Bayesian optimization is a widely used method for optimizing expensive black-box functions, with Expected Improvement being one of the most commonly used acquisition functions. In contrast, information-theoretic acquisition functions aim to reduce uncertainty about the function's optimum and are often considered fundamentally distinct from EI. In this work, we challenge this prevailing perspective by introducing a unified theoretical framework, Variational Entropy Search, which reveals that EI and information-theoretic acquisition functions are more closely related than previously recognized. We demonstrate that EI can be interpreted as a variational inference approximation of the popular information-theoretic acquisition function, named Max-value Entropy Search. Building on this insight, we propose VES-Gamma, a novel acquisition function that balances the strengths of EI and MES. Extensive empirical evaluations across both low- and high-dimensional synthetic and real-world benchmarks demonstrate that VES-Gamma is competitive with state-of-the-art acquisition functions and in many cases outperforms EI and MES.
Cross-subject variability in EEG degrades performance of current deep learning models, limiting the development of brain-computer interface (BCI). This paper proposes ISAM-MTL, which is a multi-task learning (MTL) EEG classification model based on identifiable spiking (IS) representations and associative memory (AM) networks. The proposed model treats EEG classification of each subject as an independent task and leverages cross-subject data training to facilitate feature sharing across subjects. ISAM-MTL consists of a spiking feature extractor that captures shared features across subjects and a subject-specific bidirectional associative memory network that is trained by Hebbian learning for efficient and fast within-subject EEG classification. ISAM-MTL integrates learned spiking neural representations with bidirectional associative memory for cross-subject EEG classification. The model employs label-guided variational inference to construct identifiable spike representations, enhancing classification accuracy. Experimental results on two BCI Competition datasets demonstrate that ISAM-MTL improves the average accuracy of cross-subject EEG classification while reducing performance variability among subjects. The model further exhibits the characteristics of few-shot learning and identifiable neural activity beneath EEG, enabling rapid and interpretable calibration for BCI systems.
Hyperbolic space naturally encodes hierarchical structures such as phylogenies (binary trees), where inward-bending geodesics reflect paths through least common ancestors, and the exponential growth of neighborhoods mirrors the super-exponential scaling of topologies. This scaling challenge limits the efficiency of Euclidean-based approximate inference methods. Motivated by the geometric connections between trees and hyperbolic space, we develop novel hyperbolic extensions of two sequential search algorithms: Combinatorial and Nested Combinatorial Sequential Monte Carlo (\textsc{Csmc} and \textsc{Ncsmc}). Our approach introduces consistent and unbiased estimators, along with variational inference methods (\textsc{H-Vcsmc} and \textsc{H-Vncsmc}), which outperform their Euclidean counterparts. Empirical results demonstrate improved speed, scalability and performance in high-dimensional phylogenetic inference tasks.
Transformers have emerged as the dominant architecture in the field of deep learning, with a broad range of applications and remarkable in-context learning (ICL) capabilities. While not yet fully understood, ICL has already proved to be an intriguing phenomenon, allowing transformers to learn in context -- without requiring further training. In this paper, we further advance the understanding of ICL by demonstrating that transformers can perform full Bayesian inference for commonly used statistical models in context. More specifically, we introduce a general framework that builds on ideas from prior fitted networks and continuous normalizing flows which enables us to infer complex posterior distributions for methods such as generalized linear models and latent factor models. Extensive experiments on real-world datasets demonstrate that our ICL approach yields posterior samples that are similar in quality to state-of-the-art MCMC or variational inference methods not operating in context.
In this work, we propose a novel variational Bayesian adaptive learning approach for cross-domain knowledge transfer to address acoustic mismatches between training and testing conditions, such as recording devices and environmental noise. Different from the traditional Bayesian approaches that impose uncertainties on model parameters risking the curse of dimensionality due to the huge number of parameters, we focus on estimating a manageable number of latent variables in deep neural models. Knowledge learned from a source domain is thus encoded in prior distributions of deep latent variables and optimally combined, in a Bayesian sense, with a small set of adaptation data from a target domain to approximate the corresponding posterior distributions. Two different strategies are proposed and investigated to estimate the posterior distributions: Gaussian mean-field variational inference, and empirical Bayes. These strategies address the presence or absence of parallel data in the source and target domains. Furthermore, structural relationship modeling is investigated to enhance the approximation. We evaluated our proposed approaches on two acoustic adaptation tasks: 1) device adaptation for acoustic scene classification, and 2) noise adaptation for spoken command recognition. Experimental results show that the proposed variational Bayesian adaptive learning approach can obtain good improvements on target domain data, and consistently outperforms state-of-the-art knowledge transfer methods.
Bayesian neural networks (BNNs) offer the potential for reliable uncertainty quantification and interpretability, which are critical for trustworthy AI in high-stakes domains. However, existing methods often struggle with issues such as overconfidence, hyperparameter sensitivity, and posterior collapse, leaving room for alternative approaches. In this work, we advance message passing (MP) for BNNs and present a novel framework that models the predictive posterior as a factor graph. To the best of our knowledge, our framework is the first MP method that handles convolutional neural networks and avoids double-counting training data, a limitation of previous MP methods that causes overconfidence. We evaluate our approach on CIFAR-10 with a convolutional neural network of roughly 890k parameters and find that it can compete with the SOTA baselines AdamW and IVON, even having an edge in terms of calibration. On synthetic data, we validate the uncertainty estimates and observe a strong correlation (0.9) between posterior credible intervals and its probability of covering the true data-generating function outside the training range. While our method scales to an MLP with 5.6 million parameters, further improvements are necessary to match the scale and performance of state-of-the-art variational inference methods.
We present a novel framework combining Deep Operator Networks (DeepONets) with Physics-Informed Neural Networks (PINNs) to solve partial differential equations (PDEs) and estimate their unknown parameters. By integrating data-driven learning with physical constraints, our method achieves robust and accurate solutions across diverse scenarios. Bayesian training is implemented through variational inference, allowing for comprehensive uncertainty quantification for both aleatoric and epistemic uncertainties. This ensures reliable predictions and parameter estimates even in noisy conditions or when some of the physical equations governing the problem are missing. The framework demonstrates its efficacy in solving forward and inverse problems, including the 1D unsteady heat equation and 2D reaction-diffusion equations, as well as regression tasks with sparse, noisy observations. This approach provides a computationally efficient and generalizable method for addressing uncertainty quantification in PDE surrogate modeling.
In geotechnical engineering, constitutive models play a crucial role in describing soil behavior under varying loading conditions. Data-driven deep learning (DL) models offer a promising alternative for developing predictive constitutive models. When prediction is the primary focus, quantifying the predictive uncertainty of a trained DL model and communicating this uncertainty to end users is crucial for informed decision-making. This study proposes a recursive Bayesian neural network (rBNN) framework, which builds upon recursive feedforward neural networks (rFFNNs) by introducing generalized Bayesian inference for uncertainty quantification. A significant contribution of this work is the incorporation of a sliding window approach in rFFNNs, allowing the models to effectively capture temporal dependencies across load steps. The rBNN extends this framework by treating model parameters as random variables, with their posterior distributions inferred using generalized variational inference. The proposed framework is validated on two datasets: (i) a numerically simulated consolidated drained (CD) triaxial dataset employing a hardening soil model and (ii) an experimental dataset comprising 28 CD triaxial tests on Baskarp sand. Comparative analyses with LSTM, Bi-LSTM, and GRU models demonstrate that the deterministic rFFNN achieves superior predictive accuracy, attributed to its transparent structure and sliding window design. While the rBNN marginally trails in accuracy for the experimental case, it provides robust confidence intervals, addressing data sparsity and measurement noise in experimental conditions. The study underscores the trade-offs between deterministic and probabilistic approaches and the potential of rBNNs for uncertainty-aware constitutive modeling.
In variational inference (VI), an approximation of the posterior distribution is selected from a family of distributions through numerical optimization. With the most common variational objective function, known as the evidence lower bound (ELBO), only convergence to a local optimum can be guaranteed. In this work, we instead establish the global convergence of a particular VI method. This VI method, which may be considered an instance of neural posterior estimation (NPE), minimizes an expectation of the inclusive (forward) KL divergence to fit a variational distribution that is parameterized by a neural network. Our convergence result relies on the neural tangent kernel (NTK) to characterize the gradient dynamics that arise from considering the variational objective in function space. In the asymptotic regime of a fixed, positive-definite neural tangent kernel, we establish conditions under which the variational objective admits a unique solution in a reproducing kernel Hilbert space (RKHS). Then, we show that the gradient descent dynamics in function space converge to this unique function. In ablation studies and practical problems, we demonstrate that our results explain the behavior of NPE in non-asymptotic finite-neuron settings, and show that NPE outperforms ELBO-based optimization, which often converges to shallow local optima.
Bayesian Neural Networks (BNNs) offer robust uncertainty quantification in model predictions, but training them presents a significant computational challenge. This is mainly due to the problem of sampling multimodal posterior distributions using Markov Chain Monte Carlo (MCMC) sampling and variational inference algorithms. Moreover, the number of model parameters scales exponentially with additional hidden layers, neurons, and features in the dataset. Typically, a significant portion of these densely connected parameters are redundant and pruning a neural network not only improves portability but also has the potential for better generalisation capabilities. In this study, we address some of the challenges by leveraging MCMC sampling with network pruning to obtain compact probabilistic models having removed redundant parameters. We sample the posterior distribution of model parameters (weights and biases) and prune weights with low importance, resulting in a compact model. We ensure that the compact BNN retains its ability to estimate uncertainty via the posterior distribution while retaining the model training and generalisation performance accuracy by adapting post-pruning resampling. We evaluate the effectiveness of our MCMC pruning strategy on selected benchmark datasets for regression and classification problems through empirical result analysis. We also consider two coral reef drill-core lithology classification datasets to test the robustness of the pruning model in complex real-world datasets. We further investigate if refining compact BNN can retain any loss of performance. Our results demonstrate the feasibility of training and pruning BNNs using MCMC whilst retaining generalisation performance with over 75% reduction in network size. This paves the way for developing compact BNN models that provide uncertainty estimates for real-world applications.
Recent work has demonstrated that Bayesian neural networks (BNN's) trained with mean field variational inference (MFVI) can be implemented in analog hardware, promising orders of magnitude energy savings compared to the standard digital implementations. However, while Gaussians are typically used as the variational distribution in MFVI, it is difficult to precisely control the shape of the noise distributions produced by sampling analog devices. This paper introduces a method for MFVI training using real device noise as the variational distribution. Furthermore, we demonstrate empirically that the predictive distributions from BNN's with the same weight means and variances converge to the same distribution, regardless of the shape of the variational distribution. This result suggests that analog device designers do not need to consider the shape of the device noise distribution when hardware-implementing BNNs performing MFVI.
Without any assumptions about data generation, multiple causal models may explain our observations equally well. To avoid selecting a single arbitrary model that could result in unsafe decisions if it does not match reality, it is therefore essential to maintain a notion of epistemic uncertainty about our possible candidates. This thesis studies the problem of structure learning from a Bayesian perspective, approximating the posterior distribution over the structure of a causal model, represented as a directed acyclic graph (DAG), given data. It introduces Generative Flow Networks (GFlowNets), a novel class of probabilistic models designed for modeling distributions over discrete and compositional objects such as graphs. They treat generation as a sequential decision making problem, constructing samples of a target distribution defined up to a normalization constant piece by piece. In the first part of this thesis, we present the mathematical foundations of GFlowNets, their connections to existing domains of machine learning and statistics such as variational inference and reinforcement learning, and their extensions beyond discrete problems. In the second part of this thesis, we show how GFlowNets can approximate the posterior distribution over DAG structures of causal Bayesian Networks, along with the parameters of its causal mechanisms, given observational and experimental data.
This paper is concerned with the approximation of probability distributions known up to normalization constants, with a focus on Bayesian inference for large-scale inverse problems in scientific computing. In this context, key challenges include costly repeated evaluations of forward models, multimodality, and inaccessible gradients for the forward model. To address them, we develop a variational inference framework that combines Fisher-Rao natural gradient with specialized quadrature rules to enable derivative free updates of Gaussian mixture variational families. The resulting method, termed Derivative Free Gaussian Mixture Variational Inference (DF-GMVI), guarantees covariance positivity and affine invariance, offering a stable and efficient framework for approximating complex posterior distributions. The effectiveness of DF-GMVI is demonstrated through numerical experiments on challenging scenarios, including distributions with multiple modes, infinitely many modes, and curved modes in spaces with up to 100 dimensions. The method's practicality is further demonstrated in a large-scale application, where it successfully recovers the initial conditions of the Navier-Stokes equations from solution data at positive times.
This paper presents a novel machine-learning framework for reconstructing low-order gust-encounter flow field and lift coefficients from sparse, noisy surface pressure measurements. Our study thoroughly investigates the time-varying response of sensors to gust-airfoil interactions, uncovering valuable insights into optimal sensor placement. To address uncertainties in deep learning predictions, we implement probabilistic regression strategies to model both epistemic and aleatoric uncertainties. Epistemic uncertainty, reflecting the model's confidence in its predictions, is modeled using Monte Carlo dropout, as an approximation to the variational inference in the Bayesian framework, treating the neural network as a stochastic entity. On the other hand, aleatoric uncertainty, arising from noisy input measurements, is captured via learned statistical parameters, which propagates measurement noise through the network into the final predictions. Our results showcase the efficacy of this dual uncertainty quantification strategy in accurately predicting aerodynamic behavior under extreme conditions while maintaining computational efficiency, underscoring its potential to improve online sensor-based flow estimation in real-world applications.
Variational inference is a fast and scalable alternative to Markov chain Monte Carlo and has been widely applied to posterior inference tasks in statistics and machine learning. A traditional approach for implementing mean-field variational inference (MFVI) is coordinate ascent variational inference (CAVI), which relies crucially on parametric assumptions on complete conditionals. In this paper, we introduce a novel particle-based algorithm for mean-field variational inference, which we term PArticle VI (PAVI). Notably, our algorithm does not rely on parametric assumptions on complete conditionals, and it applies to the nonparametric setting. We provide non-asymptotic finite-particle convergence guarantee for our algorithm. To our knowledge, this is the first end-to-end guarantee for particle-based MFVI.
The signature kernel is a kernel between time series of arbitrary length and comes with strong theoretical guarantees from stochastic analysis. It has found applications in machine learning such as covariance functions for Gaussian processes. A strength of the underlying signature features is that they provide a structured global description of a time series. However, this property can quickly become a curse when local information is essential and forgetting is required; so far this has only been addressed with ad-hoc methods such as slicing the time series into subsegments. To overcome this, we propose a principled, data-driven approach by introducing a novel forgetting mechanism for signatures. This allows the model to dynamically adapt its context length to focus on more recent information. To achieve this, we revisit the recently introduced Random Fourier Signature Features, and develop Random Fourier Decayed Signature Features (RFDSF) with Gaussian processes (GPs). This results in a Bayesian time series forecasting algorithm with variational inference, that offers a scalable probabilistic algorithm that processes and transforms a time series into a joint predictive distribution over time steps in one pass using recurrence. For example, processing a sequence of length $10^4$ steps in $\approx 10^{-2}$ seconds and in $< 1\text{GB}$ of GPU memory. We demonstrate that it outperforms other GP-based alternatives and competes with state-of-the-art probabilistic time series forecasting algorithms.
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov Chain Monte Carlo methods face slow convergence and computational burdens. Existing Variational Inference methods, which require pre-generated topologies and typically treat tree structures and branch lengths independently, may overlook critical sequence features, limiting their accuracy and flexibility. We propose PhyloGen, a novel method leveraging a pre-trained genomic language model to generate and optimize phylogenetic trees without dependence on evolutionary models or aligned sequence constraints. PhyloGen views phylogenetic inference as a conditionally constrained tree structure generation problem, jointly optimizing tree topology and branch lengths through three core modules: (i) Feature Extraction, (ii) PhyloTree Construction, and (iii) PhyloTree Structure Modeling. Meanwhile, we introduce a Scoring Function to guide the model towards a more stable gradient descent. We demonstrate the effectiveness and robustness of PhyloGen on eight real-world benchmark datasets. Visualization results confirm PhyloGen provides deeper insights into phylogenetic relationships.
Recent advances in statistical learning theory have revealed profound connections between mutual information (MI) bounds, PAC-Bayesian theory, and Bayesian nonparametrics. This work introduces a novel mutual information bound for statistical models. The derived bound has wide-ranging applications in statistical inference. It yields improved contraction rates for fractional posteriors in Bayesian nonparametrics. It can also be used to study a wide range of estimation methods, such as variational inference or Maximum Likelihood Estimation (MLE). By bridging these diverse areas, this work advances our understanding of the fundamental limits of statistical inference and the role of information in learning from data. We hope that these results will not only clarify connections between statistical inference and information theory but also help to develop a new toolbox to study a wide range of estimators.
We propose a probabilistic framework for developing computational models of biological neural systems. In this framework, physiological recordings are viewed as discrete-time partial observations of an underlying continuous-time stochastic dynamical system which implements computations through its state evolution. To model this dynamical system, we employ a system of coupled stochastic differential equations with differentiable drift and diffusion functions and use variational inference to infer its states and parameters. This formulation enables seamless integration of existing mathematical models in the literature, neural networks, or a hybrid of both to learn and compare different models. We demonstrate this in our framework by developing a generative model that combines coupled oscillators with neural networks to capture latent population dynamics from single-cell recordings. Evaluation across three neuroscience datasets spanning different species, brain regions, and behavioral tasks show that these hybrid models achieve competitive performance in predicting stimulus-evoked neural and behavioral responses compared to sophisticated black-box approaches while requiring an order of magnitude fewer parameters, providing uncertainty estimates, and offering a natural language for interpretation.
Ou et al. (2022) introduce the problem of learning set functions from data generated by a so-called optimal subset oracle. Their approach approximates the underlying utility function with an energy-based model, whose parameters are estimated via mean-field variational inference. Ou et al. (2022) show this reduces to fixed point iterations; however, as the number of iterations increases, automatic differentiation quickly becomes computationally prohibitive due to the size of the Jacobians that are stacked during backpropagation. We address this challenge with implicit differentiation and examine the convergence conditions for the fixed-point iterations. We empirically demonstrate the efficiency of our method on synthetic and real-world subset selection applications including product recommendation, set anomaly detection and compound selection tasks.