The sample efficiency of Bayesian optimization algorithms depends on carefully crafted acquisition functions (AFs) guiding the sequential collection of function evaluations. The best-performing AFs can vary significantly across optimization problems, often requiring ad-hoc and problem-specific choices. This work tackles the challenge of designing novel AFs that perform well across a variety of experimental settings. Based on FunSearch, a recent work using Large Language Models (LLMs) for discovery in mathematical sciences, we propose FunBO, an LLM-based method that can be used to learn new AFs written in computer code by leveraging access to a number of evaluations for a limited set of objective functions. We provide the analytic expression of all discovered AFs and evaluate them on various global optimization benchmarks and hyperparameter optimization tasks. We show how FunBO identifies AFs that generalize well both in and out of the training distribution of functions, thus outperforming established general-purpose AFs and achieving competitive performance against AFs that are customized to specific function types and are learned via transfer-learning algorithms.

We consider the problem of fitting autoregressive graph generative models via maximum likelihood estimation (MLE). MLE is intractable for graph autoregressive models because the nodes in a graph can be arbitrarily reordered; thus the exact likelihood involves a sum over all possible node orders leading to the same graph. In this work, we fit the graph models by maximizing a variational bound, which is built by first deriving the joint probability over the graph and the node order of the autoregressive process. This approach avoids the need to specify ad-hoc node orders, since an inference network learns the most likely node sequences that have generated a given graph. We improve the approach by developing a graph generative model based on attention mechanisms and an inference network based on routing search. We demonstrate empirically that fitting autoregressive graph models via variational inference improves their qualitative and quantitative performance, and the improved model and inference network further boost the performance.

A graph generative model defines a distribution over graphs. Typically, the model consists of a sequential process that creates and adds nodes and edges. Such sequential process defines an ordering of the nodes in the graph. The computation of the model’s likelihood requires to marginalize the node orderings; this makes maximum likelihood estimation (MLE) challenging due to the (factorial) number of possible permutations. In this work, we provide an expression for the likelihood of a graph generative model and show that its calculation is closely related to the problem of graph automorphism. In addition, we derive a variational inference (VI) algorithm for fitting a graph generative model that is based on the maximization of a variational bound of the log-likelihood. This allows the model to be trained with node orderings from the approximate posterior instead of ad-hoc orderings. Our experiments show that our log-likelihood bound is significantly tighter than the bound of previous schemes. The models fitted with the VI algorithm are able to generate high-quality graphs that match the structures of target graphs not seen during training.

The variational auto-encoder (VAE) is a deep latent variable model that has two neural networks in an autoencoder-like architecture; one of them parameterizes the model’s likelihood. Fitting its parameters via maximum likelihood (ML) is challenging since the computation of the marginal likelihood involves an intractable integral over the latent space; thus the VAE is trained instead by maximizing a variational lower bound. Here, we develop a ML training scheme for VAEs by introducing unbiased estimators of the log-likelihood gradient. We obtain the estimators by augmenting the latent space with a set of importance samples, similarly to the importance weighted auto-encoder (IWAE), and then constructing a Markov chain Monte Carlo coupling procedure on this augmented space. We provide the conditions under which the estimators can be computed in finite time and with finite variance. We show experimentally that VAEs fitted with unbiased estimators exhibit better predictive performance.

We formulate meta learning using information theoretic concepts; namely, mutual information and the information bottleneck. The idea is to learn a stochastic representation or encoding of the task description, given by a training set, that is highly informative about predicting the validation set. By making use of variational approximations to the mutual information, we derive a general and tractable framework for meta learning. This framework unifies existing gradient-based algorithms and also allows us to derive new algorithms. In particular, we develop a memory-based algorithm that uses Gaussian processes to obtain non-parametric encoding representations. We demonstrate our method on a few-shot regression problem and on four few-shot classification problems, obtaining competitive accuracy when compared to existing baselines.

We analyse the properties of an unbiased gradient estimator of the ELBO for variational inference, based on the score function method with leave-one-out control variates. We show that this gradient estimator can be obtained using a new loss, defined as the variance of the log-ratio between the exact posterior and the variational approximation, which we call the log-variance loss. Under certain conditions, the gradient of the log-variance loss equals the gradient of the (negative) ELBO. We show theoretically that this gradient estimator, which we call VarGrad due to its connection to the log-variance loss, exhibits lower variance than the score function method in certain settings, and that the leave-one-out control variate coefficients are close to the optimal ones. We empirically demonstrate that VarGrad offers a favourable variance versus computation trade-off compared to other state-of-the-art estimators on a discrete VAE.

Topic modeling analyzes documents to learn meaningful patterns of words. However, existing topic models fail to learn interpretable topics when working with large and heavy-tailed vocabularies. To this end, we develop the embedded topic model (etm), a generative model of documents that marries traditional topic models with word embeddings. More specifically, the etm models each word with a categorical distribution whose natural parameter is the inner product between the word’s embedding and an embedding of its assigned topic. To fit the etm, we develop an efficient amortized variational inference algorithm. The etm discovers interpretable topics even with large vocabularies that include rare words and stop words. It outperforms existing document models, such as latent Dirichlet allocation, in terms of both topic quality and predictive performance.

We develop unbiased implicit variational inference (UIVI), a method that expands the applicability of variational inference by defining an expressive variational family. UIVI considers an implicit variational distribution obtained in a hierarchical manner using a simple reparameterizable distribution whose variational parameters are defined by arbitrarily flexible deep neural networks. Unlike previous works, UIVI directly optimizes the evidence lower bound (ELBO) rather than an approximation to the ELBO. We demonstrate UIVI on several models, including Bayesian multinomial logistic regression and variational autoencoders, and show that UIVI achieves both tighter ELBO and better predictive performance than existing approaches at a similar computational cost.

We develop a method to combine Markov chain Monte Carlo (MCMC) and variational inference (VI), leveraging the advantages of both inference approaches. Specifically, we improve the variational distribution by running a few MCMC steps. To make inference tractable, we introduce the variational contrastive divergence (VCD), a new divergence that replaces the standard Kullback-Leibler (KL) divergence used in VI. The VCD captures a notion of discrepancy between the initial variational distribution and its improved version (obtained after running the MCMC steps), and it converges asymptotically to the symmetrized KL divergence between the variational distribution and the posterior of interest. The VCD objective can be optimized efficiently with respect to the variational parameters via stochastic optimization. We show experimentally that optimizing the VCD leads to better predictive performance on two latent variable models: logistic matrix factorization and variational autoencoders (VAEs).

Categorical distributions are ubiquitous in machine learning, e.g., in classification, language models, and recommendation systems. However, when the number of possible outcomes is very large, using categorical distributions becomes computationally expensive, as the complexity scales linearly with the number of outcomes. To address this problem, we propose augment and reduce (A&R), a method to alleviate the computational complexity. A&R uses two ideas: latent variable augmentation and stochastic variational inference. It maximizes a lower bound on the marginal likelihood of the data. Unlike existing methods which are specific to softmax, A&R is more general and is amenable to other categorical models, such as multinomial probit. On several large-scale classification problems, we show that A&R provides a tighter bound on the marginal likelihood and has better predictive performance than existing approaches.

Variational inference using the reparameterization trick has enabled large-scale approximate Bayesian inference in complex probabilistic models, leveraging stochastic optimization to sidestep intractable expectations. The reparameterization trick is applicable when we can simulate a random variable by applying a differentiable deterministic function on an auxiliary random variable whose distribution is fixed. For many distributions of interest (such as the gamma or Dirichlet), simulation of random variables relies on acceptance-rejection sampling. The discontinuity introduced by the accept-reject step means that standard reparameterization tricks are not applicable. We propose a new method that lets us leverage reparameterization gradients even when variables are outputs of a acceptance-rejection sampling algorithm. Our approach enables reparameterization on a larger class of variational distributions. In several studies of real and synthetic data, we show that the variance of the estimator of the gradient is significantly lower than other state-of-the-art methods. This leads to faster convergence of stochastic gradient variational inference.

Word embeddings are an effective tool to analyze language. They have been recently extended to model other types of data beyond text, such as items in recommendation systems. Embedding models consider the probability of a target observation (a word or an item) conditioned on the elements in the context (other words or items). In this paper, we show that conditioning on all the elements in the context is not optimal. Instead, we model the probability of the target conditioned on a learned subset of the elements in the context. We use amortized variational inference to automatically choose this subset. Compared to standard embedding models, this method improves predictions and the quality of the embeddings.

Word embeddings are a powerful approach for analyzing language, and exponential family embeddings (EFE) extend them to other types of data. Here we develop structured exponential family embeddings (S-EFE), a method for discovering embeddings that vary across related groups of data. We study how the word usage of U.S. Congressional speeches varies across states and party affiliation, how words are used differently across sections of the ArXiv, and how the co-purchase patterns of groceries can vary across seasons. Key to the success of our method is that the groups share statistical information. We develop two sharing strategies: hierarchical modeling and amortization. We demonstrate the benefits of this approach in empirical studies of speeches, abstracts, and shopping baskets. We show how SEFE enables group-specific interpretation of word usage, and outperforms EFE in predicting held-out data.

Word embeddings are a powerful approach to capturing semantic similarity among terms in a vocabulary. In this paper, we develop exponential family embeddings, which extends the idea of word embeddings to other types of high-dimensional data. As examples, we studied several types of data: neural data with real-valued observations, count data from a market basket analysis, and ratings data from a movie recommendation system. The main idea is that each observation is modeled conditioned on a set of latent embeddings and other observations, called the context, where the way the context is defined depends on the problem. In language the context is the surrounding words; in neuroscience the context is close-by neurons; in market basket data the context is other items in the shopping cart. Each instance of an embedding defines the context, the exponential family of conditional distributions, and how the embedding vectors are shared across data. We infer the embeddings with stochastic gradient descent, with an algorithm that connects closely to generalized linear models. On all three of our applications—neural activity of zebrafish, users’ shopping behavior, and movie ratings—we found that exponential family embedding models are more effective than other dimension reduction methods. They better reconstruct held-out data and find interesting qualitative structure.

The reparameterization gradient has become a widely used method to obtain Monte Carlo gradients to optimize the variational objective. However, this technique does not easily apply to commonly used distributions such as beta or gamma without further approximations, and most practical applications of the reparameterization gradient fit Gaussian distributions. In this paper, we introduce the generalized reparameterization gradient, a method that extends the reparameterization gradient to a wider class of variational distributions. Generalized reparameterizations use invertible transformations of the latent variables which lead to transformed distributions that weakly depend on the variational parameters. This results in new Monte Carlo gradients that combine reparameterization gradients and score function gradients. We demonstrate our approach on variational inference for two complex probabilistic models. The generalized reparameterization is effective: even a single sample from the variational distribution is enough to obtain a low-variance gradient.

We aim at finding the comorbidity patterns of substance abuse, mood and personality disorders using the diagnoses from the National Epidemiologic Survey on Alcohol and Related Conditions database. To this end, we propose a novel Bayesian nonparametric latent feature model for categorical observations, based on the Indian buffet process, in which the latent variables can take values between 0 and 1. The proposed model has several interesting features for modeling psychiatric disorders. First, the latent features might be off, which allows distinguishing between the subjects who suffer a condition and those who do not. Second, the active latent features take positive values, which allows modeling the extent to which the patient has that condition. We also develop a new Markov chain Monte Carlo inference algorithm for our model that makes use of a nested expectation propagation procedure.

There are many scenarios in artificial intelligence, signal processing or medicine, in which a temporal sequence consists of several unknown overlapping independent causes, and we are interested in accurately recovering those canonical causes. Factorial hidden Markov models (FHMMs) present the versatility to provide a good fit to these scenarios. However, in some scenarios, the number of causes or the number of states of the FHMM cannot be known or limited a priori. In this paper, we propose an infinite factorial unbounded-state hidden Markov model (IFUHMM), in which the number of parallel hidden Markovmodels (HMMs) and states in each HMM are potentially unbounded. We rely on a Bayesian nonparametric (BNP) prior over integer-valued matrices, in which the columns represent the Markov chains, the rows the time indexes, and the integers the state for each chain and time instant. First, we extend the existent infinite factorial binary-state HMM to allow for any number of states. Then, we modify this model to allow for an unbounded number of states and derive an MCMC-based inference algorithm that properly deals with the trade-off between the unbounded number of states and chains. We illustrate the performance of our proposed models in the power disaggregation problem.

We propose the infinite factorial dynamic model (iFDM), a general Bayesian nonparametric model for source separation. Our model builds on the Markov Indian buffet process to consider a potentially unbounded number of hidden Markov chains (sources) that evolve independently according to some dynamics, in which the state space can be either discrete or continuous. For posterior inference, we develop an algorithm based on particle Gibbs with ancestor sampling that can be efficiently applied to a wide range of source separation problems. We evaluate the performance of our iFDM on four well-known applications: multitarget tracking, cocktail party, power disaggregation, and multiuser detection. Our experimental results show that our approach for source separation does not only outperform previous approaches, but it can also handle problems that were computationally intractable for existing approaches.

We develop a Bayesian nonparametric Poisson factorization model for recommendation systems. Poisson factorization implicitly models each user’s limited budget of attention (or money) that allows consumption of only a small subset of the available items. In our Bayesian nonparametric variant, the number of latent components is theoretically unbounded and effectively estimated when computing a posterior with observed user behavior data. To approximate the posterior, we develop an efficient variational inference algorithm. It adapts the dimensionality of the latent components to the data, only requires iteration over the user/item pairs that have been rated, and has computational complexity on the same order as for a parametric model with fixed dimensionality. We studied our model and algorithm with large real-world data sets of user-movie preferences. Our model eases the computational burden of searching for the number of latent components and gives better predictive performance than its parametric counterpart.

The National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) database contains a large amount of information, regarding the way of life, medical conditions, depression, etc., of a representative sample of the U.S. population. In the present paper, we are interested in seeking the hidden causes behind the suicide attempts, for which we propose to model the subjects using a nonparametric latent model based on the Indian Buffet Process (IBP). Due to the nature of the data, we need to adapt the observation model for discrete random variables. We propose a generative model in which the observations are drawn from a multinomial-logit distribution given the IBP matrix. The implementation of an efficient Gibbs sampler is accomplished using the Laplace approximation, which allows us to integrate out the weighting factors of the multinomial-logit likelihood model. Finally, the experiments over the NESARC database show that our model properly captures some of the hidden causes that model suicide attempts.

In this paper, we propose nontrivial codes that achieve a non-zero zero-error rate for several odd-letter noisy-typewriter channels. Some of these codes (specifically, those which are defined for a number of letters of the channel of the form 2n+ 1) achieve the best-known lower bound on the zero-error capacity. We build the codes using linear codes over rings, as we do not require the multiplicative inverse to build the codes.