With the increased use of data-driven approaches and machine learning-based methods in material science, the importance of reliable uncertainty quantification (UQ) of the predicted variables for informed decision-making cannot be overstated. UQ in material property prediction poses unique challenges, including the multi-scale and multi-physics nature of advanced materials, intricate interactions between numerous factors, limited availability of large curated datasets for model training, etc. Recently, Bayesian Neural Networks (BNNs) have emerged as a promising approach for UQ, offering a probabilistic framework for capturing uncertainties within neural networks. In this work, we introduce an approach for UQ within physics-informed BNNs, which integrates knowledge from governing laws in material modeling to guide the models toward physically consistent predictions. To evaluate the effectiveness of this approach, we present case studies for predicting the creep rupture life of steel alloys. Experimental validation with three datasets of collected measurements from creep tests demonstrates the ability of BNNs to produce accurate point and uncertainty estimates that are competitive or exceed the performance of the conventional method of Gaussian Process Regression. Similarly, we evaluated the suitability of BNNs for UQ in an active learning application and reported competitive performance. The most promising framework for creep life prediction is BNNs based on Markov Chain Monte Carlo approximation of the posterior distribution of network parameters, as it provided more reliable results in comparison to BNNs based on variational inference approximation or related NNs with probabilistic outputs. The codes are available at: https://github.com/avakanski/Creep-uncertainty-quantification.
Randomized controlled trials (RCTs) are the accepted standard for treatment effect estimation but they can be infeasible due to ethical reasons and prohibitive costs. Single-arm trials, where all patients belong to the treatment group, can be a viable alternative but require access to an external control group. We propose an identifiable deep latent-variable model for this scenario that can also account for missing covariate observations by modeling their structured missingness patterns. Our method uses amortized variational inference to learn both group-specific and identifiable shared latent representations, which can subsequently be used for {\em (i)} patient matching if treatment outcomes are not available for the treatment group, or for {\em (ii)} direct treatment effect estimation assuming outcomes are available for both groups. We evaluate the model on a public benchmark as well as on a data set consisting of a published RCT study and real-world electronic health records. Compared to previous methods, our results show improved performance both for direct treatment effect estimation as well as for effect estimation via patient matching.
We propose Diffusion Model Variational Inference (DMVI), a novel method for automated approximate inference in probabilistic programming languages (PPLs). DMVI utilizes diffusion models as variational approximations to the true posterior distribution by deriving a novel bound to the marginal likelihood objective used in Bayesian modelling. DMVI is easy to implement, allows hassle-free inference in PPLs without the drawbacks of, e.g., variational inference using normalizing flows, and does not make any constraints on the underlying neural network model. We evaluate DMVI on a set of common Bayesian models and show that its posterior inferences are in general more accurate than those of contemporary methods used in PPLs while having a similar computational cost and requiring less manual tuning.
We introduce Support Decomposition Variational Inference (SDVI), a new variational inference (VI) approach for probabilistic programs with stochastic support. Existing approaches to this problem rely on designing a single global variational guide on a variable-by-variable basis, while maintaining the stochastic control flow of the original program. SDVI instead breaks the program down into sub-programs with static support, before automatically building separate sub-guides for each. This decomposition significantly aids in the construction of suitable variational families, enabling, in turn, substantial improvements in inference performance.
Variational inference is a technique that approximates a target distribution by optimizing within the parameter space of variational families. On the other hand, Wasserstein gradient flows describe optimization within the space of probability measures where they do not necessarily admit a parametric density function. In this paper, we bridge the gap between these two methods. We demonstrate that, under certain conditions, the Bures-Wasserstein gradient flow can be recast as the Euclidean gradient flow where its forward Euler scheme is the standard black-box variational inference algorithm. Specifically, the vector field of the gradient flow is generated via the path-derivative gradient estimator. We also offer an alternative perspective on the path-derivative gradient, framing it as a distillation procedure to the Wasserstein gradient flow. Distillations can be extended to encompass $f$-divergences and non-Gaussian variational families. This extension yields a new gradient estimator for $f$-divergences, readily implementable using contemporary machine learning libraries like PyTorch or TensorFlow.
In this paper, we introduce ProNet, an novel deep learning approach designed for multi-horizon time series forecasting, adaptively blending autoregressive (AR) and non-autoregressive (NAR) strategies. Our method involves dividing the forecasting horizon into segments, predicting the most crucial steps in each segment non-autoregressively, and the remaining steps autoregressively. The segmentation process relies on latent variables, which effectively capture the significance of individual time steps through variational inference. In comparison to AR models, ProNet showcases remarkable advantages, requiring fewer AR iterations, resulting in faster prediction speed, and mitigating error accumulation. On the other hand, when compared to NAR models, ProNet takes into account the interdependency of predictions in the output space, leading to improved forecasting accuracy. Our comprehensive evaluation, encompassing four large datasets, and an ablation study, demonstrate the effectiveness of ProNet, highlighting its superior performance in terms of accuracy and prediction speed, outperforming state-of-the-art AR and NAR forecasting models.
Adaptive importance sampling (AIS) algorithms are widely used to approximate expectations with respect to complicated target probability distributions. When the target has heavy tails, existing AIS algorithms can provide inconsistent estimators or exhibit slow convergence, as they often neglect the target's tail behaviour. To avoid this pitfall, we propose an AIS algorithm that approximates the target by Student-t proposal distributions. We adapt location and scale parameters by matching the escort moments - which are defined even for heavy-tailed distributions - of the target and the proposal. These updates minimize the $\alpha$-divergence between the target and the proposal, thereby connecting with variational inference. We then show that the $\alpha$-divergence can be approximated by a generalized notion of effective sample size and leverage this new perspective to adapt the tail parameter with Bayesian optimization. We demonstrate the efficacy of our approach through applications to synthetic targets and a Bayesian Student-t regression task on a real example with clinical trial data.
Natural gradient methods have been used to optimise the parameters of probability distributions in a variety of settings, often resulting in fast-converging procedures. Unfortunately, for many distributions of interest, computing the natural gradient has a number of challenges. In this work we propose a novel technique for tackling such issues, which involves reframing the optimisation as one with respect to the parameters of a surrogate distribution, for which computing the natural gradient is easy. We give several examples of existing methods that can be interpreted as applying this technique, and propose a new method for applying it to a wide variety of problems. Our method expands the set of distributions that can be efficiently targeted with natural gradients. Furthermore, it is fast, easy to understand, simple to implement using standard autodiff software, and does not require lengthy model-specific derivations. We demonstrate our method on maximum likelihood estimation and variational inference tasks.
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.
Discovering causal relationships from time series data is significant in fields such as finance, climate science, and neuroscience. However, contemporary techniques rely on the simplifying assumption that data originates from the same causal model, while in practice, data is heterogeneous and can stem from different causal models. In this work, we relax this assumption and perform causal discovery from time series data originating from a mixture of causal models. We propose a general variational inference-based framework called MCD to infer the underlying causal models as well as the mixing probability of each sample. Our approach employs an end-to-end training process that maximizes an evidence-lower bound for the data likelihood. We present two variants: MCD-Linear for linear relationships and independent noise, and MCD-Nonlinear for nonlinear causal relationships and history-dependent noise. We demonstrate that our method surpasses state-of-the-art benchmarks in causal discovery tasks through extensive experimentation on synthetic and real-world datasets, particularly when the data emanates from diverse underlying causal graphs. Theoretically, we prove the identifiability of such a model under some mild assumptions.
Backdoor adjustment is a technique in causal inference for estimating interventional quantities from purely observational data. For example, in medical settings, backdoor adjustment can be used to control for confounding and estimate the effectiveness of a treatment. However, high dimensional treatments and confounders pose a series of potential pitfalls: tractability, identifiability, optimization. In this work, we take a generative modeling approach to backdoor adjustment for high dimensional treatments and confounders. We cast backdoor adjustment as an optimization problem in variational inference without reliance on proxy variables and hidden confounders. Empirically, our method is able to estimate interventional likelihood in a variety of high dimensional settings, including semi-synthetic X-ray medical data. To the best of our knowledge, this is the first application of backdoor adjustment in which all the relevant variables are high dimensional.
Multi-source domain adaptation (MSDA) methods aim to transfer knowledge from multiple labeled source domains to an unlabeled target domain. Although current methods achieve target joint distribution identifiability by enforcing minimal changes across domains, they often necessitate stringent conditions, such as an adequate number of domains, monotonic transformation of latent variables, and invariant label distributions. These requirements are challenging to satisfy in real-world applications. To mitigate the need for these strict assumptions, we propose a subspace identification theory that guarantees the disentanglement of domain-invariant and domain-specific variables under less restrictive constraints regarding domain numbers and transformation properties, thereby facilitating domain adaptation by minimizing the impact of domain shifts on invariant variables. Based on this theory, we develop a Subspace Identification Guarantee (SIG) model that leverages variational inference. Furthermore, the SIG model incorporates class-aware conditional alignment to accommodate target shifts where label distributions change with the domains. Experimental results demonstrate that our SIG model outperforms existing MSDA techniques on various benchmark datasets, highlighting its effectiveness in real-world applications.
We present VBPI-Mixtures, an algorithm designed to enhance the accuracy of phylogenetic posterior distributions, particularly for tree-topology and branch-length approximations. Despite the Variational Bayesian Phylogenetic Inference (VBPI), a leading-edge black-box variational inference (BBVI) framework, achieving remarkable approximations of these distributions, the multimodality of the tree-topology posterior presents a formidable challenge to sampling-based learning techniques such as BBVI. Advanced deep learning methodologies such as normalizing flows and graph neural networks have been explored to refine the branch-length posterior approximation, yet efforts to ameliorate the posterior approximation over tree topologies have been lacking. Our novel VBPI-Mixtures algorithm bridges this gap by harnessing the latest breakthroughs in mixture learning within the BBVI domain. As a result, VBPI-Mixtures is capable of capturing distributions over tree-topologies that VBPI fails to model. We deliver state-of-the-art performance on difficult density estimation tasks across numerous real phylogenetic datasets.
Integrating first-order logic constraints (FOLCs) with neural networks is a crucial but challenging problem since it involves modeling intricate correlations to satisfy the constraints. This paper proposes a novel neural layer, LogicMP, whose layers perform mean-field variational inference over an MLN. It can be plugged into any off-the-shelf neural network to encode FOLCs while retaining modularity and efficiency. By exploiting the structure and symmetries in MLNs, we theoretically demonstrate that our well-designed, efficient mean-field iterations effectively mitigate the difficulty of MLN inference, reducing the inference from sequential calculation to a series of parallel tensor operations. Empirical results in three kinds of tasks over graphs, images, and text show that LogicMP outperforms advanced competitors in both performance and efficiency.
We release a new Bayesian neural network library for PyTorch for large-scale deep networks. Our library implements mainstream approximate Bayesian inference algorithms: variational inference, MC-dropout, stochastic-gradient MCMC, and Laplace approximation. The main differences from other existing Bayesian neural network libraries are as follows: 1) Our library can deal with very large-scale deep networks including Vision Transformers (ViTs). 2) We need virtually zero code modifications for users (e.g., the backbone network definition codes do not neet to be modified at all). 3) Our library also allows the pre-trained model weights to serve as a prior mean, which is very useful for performing Bayesian inference with the large-scale foundation models like ViTs that are hard to optimise from scratch with the downstream data alone. Our code is publicly available at: \url{https://github.com/SamsungLabs/BayesDLL}\footnote{A mirror repository is also available at: \url{https://github.com/minyoungkim21/BayesDLL}.}.
Deep Gaussian Process (DGP) models offer a powerful nonparametric approach for Bayesian inference, but exact inference is typically intractable, motivating the use of various approximations. However, existing approaches, such as mean-field Gaussian assumptions, limit the expressiveness and efficacy of DGP models, while stochastic approximation can be computationally expensive. To tackle these challenges, we introduce Neural Operator Variational Inference (NOVI) for Deep Gaussian Processes. NOVI uses a neural generator to obtain a sampler and minimizes the Regularized Stein Discrepancy in L2 space between the generated distribution and true posterior. We solve the minimax problem using Monte Carlo estimation and subsampling stochastic optimization techniques. We demonstrate that the bias introduced by our method can be controlled by multiplying the Fisher divergence with a constant, which leads to robust error control and ensures the stability and precision of the algorithm. Our experiments on datasets ranging from hundreds to tens of thousands demonstrate the effectiveness and the faster convergence rate of the proposed method. We achieve a classification accuracy of 93.56 on the CIFAR10 dataset, outperforming SOTA Gaussian process methods. Furthermore, our method guarantees theoretically controlled prediction error for DGP models and demonstrates remarkable performance on various datasets. We are optimistic that NOVI has the potential to enhance the performance of deep Bayesian nonparametric models and could have significant implications for various practical applications
Deep learning's immense capabilities are often constrained by the complexity of its models, leading to an increasing demand for effective sparsification techniques. Bayesian sparsification for deep learning emerges as a crucial approach, facilitating the design of models that are both computationally efficient and competitive in terms of performance across various deep learning applications. The state-of-the-art -- in Bayesian sparsification of deep neural networks -- combines structural shrinkage priors on model weights with an approximate inference scheme based on stochastic variational inference. However, model inversion of the full generative model is exceptionally computationally demanding, especially when compared to standard deep learning of point estimates. In this context, we advocate for the use of Bayesian model reduction (BMR) as a more efficient alternative for pruning of model weights. As a generalization of the Savage-Dickey ratio, BMR allows a post-hoc elimination of redundant model weights based on the posterior estimates under a straightforward (non-hierarchical) generative model. Our comparative study highlights the advantages of the BMR method relative to established approaches based on hierarchical horseshoe priors over model weights. We illustrate the potential of BMR across various deep learning architectures, from classical networks like LeNet to modern frameworks such as Vision Transformers and MLP-Mixers.
Topic models have a rich history with various applications and have recently been reinvigorated by neural topic modeling. However, these numerous topic models adopt totally distinct datasets, implementations, and evaluations. This impedes quick utilization and fair comparisons, and thereby hinders their research progress and applications. To tackle this challenge, we in this paper propose a Topic Modeling System Toolkit (TopMost). Compared to existing toolkits, TopMost stands out by supporting more extensive features. It covers a broader spectrum of topic modeling scenarios with their complete lifecycles, including datasets, preprocessing, models, training, and evaluations. Thanks to its highly cohesive and decoupled modular design, TopMost enables rapid utilization, fair comparisons, and flexible extensions of diverse cutting-edge topic models. Our code, tutorials, and documentation are available at https://github.com/bobxwu/topmost.
Developing efficient solutions for inference problems in intelligent sensor networks is crucial for the next generation of location, tracking, and mapping services. This paper develops a scalable distributed probabilistic inference algorithm that applies to continuous variables, intractable posteriors and large-scale real-time data in sensor networks. In a centralized setting, variational inference is a fundamental technique for performing approximate Bayesian estimation, in which an intractable posterior density is approximated with a parametric density. Our key contribution lies in the derivation of a separable lower bound on the centralized estimation objective, which enables distributed variational inference with one-hop communication in a sensor network. Our distributed evidence lower bound (DELBO) consists of a weighted sum of observation likelihood and divergence to prior densities, and its gap to the measurement evidence is due to consensus and modeling errors. To solve binary classification and regression problems while handling streaming data, we design an online distributed algorithm that maximizes DELBO, and specialize it to Gaussian variational densities with non-linear likelihoods. The resulting distributed Gaussian variational inference (DGVI) efficiently inverts a $1$-rank correction to the covariance matrix. Finally, we derive a diagonalized version for online distributed inference in high-dimensional models, and apply it to multi-robot probabilistic mapping using indoor LiDAR data.
Meta-learning is a framework in which machine learning models train over a set of datasets in order to produce predictions on new datasets at test time. Probabilistic meta-learning has received an abundance of attention from the research community in recent years, but a problem shared by many existing probabilistic meta-models is that they require a very large number of datasets in order to produce high-quality predictions with well-calibrated uncertainty estimates. In many applications, however, such quantities of data are simply not available. In this dissertation we present a significantly more data-efficient approach to probabilistic meta-learning through per-datapoint amortisation of inference in Bayesian neural networks, introducing the Amortised Pseudo-Observation Variational Inference Bayesian Neural Network (APOVI-BNN). First, we show that the approximate posteriors obtained under our amortised scheme are of similar or better quality to those obtained through traditional variational inference, despite the fact that the amortised inference is performed in a single forward pass. We then discuss how the APOVI-BNN may be viewed as a new member of the neural process family, motivating the use of neural process training objectives for potentially better predictive performance on complex problems as a result. Finally, we assess the predictive performance of the APOVI-BNN against other probabilistic meta-models in both a one-dimensional regression problem and in a significantly more complex image completion setting. In both cases, when the amount of training data is limited, our model is the best in its class.