Faced with complex problems, the human brain demonstrates a remarkable capacity to transcend sensory input and form latent understandings of perceived world patterns. However, this cognitive capacity is not explicitly considered or encoded in current large language models (LLMs). As a result, LLMs often struggle to capture latent structures and model uncertainty in complex compositional reasoning tasks. This work introduces a novel Bayesian prompting approach that facilitates training-free Bayesian inference with LLMs by using a verbalized Probabilistic Graphical Model (PGM). While traditional Bayesian approaches typically depend on extensive data and predetermined mathematical structures for learning latent factors and dependencies, our approach efficiently reasons latent variables and their probabilistic dependencies by prompting LLMs to adhere to Bayesian principles. We evaluated our model on several compositional reasoning tasks, both close-ended and open-ended. Our results indicate that the model effectively enhances confidence elicitation and text generation quality, demonstrating its potential to improve AI language understanding systems, especially in modeling uncertainty.

An example of this is question answering (QA): given a question from the user, the model may provide a brief answer, but it may also follow with supporting facts and explanations, which can vary in form and detail. The user can be satisfied by a wide variety of responses, irrespective of their style or (to some extent) the choice of supporting facts included. Free-form NLG poses significant challenges to uncertainty quantification: some aspects of generation are irrelevant to the task's purpose and best excluded from uncertainty quantification, but it often appears that we are unable to characterize them precisely. If left unaddressed, however, the model's variation in the irrelevant aspects may dominate in standard uncertainty measures such as token-level entropy (Kuhn et al., 2023), making them uninformative about the model's actual performance on the task. Starting from Kuhn et al. (2023), a recent line of work (Kuhn et al., 2023; Lin et al., 2024; Zhang et al., 2023; Aichberger et al., 2024) studied this issue and proposed measuring the "semantic uncertainty" of generation; "semantics" is defined as the equivalence class of textual responses that logically entail one another. Empirical improvements in downstream tasks evidenced their contributions and highlighted the importance of task-specific uncertainty quantification, but important conceptual and practical issues remain. From a practical perspective, semantic equivalence is estimated using machine learning models, resulting in imprecise estimates that do not necessarily define an equivalence relation.

A Bayesian nonparametric model known as the Wishart process has been shown to be effective in this situation, but its inference remains highly challenging. In this work, we introduce a Sequential Monte Carlo (SMC) sampler for the Wishart process, and show how it compares to conventional inference approaches, namely MCMC and variational inference. Using simulations we show that SMC sampling results in the most robust estimates and out-of-sample predictions of dynamic covariance. SMC especially outperforms the alternative approaches when using composite covariance functions with correlated parameters. We demonstrate the practical applicability of our proposed approach on a dataset of clinical depression (n = 1), and show how using an accurate representation of the posterior distribution can be used to test for dynamics on covariance.

We investigate how to select the number of communities for weighted networks without a full likelihood modeling. First, we propose a novel weighted degree-corrected stochastic block model (DCSBM), in which the mean adjacency matrix is modeled as the same as in standard DCSBM, while the variance profile matrix is assumed to be related to the mean adjacency matrix through a given variance function. Our method of selection the number of communities is based on a sequential testing framework, in each step the weighed DCSBM is fitted via some spectral clustering method. A key step is to carry out matrix scaling on the estimated variance profile matrix. The resulting scaling factors can be used to normalize the adjacency matrix, from which the testing statistic is obtained. Under mild conditions on the weighted DCSBM, our proposed procedure is shown to be consistent in estimating the true number of communities. Numerical experiments on both simulated and real network data also demonstrate the desirable empirical properties of our method.

A common objective in the analysis of tabular data is estimating the conditional distribution (in contrast to only producing predictions) of a set of "outcome" variables given a set of "covariates", which is sometimes referred to as the "density regression" problem. Beyond estimation on the conditional distribution, the generative ability of drawing synthetic samples from the learned conditional distribution is also desired as it further widens the range of applications. We propose a flow-based generative model tailored for the density regression task on tabular data. Our flow applies a sequence of tree-based piecewise-linear transforms on initial uniform noise to eventually generate samples from complex conditional densities of (univariate or multivariate) outcomes given the covariates and allows efficient analytical evaluation of the fitted conditional density on any point in the sample space. We introduce a training algorithm for fitting the tree-based transforms using a divide-and-conquer strategy that transforms maximum likelihood training of the tree-flow into training a collection of binary classifiers--one at each tree split--under cross-entropy loss. We assess the performance of our method under out-of-sample likelihood evaluation and compare it with a variety of state-of-the-art conditional density learners on a range of simulated and real benchmark tabular datasets. Our method consistently achieves comparable or superior performance at a fraction of the training and sampling budget. Finally, we demonstrate the utility of our method's generative ability through an application to generating synthetic longitudinal microbiome compositional data based on training our flow on a publicly available microbiome study.

The limitations of purely neural learning have sparked an interest in probabilistic neurosymbolic models, which combine neural networks with probabilistic logical reasoning. As these neurosymbolic models are trained with gradient descent, we study the complexity of differentiating probabilistic reasoning. We prove that although approximating these gradients is intractable in general, it becomes tractable during training. Furthermore, we introduce WeightME, an unbiased gradient estimator based on model sampling. Under mild assumptions, WeightME approximates the gradient with probabilistic guarantees using a logarithmic number of calls to a SAT solver. Lastly, we evaluate the necessity of these guarantees on the gradient. Our experiments indicate that the existing biased approximations indeed struggle to optimize even when exact solving is still feasible.

Random effects meta-analysis model is an important tool for integrating results from multiple independent studies. However, the standard model is based on the assumption of normal distributions for both random effects and within-study errors, making it susceptible to outlying studies. Although robust modeling using the $t$ distribution is an appealing idea, the existing work, that explores the use of the $t$ distribution only for random effects, involves complicated numerical integration and numerical optimization. In this paper, a novel robust meta-analysis model using the $t$ distribution is proposed ($t$Meta). The novelty is that the marginal distribution of the effect size in $t$Meta follows the $t$ distribution, enabling that $t$Meta can simultaneously accommodate and detect outlying studies in a simple and adaptive manner. A simple and fast EM-type algorithm is developed for maximum likelihood estimation. Due to the mathematical tractability of the $t$ distribution, $t$Meta frees from numerical integration and allows for efficient optimization. Experiments on real data demonstrate that $t$Meta is compared favorably with related competitors in situations involving mild outliers. Moreover, in the presence of gross outliers, while related competitors may fail, $t$Meta continues to perform consistently and robustly.

The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on biological processes but introduce challenging inverse problems. Learning-based approaches have emerged as accurate and efficient methods to solve these inverse problems for 3D structure determination, but are specialized for a predefined type of measurement. Here, we introduce a versatile framework to turn raw biophysical measurements of varying types into 3D atomic models. Our method combines a physics-based forward model of the measurement process with a pretrained generative model providing a task-agnostic, data-driven prior. Our method outperforms posterior sampling baselines on both linear and non-linear inverse problems. In particular, it is the first diffusion-based method for refining atomic models from cryo-EM density maps.

Recent advances in probabilistic deep learning enable efficient amortized Bayesian inference in settings where the likelihood function is only implicitly defined by a simulation program (simulation-based inference; SBI). But how faithful is such inference if the simulation represents reality somewhat inaccurately, that is, if the true system behavior at test time deviates from the one seen during training? We conceptualize the types of such model misspecification arising in SBI and systematically investigate how the performance of neural posterior approximators gradually deteriorates as a consequence, making inference results less and less trustworthy. To notify users about this problem, we propose a new misspecification measure that can be trained in an unsupervised fashion (i.e., without training data from the true distribution) and reliably detects model misspecification at test time. Our experiments clearly demonstrate the utility of our new measure both on toy examples with an analytical ground-truth and on representative scientific tasks in cell biology, cognitive decision making, disease outbreak dynamics, and computer vision. We show how the proposed misspecification test warns users about suspicious outputs, raises an alarm when predictions are not trustworthy, and guides model designers in their search for better simulators.

In recent years, solving optimization problems involving black-box simulators has become a point of focus for the machine learning community due to their ubiquity in science and engineering. The simulators describe a forward process $f_{\mathrm{sim}}: (\psi, x) \rightarrow y$ from simulation parameters $\psi$ and input data $x$ to observations $y$, and the goal of the optimization problem is to find parameters $\psi$ that minimize a desired loss function. Sophisticated optimization algorithms typically require gradient information regarding the forward process, $f_{\mathrm{sim}}$, with respect to the parameters $\psi$. However, obtaining gradients from black-box simulators can often be prohibitively expensive or, in some cases, impossible. Furthermore, in many applications, practitioners aim to solve a set of related problems. Thus, starting the optimization ``ab initio", i.e. from scratch, each time might be inefficient if the forward model is expensive to evaluate. To address those challenges, this paper introduces a novel method for solving classes of similar black-box optimization problems by learning an active learning policy that guides a differentiable surrogate's training and uses the surrogate's gradients to optimize the simulation parameters with gradient descent. After training the policy, downstream optimization of problems involving black-box simulators requires up to $\sim$90\% fewer expensive simulator calls compared to baselines such as local surrogate-based approaches, numerical optimization, and Bayesian methods.