-likelihood for model selection, and (iii) the frequentist solution paths through simulated annealing in the MAP limit.

Paper

References (52)

Scroll for more · 38 remaining

Similar papers

Peer review

Reviewer vqBu6/10 · confidence 3/52023-06-27

Summary

This work proposed a framework for performing inference on Gaussian Graphical Models by approximating the posterior with a normalizing flow over PSD matrices. In this way, the authors can investigate $l_p$-norm regularized GGMs for any value of $p$ in an efficient way.

Strengths

The idea of using normalizing flows for GGM inference definitely brings in advantages of both Bayesian and frequentist worlds; to me, that's an innovative idea.

Weaknesses

The main weakness that I identified is the lack of comparison between the proposed framework and the well-studied graphical lasso with concave approximations of the $l_0$-norm. More precisely, the authors show that their framework obtains frequentist solution paths through simulated annealing, therefore, it'd be of great interest to see a comparison between these solution paths and those obtained by iterative algorithms such as iterative reweighted l1-norm for graphical lasso.

Questions

- in the frequentist case, how does the proposed framework compares against more classical techniques to obtain the solution paths, e.g., iterative reweighted l1-norm?

Rating

6: Weak Accept: Technically solid, moderate-to-high impact paper, with no major concerns with respect to evaluation, resources, reproducibility, ethical considerations.

Confidence

3: You are fairly confident in your assessment. It is possible that you did not understand some parts of the submission or that you are unfamiliar with some pieces of related work. Math/other details were not carefully checked.

Soundness

3 good

Presentation

3 good

Contribution

3 good

Limitations

The authors adequately addressed the limitations of their proposed framework.

Reviewer 3sWQ5/10 · confidence 3/52023-07-03

Summary

This paper proposes a method that can be used to infer conditional independencies in a Gaussian model. These conditional independencies are related to zeros in the precision matrix. Typically, sparse enforcing norms are used to estimate the precision matrix while enforcing zeros in the elements outside of the diagonal. In this paper a Bayesian approach is considered. For this a pseudo-distribution for the data is considered by taking the exponential to the p-norm. The method is trained via variational inference combined with normalizing flows to increase the accuracy of the posterior approximation. The variational distribution is tuned via simulated annealing and a temperature parameter allows to interpolate between the Bayesian and the Map solution.

Strengths

- Well written paper. - Illustrative toy experiments.

Weaknesses

- The proposed method is a combination of already known techniques. - The experimental section is weak as only a single real problem is considered. - Although the proposed method is a generalization of several known techniques, I have found in the experimental section a lack of comparisons with other related methods. My main point of criticism is the weak experimental section which only considers a single real problem and no comparisons with other related methods are carried out in real problems. Another point of criticism is that, for some particular values of the p parameter one does not actually observe sparsity in the Bayesian solution. For example, when sampling from the Laplace distribution one never observes zeros in practice. Spike and slab priors (a mix between a Gaussian and a point of mass center at zero) are the ones that actually lead to zeros.

Questions

None

Rating

5: Borderline accept: Technically solid paper where reasons to accept outweigh reasons to reject, e.g., limited evaluation. Please use sparingly.

Confidence

3: You are fairly confident in your assessment. It is possible that you did not understand some parts of the submission or that you are unfamiliar with some pieces of related work. Math/other details were not carefully checked.

Soundness

2 fair

Presentation

3 good

Contribution

2 fair

Limitations

The authors have not commented on the limitations of their approach.

Reviewer pTVu6/10 · confidence 3/52023-07-07

Summary

This paper targets the structure learning problem in Gaussian Graphical Models via (Normalising) Flow-based Variational approximation of the elements of weight metrics that correspond to the Gaussian Bayesian network. They use sub-l1 pseudo norms to penalize dense precision metrics (which correspond to graphs with numerous links) without imposing an extra high penalty for large non-zero values (which typically occurs if $l_{\geq1}$ is used).

Strengths

1. Up to my knowledge, this is the first time flows are applied to the space of positive definite matrices. 2. The proposed approach is flexible meaning the class of applicable prior and likelihood functions is quite large. 3. Using sub-l1 norm is suitable for structure learning. 4. The proposed algorithm is mathematically sound (as far as I can follow) and is quite interesting. 5. The paper is well-written, and the relevant work is sufficiently discussed. 6. Due to its flexibility, the proposed method has the potential of having a large impact.

Weaknesses

Due to the factors mentioned in the previous section, I find this work impressive and beautiful. However, unfortunately, the carried out experiments are minimal. Most notably, the algorithm is compared to no alternative work (neither in the main paper nor in the supplementary material). With no quantitative comparisons, it is impossible to evaluate the performance of the proposed algorithm compared to the existing methods. NOTE: In the Rebuttal, some experiments are carried out (though the code is still not accessible). Minor suggestion: 1. Though it is clear in the context, I suggest that the authors do not use the same letter "p" (with the same font) for both probability density and norm parameter. 2. Fix minor typos e.g. the end sentence period in line 214.

Questions

* In line 141, what do you mean by "contradiction"?

Rating

6: Weak Accept: Technically solid, moderate-to-high impact paper, with no major concerns with respect to evaluation, resources, reproducibility, ethical considerations.

Confidence

3: You are fairly confident in your assessment. It is possible that you did not understand some parts of the submission or that you are unfamiliar with some pieces of related work. Math/other details were not carefully checked.

Soundness

3 good

Presentation

4 excellent

Contribution

2 fair

Limitations

The authors should compare their method with the relevant structure learning lierature and reveal its points of strength as well as its limitations. This work is theoretical/methodological and does not have any positive or negative social/ethical impact on its own.

Reviewer CnQu6/10 · confidence 4/52023-07-07

Summary

This paper concerns the estimation of precision matrix under $l_p$ norm sparcity penal. The solution is a variational inference through normalizing flow, which is a function of shrinkage parameter $\lambda$ and non-negative norm parameter $p$. It allows for straightforward computation of solution paths for the intervals of $\lambda$ and $p$, and was empirically evaluated on two relatively small data sets.

Strengths

Framework for GGM estimation based on conditional normalizing flows, indeed appears novel. Supporting math seems solid. Using simulated annealing algorithm to recover a path of solutions for varying $\lambda$ and $p$ is useful, in particular for the case of $p$, as in case of $\lambda$ it was fairly straightforward to perform it with other methods too. I am just wondering how costly and scalable it is under the new framework, an empirical/theoretical analysis would be appreciated.

Weaknesses

Empirical evaluation appears limited. It does not contain comparison with other (e.g. frequentist) approaches to derive the solution paths. Both in terms of estimation accuracy and in terms of computational cost.

Questions

In synthetic data example, why did you choose to have more samples than dimensions ( $n>d$ )? Since in that case GGM can be obtained with matrix inverse, and no need for penalized objective.

Rating

6: Weak Accept: Technically solid, moderate-to-high impact paper, with no major concerns with respect to evaluation, resources, reproducibility, ethical considerations.

Confidence

4: You are confident in your assessment, but not absolutely certain. It is unlikely, but not impossible, that you did not understand some parts of the submission or that you are unfamiliar with some pieces of related work.

Soundness

3 good

Presentation

3 good

Contribution

3 good

Limitations

Limitations were not discussed.

Program Chairsdecision2023-09-21

Decision

Accept (poster)

© 2026 NYSGPT2525 LLC