Normalizing Flows have emerged as a powerful brand of generative models, as they not only allow for efficient sampling of complicated target distributions, but also deliver density estimation by construction. We propose here an in-depth comparison of coupling and autoregressive flows, both of the affine and rational quadratic spline type, considering four different architectures: Real-valued Non-Volume Preserving (RealNVP), Masked Autoregressive Flow (MAF), Coupling Rational Quadratic Spline (C-RQS), and Autoregressive Rational Quadratic Spline (A-RQS). We focus on different target distributions of increasing complexity with dimensionality ranging from 4 to 1000. The performances are discussed in terms of different figures of merit: the one-dimensional Wasserstein distance, the one-dimensional Kolmogorov-Smirnov test, the Frobenius norm of the difference between correlation matrices, and the training time. Our results indicate that the A-RQS algorithm stands out both in terms of accuracy and training speed. Nonetheless, all the algorithms are generally able, without much fine-tuning, to learn complex distributions with limited training data and in a reasonable time, of the order of hours on a Tesla V100 GPU. The only exception is the C-RQS, which takes significantly longer to train, and does not always provide good accuracy. All algorithms have been implemented using TensorFlow2 and TensorFlow Probability and made available on GitHub.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

Training deep graph neural networks (GNNs) poses a challenging task, as the performance of GNNs may suffer from the number of hidden message-passing layers. The literature has focused on the proposals of {over-smoothing} and {under-reaching} to explain the performance deterioration of deep GNNs. In this paper, we propose a new explanation for such deteriorated performance phenomenon, {mis-simplification}, that is, mistakenly simplifying graphs by preventing self-loops and forcing edges to be unweighted. We show that such simplifying can reduce the potential of message-passing layers to capture the structural information of graphs. In view of this, we propose a new framework, edge enhanced graph neural network (EEGNN). EEGNN uses the structural information extracted from the proposed Dirichlet mixture Poisson graph model (DMPGM), a Bayesian nonparametric model for graphs, to improve the performance of various deep message-passing GNNs. We propose a Markov chain Monte Carlo inference framework for DMPGM. Experiments over different datasets show that our method achieves considerable performance increase compared to baselines.

Probabilistic circuits (PCs) are a prominent representation of probability distributions with tractable inference. While parameter learning in PCs is rigorously studied, structure learning is often more based on heuristics than on principled objectives. In this paper, we develop Bayesian structure scores for deterministic PCs, i.e., the structure likelihood with parameters marginalized out, which are well known as rigorous objectives for structure learning in probabilistic graphical models. When used within a greedy cutset algorithm, our scores effectively protect against overfitting and yield a fast and almost hyper-parameter-free structure learner, distinguishing it from previous approaches. In experiments, we achieve good trade-offs between training time and model fit in terms of log-likelihood. Moreover, the principled nature of Bayesian scores unlocks PCs for accommodating frameworks such as structural expectation-maximization.

A promising approach for scalable Gaussian processes (GPs) is the Karhunen-Lo\`eve (KL) decomposition, in which the GP kernel is represented by a set of basis functions which are the eigenfunctions of the kernel operator. Such decomposed kernels have the potential to be very fast, and do not depend on the selection of a reduced set of inducing points. However KL decompositions lead to high dimensionality, and variable selection becomes paramount. This paper reports a new method of forward variable selection, enabled by the ordered nature of the basis functions in the KL expansion of the Bayesian Smoothing Spline ANOVA kernel (BSS-ANOVA), coupled with fast Gibbs sampling in a fully Bayesian approach. It quickly and effectively limits the number of terms, yielding a method with competitive accuracies, training and inference times for tabular datasets of low feature set dimensionality. The inference speed and accuracy makes the method especially useful for dynamic systems identification, by modeling the dynamics in the tangent space as a static problem, then integrating the learned dynamics using a high-order scheme. The methods are demonstrated on two dynamic datasets: a `Susceptible, Infected, Recovered' (SIR) toy problem, with the transmissibility used as forcing function, along with the experimental `Cascaded Tanks' benchmark dataset. Comparisons on the static prediction of time derivatives are made with a random forest (RF), a residual neural network (ResNet), and the Orthogonal Additive Kernel (OAK) inducing points scalable GP, while for the timeseries prediction comparisons are made with LSTM and GRU recurrent neural networks (RNNs) along with the SINDy package.

Gradient boosting machines (GBMs) based on decision trees consistently demonstrate state-of-the-art results on regression and classification tasks with tabular data, often outperforming deep neural networks. However, these models do not provide well-calibrated predictive uncertainties, which prevents their use for decision making in high-risk applications. The Bayesian treatment is known to improve predictive uncertainty calibration, but previously proposed Bayesian GBM methods are either computationally expensive, or resort to crude approximations. Variational inference is often used to implement Bayesian neural networks, but is difficult to apply to GBMs, because the decision trees used as weak learners are non-differentiable. In this paper, we propose to implement Bayesian GBMs using variational inference with soft decision trees, a fully differentiable alternative to standard decision trees introduced by Irsoy et al. Our experiments demonstrate that variational soft trees and variational soft GBMs provide useful uncertainty estimates, while retaining good predictive performance. The proposed models show higher test likelihoods when compared to the state-of-the-art Bayesian GBMs in 7/10 tabular regression datasets and improved out-of-distribution detection in 5/10 datasets.

Explaining algorithmic decisions and recommending actionable feedback is increasingly important for machine learning applications. Recently, significant efforts have been invested in finding a diverse set of recourses to cover the wide spectrum of users' preferences. However, existing works often neglect the requirement that the recourses should be close to the data manifold; hence, the constructed recourses might be implausible and unsatisfying to users. To address these issues, we propose a novel approach that explicitly directs the diverse set of actionable recourses towards the data manifold. We first find a diverse set of prototypes in the favorable class that balances the trade-off between diversity and proximity. We demonstrate two specific methods to find these prototypes: either by finding the maximum a posteriori estimate of a determinantal point process or by solving a quadratic binary program. To ensure the actionability constraints, we construct an actionability graph in which the nodes represent the training samples and the edges indicate the feasible action between two instances. We then find a feasible path to each prototype, and this path demonstrates the feasible actions for each recourse in the plan. The experimental results show that our method produces a set of recourses that are close to the data manifold while delivering a better cost-diversity trade-off than existing approaches.

Bernstein's condition is a key assumption that guarantees fast rates in machine learning. For example, the Gibbs algorithm with prior $\pi$ has an excess risk in $O(d_{\pi}/n)$, as opposed to the standard $O(\sqrt{d_{\pi}/n})$, where $n$ denotes the number of observations and $d_{\pi}$ is a complexity parameter which depends on the prior $\pi$. In this paper, we examine the Gibbs algorithm in the context of meta-learning, i.e., when learning the prior $\pi$ from $T$ tasks (with $n$ observations each) generated by a meta distribution. Our main result is that Bernstein's condition always holds at the meta level, regardless of its validity at the observation level. This implies that the additional cost to learn the Gibbs prior $\pi$, which will reduce the term $d_\pi$ across tasks, is in $O(1/T)$, instead of the expected $O(1/\sqrt{T})$. We further illustrate how this result improves on standard rates in three different settings: discrete priors, Gaussian priors and mixture of Gaussians priors.

We introduce GAUCHE, a library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to chemical representations, however, is nontrivial, necessitating kernels defined over structured inputs such as graphs, strings and bit vectors. By defining such kernels in GAUCHE, we seek to open the door to powerful tools for uncertainty quantification and Bayesian optimisation in chemistry. Motivated by scenarios frequently encountered in experimental chemistry, we showcase applications for GAUCHE in molecular discovery and chemical reaction optimisation. The codebase is made available at https://github.com/leojklarner/gauche

With the growth of neural network size, model compression has attracted increasing interest in recent research. As one of the most common techniques, pruning has been studied for a long time. By exploiting the structured sparsity of the neural network, existing methods can prune neurons instead of individual weights. However, in most existing pruning methods, surviving neurons are randomly connected in the neural network without any structure, and the non-zero weights within each neuron are also randomly distributed. Such irregular sparse structure can cause very high control overhead and irregular memory access for the hardware and even increase the neural network computational complexity. In this paper, we propose a three-layer hierarchical prior to promote a more regular sparse structure during pruning. The proposed three-layer hierarchical prior can achieve per-neuron weight-level structured sparsity and neuron-level structured sparsity. We derive an efficient Turbo-variational Bayesian inferencing (Turbo-VBI) algorithm to solve the resulting model compression problem with the proposed prior. The proposed Turbo-VBI algorithm has low complexity and can support more general priors than existing model compression algorithms. Simulation results show that our proposed algorithm can promote a more regular structure in the pruned neural networks while achieving even better performance in terms of compression rate and inferencing accuracy compared with the baselines.