NeurIPS 2023 论文列表

Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic features which would require domain expertise and may suffer from limited approximation capability. In this paper, we propose a deep autoregressive model for phylogenetic inference based on graph neural networks (GNNs), called ARTree. By decomposing a tree topology into a sequence of leaf node addition operations and modeling the involved conditional distributions based on learnable topological features via GNNs, ARTree can provide a rich family of distributions over tree topologies that have simple sampling algorithms, without using heuristic features. We demonstrate the effectiveness and efficiency of our method on a benchmark of challenging real data tree topology density estimation and variational Bayesian phylogenetic inference problems.

We study data-driven decision-making problems in the Bayesian framework, where the expectation in the Bayes risk is replaced by a risk-sensitive entropic risk measure with respect to the posterior distribution. We focus on problems where calculating the posterior distribution is intractable, a typical situation in modern applications with large datasets and complex data generating models. We leverage a dual representation of the entropic risk measure to introduce a novel risk-sensitive variational Bayesian (RSVB) framework for jointly computing a risk-sensitive posterior approximation and the corresponding decision rule. Our general framework includes \textit{loss-calibrated} VB (Lacoste-Julien et al. [2011] ) as a special case. We also study the impact of these computational approximations on the predictive performance of the inferred decision rules. We compute the convergence rates of the RSVB approximate posterior and the corresponding optimal value. We illustrate our theoretical findings in parametric and nonparametric settings with the help of three examples.

The Naïve Mean Field (NMF) approximation is widely employed in modern Machine Learning due to the huge computational gains it bestows on the statistician. Despite its popularity in practice, theoretical guarantees for high-dimensional problems are only available under strong structural assumptions (e.g. sparsity). Moreover, existing theory often does not explain empirical observations noted in the existing literature. In this paper, we take a step towards addressing these problems by deriving sharp asymptotic characterizations for the NMF approximation in high-dimensional linear regression. Our results apply to a wide class of natural priors and allow for model mismatch (i.e. the underlying statistical model can be different from the fitted model). We work under an iid Gaussian design and the proportional asymptotic regime, where the number of features and number of observations grow at a proportional rate. As a consequence of our asymptotic characterization, we establish two concrete corollaries: (a) we establish the inaccuracy of the NMF approximation for the log-normalizing constant in this regime, and (b) we provide theoretical results backing the empirical observation that the NMF approximation can be overconfident in terms of uncertainty quantification. Our results utilize recent advances in the theory of Gaussian comparison inequalities. To the best of our knowledge, this is the first application of these ideas to the analysis of Bayesian variational inference problems. Our theoretical results are corroborated by numerical experiments. Lastly, we believe our results can be generalized to non-Gaussian designs and provide empirical evidence to support it.

By now Bayesian methods are routinely used in practice for solving inverse problems. In inverse problems the parameter or signal of interest is observed only indirectly, as an image of a given map, and the observations are typically further corrupted with noise. Bayes offers a natural way to regularize these problems via the prior distribution and provides a probabilistic solution, quantifying the remaining uncertainty in the problem. However, the computational costs of standard, sampling based Bayesian approaches can be overly large in such complex models. Therefore, in practice variational Bayes is becoming increasingly popular. Nevertheless, the theoretical understanding of these methods is still relatively limited, especially in context of inverse problems. In our analysis we investigate variational Bayesian methods for Gaussian process priors to solve linear inverse problems. We consider both mildly and severely ill-posed inverse problems and work with the popular inducing variable variational Bayes approach proposed by Titsias [Titsias, 2009]. We derive posterior contraction rates for the variational posterior in general settings and show that the minimax estimation rate can be attained by correctly tunned procedures. As specific examples we consider a collection of inverse problems including the heat equation, Volterra operator and Radon transform and inducing variable methods based on population and empirical spectral features.

Exact inference of marginals in probabilistic graphical models (PGM) is known to be intractable, necessitating the use of approximate methods. Most of the existing variational techniques perform iterative message passing in loopy graphs which is slow to converge for many benchmarks. In this paper, we propose a new algorithm for marginal inference that is based on the incremental build-infer-approximate (IBIA) paradigm. Our algorithm converts the PGM into a sequence of linked clique tree forests (SLCTF) with bounded clique sizes, and then uses a heuristic belief update algorithm to infer the marginals. For the special case of Bayesian networks, we show that if the incremental build step in IBIA uses the topological order of variables then (a) the prior marginals are consistent in all CTFs in the SLCTF and (b) the posterior marginals are consistent once all evidence variables are added to the SLCTF. In our approach, the belief propagation step is non-iterative and the accuracy-complexity trade-off is controlled using user-defined clique size bounds. Results for several benchmark sets from recent UAI competitions show that our method gives either better or comparable accuracy than existing variational and sampling based methods, with smaller runtimes.

Kernel density estimation (KDE) is integral to a range of generative and discriminative tasks in machine learning. Drawing upon tools from the multidimensional calculus of variations, we derive an optimal weight function that reduces bias in standard kernel density estimates for density ratios, leading to improved estimates of prediction posteriors and information-theoretic measures. In the process, we shed light on some fundamental aspects of density estimation, particularly from the perspective of algorithms that employ KDEs as their main building blocks.

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.

Simulation-Based Inference (SBI) is a common name for an emerging family of approaches that infer the model parameters when the likelihood is intractable. Existing SBI methods either approximate the likelihood, such as Approximate Bayesian Computation (ABC) or directly model the posterior, such as Sequential Neural Posterior Estimation (SNPE). While ABC is efficient on low-dimensional problems, on higher-dimensional tasks, it is generally outperformed by SNPE, which leverages function approximation. In this paper, we propose Pseudo-Likelihood Inference (PLI), a new method that brings neural approximation into ABC, making it competitive on challenging Bayesian system identification tasks. By utilizing integral probability metrics, we introduce a smooth likelihood kernel with an adaptive bandwidth that is updated based on information-theoretic trust regions. Thanks to this formulation, our method (i) allows for optimizing neural posteriors via gradient descent, (ii) does not rely on summary statistics, and (iii) enables multiple observations as input. In comparison to SNPE, it leads to improved performance when more data is available. The effectiveness of PLI is evaluated on four classical SBI benchmark tasks and on a highly dynamic physical system, showing particular advantages on stochastic simulations and multi-modal posterior landscapes.

Stein Variational Gradient Descent (SVGD) is a popular particle-based variational inference algorithm with impressive empirical performance across various domains. Although the population (i.e, infinite-particle) limit dynamics of SVGD is well characterized, its behavior in the finite-particle regime is far less understood. To this end, our work introduces the notion of *virtual particles* to develop novel stochastic approximations of population-limit SVGD dynamics in the space of probability measures, that are exactly realizable using finite particles. As a result, we design two computationally efficient variants of SVGD, namely VP-SVGD and GB-SVGD, with provably fast finite-particle convergence rates. Our algorithms can be viewed as specific random-batch approximations of SVGD, which are computationally more efficient than ordinary SVGD. We show that the $n$ particles output by VP-SVGD and GB-SVGD, run for $T$ steps with batch-size $K$, are at-least as good as i.i.d samples from a distribution whose Kernel Stein Discrepancy to the target is at most $O(\tfrac{d^{1/3}}{(KT)^{1/6}})$ under standard assumptions. Our results also hold under a mild growth condition on the potential function, which is much weaker than the isoperimetric (e.g. Poincare Inequality) or information-transport conditions (e.g. Talagrand's Inequality $\mathsf{T}_1$) generally considered in prior works. As a corollary, we analyze the convergence of the empirical measure (of the particles output by VP-SVGD and GB-SVGD) to the target distribution and demonstrate a **double exponential improvement** over the best known finite-particle analysis of SVGD. Beyond this, our results present the **first known oracle complexities for this setting with polynomial dimension dependence**, thereby completely eliminating the curse of dimensionality exhibited by previously known finite-particle rates.

We study pointwise estimation and uncertainty quantification for a sparse variational Gaussian process method with eigenvector inducing variables. For a rescaled Brownian motion prior, we derive theoretical guarantees and limitations for the frequentist size and coverage of pointwise credible sets. For sufficiently many inducing variables, we precisely characterize the asymptotic frequentist coverage, deducing when credible sets from this variational method are conservative and when overconfident/misleading. We numerically illustrate the applicability of our results and discuss connections with other common Gaussian process priors.

In this paper, we investigate the impact of numerical instability on the reliability of sampling, density evaluation, and evidence lower bound (ELBO) estimation in variational flows. We first empirically demonstrate that common flows can exhibit a catastrophic accumulation of error: the numerical flow map deviates significantly from the exact map---which affects sampling---and the numerical inverse flow map does not accurately recover the initial input---which affects density and ELBO computations. Surprisingly though, we find that results produced by flows are often accurate enough for applications despite the presence of serious numerical instability. In this work, we treat variational flows as chaotic dynamical systems, and leverage shadowing theory to elucidate this behavior via theoretical guarantees on the error of sampling, density evaluation, and ELBO estimation. Finally, we develop and empirically test a diagnostic procedure that can be used to validate results produced by numerically unstable flows in practice.

Matrix completion aims to estimate missing entries in a data matrix, using the assumption of a low-complexity structure (e.g., low-rankness) so that imputation is possible. While many effective estimation algorithms exist in the literature, uncertainty quantification for this problem has proved to be challenging, and existing methods are extremely sensitive to model misspecification. In this work, we propose a distribution-free method for predictive inference in the matrix completion problem. Our method adapts the framework of conformal prediction, which provides prediction intervals with guaranteed distribution-free validity in the setting of regression, to the problem of matrix completion. Our resulting method, conformalized matrix completion (cmc), offers provable predictive coverage regardless of the accuracy of the low-rank model. Empirical results on simulated and real data demonstrate that cmc is robust to model misspecification while matching the performance of existing model-based methods when the model is correct.

We consider the problem of inferring latent stochastic differential equations (SDEs) with a time and memory cost that scales independently with the amount of data, the total length of the time series, and the stiffness of the approximate differential equations. This is in stark contrast to typical methods for inferring latent differential equations which, despite their constant memory cost, have a time complexity that is heavily dependent on the stiffness of the approximate differential equation. We achieve this computational advancement by removing the need to solve differential equations when approximating gradients using a novel amortization strategy coupled with a recently derived reparametrization of expectations under linear SDEs. We show that, in practice, this allows us to achieve similar performance to methods based on adjoint sensitivities with more than an order of magnitude fewer evaluations of the model in training.

Variational inference (VI) is a method to approximate the computationally intractable posterior distributions that arise in Bayesian statistics. Typically, VI fits a simple parametric distribution to be close to the target posterior, optimizing an appropriate objective such as the evidence lower bound (ELBO). In this work, we present a new approach to VI. Our method is based on the principle of score matching---namely, that if two distributions are equal then their score functions (i.e., gradients of the log density) are equal at every point on their support. With this principle, we develop score-matching VI, an iterative algorithm that seeks to match the scores between the variational approximation and the exact posterior. At each iteration, score-matching VI solves an inner optimization, one that minimally adjusts the current variational estimate to match the scores at a newly sampled value of the latent variables. We show that when the variational family is a Gaussian, this inner optimization enjoys a closed-form solution, which we call Gaussian score matching VI (GSM-VI). GSM-VI is a ``black box'' variational algorithm in that it only requires a differentiable joint distribution, and as such it can be applied to a wide class of models. We compare GSM-VI to black box variational inference (BBVI), which has similar requirements but instead optimizes the ELBO. We first study how GSM-VI behaves as a function of the problem dimensionality, the condition number of the target covariance matrix (when the target is Gaussian), and the degree of mismatch between the approximating and exact posterior distribution. We then study GSM-VI on a collection of real-world Bayesian inference problems from the posteriorDB database of datasets and models. We find that GSM-VI is faster than BBVI and equally or more accurate. Specifically, over a wide range of target posteriors, GSM-VI requires 10-100x fewer gradient evaluations than BBVI to obtain a comparable quality of approximation.

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.

Attention mechanisms play a crucial role in cognitive systems by allowing them to flexibly allocate cognitive resources. Transformers, in particular, have become a dominant architecture in machine learning, with attention as their central innovation. However, the underlying intuition and formalism of attention in Transformers is based on ideas of keys and queries in database management systems. In this work, we pursue a structural inference perspective, building upon, and bringing together, previous theoretical descriptions of attention such as; Gaussian Mixture Models, alignment mechanisms and Hopfield Networks. Specifically, we demonstrate that attention can be viewed as inference over an implicitly defined set of possible adjacency structures in a graphical model, revealing the generality of such a mechanism. This perspective unifies different attentional architectures in machine learning and suggests potential modifications and generalizations of attention. Here we investigate two and demonstrate their behaviour on explanatory toy problems: (a) extending the value function to incorporate more nodes of a graphical model yielding a mechanism with a bias toward attending multiple tokens; (b) introducing a geometric prior (with conjugate hyper-prior) over the adjacency structures producing a mechanism which dynamically scales the context window depending on input. Moreover, by describing a link between structural inference and precision-regulation in Predictive Coding Networks, we discuss how this framework can bridge the gap between attentional mechanisms in machine learning and Bayesian conceptions of attention in Neuroscience. We hope by providing a new lens on attention architectures our work can guide the development of new and improved attentional mechanisms.