贝叶斯深度学习

Although deep neural networks have demonstrated significant success due to their powerful expressiveness, most models struggle to meet practical requirements for uncertainty estimation. Concurrently, the entangled nature of deep neural net- works leads to a multifaceted problem, where various localized explanation tech- niques reveal that multiple unrelated features influence the decisions, thereby un- dermining interpretability. To address these challenges, we develop a Bayesian Nonnegative Decision Layer (BNDL), which reformulates deep neural networks as a conditional Bayesian non-negative factor analysis. By leveraging stochastic latent variables, the BNDL can model complex dependencies and provide robust uncertainty estimation. Moreover, the sparsity and non-negativity of the latent variables encourage the model to learn disentangled representations and decision layers, thereby improving interpretability. We also offer theoretical guarantees that BNDL can achieve effective disentangled learning. In addition, we developed a corresponding variational inference method utilizing a Weibull variational in- ference network to approximate the posterior distribution of the latent variables. Our experimental results demonstrate that with enhanced disentanglement capa- bilities, BNDL not only improves the model’s accuracy but also provides reliable uncertainty estimation and improved interpretability.

Over recent years, deep learning based image registration has achieved impressive accuracy in many domains, including medical imaging and, specifically, human neuroimaging with magnetic resonance imaging (MRI). However, the uncertainty estimation associated with these methods has been largely limited to the application of generic techniques (e.g., Monte Carlo dropout) that do not exploit the peculiarities of the problem domain, particularly spatial modeling. Here, we propose a principled way to propagate uncertainties (epistemic or aleatoric) estimated at the level of spatial location by these methods, to the level of global transformation models, and further to downstream tasks. Specifically, we justify the choice of a Gaussian distribution for the local uncertainty modeling, and then propose a framework where uncertainties spread across hierarchical levels, depending on the choice of transformation model. Experiments on publicly available data sets show that Monte Carlo dropout correlates very poorly with the reference registration error, whereas our uncertainty estimates correlate much better. Crucially, the results also show that uncertainty-aware fitting of transformations improves the registration accuracy of brain MRI scans. Finally, we illustrate how sampling from the posterior distribution of the transformations can be used to propagate uncertainties to downstream neuroimaging tasks. Code is available at: https://github.com/HuXiaoling/Regre4Regis.

Neal (1996) proved that infinitely wide shallow Bayesian neural networks (BNN) converge to Gaussian processes (GP), when the network weights have bounded prior variance. Cho & Saul (2009) provided a useful recursive formula for deep kernel processes for relating the covariance kernel of each layer to the layer immediately below. Moreover, they worked out the form of the layer-wise covariance kernel in an explicit manner for several common activation functions, including the ReLU. Subsequent works have made the connection between these two works, and provided useful results on the covariance kernel of a deep GP arising as wide limits of various deep Bayesian network architectures. However, recent works, including Aitchison et al. (2021), have highlighted that the covariance kernels obtained in this manner are deterministic and hence, precludes any possibility of representation learning, which amounts to learning a non-degenerate posterior of a random kernel given the data. To address this, they propose adding artificial noise to the kernel to retain stochasticity, and develop deep kernel Wishart and inverse Wishart processes. Nonetheless, this artificial noise injection could be critiqued in that it would not naturally emerge in a classic BNN architecture under an infinite-width limit. To address this, we show that a Bayesian deep neural network, where each layer width approaches infinity, and all network weights are elliptically distributed with infinite variance, converges to a process with $\alpha$-stable marginals in each layer that has a conditionally Gaussian representation. These conditional random covariance kernels could be recursively linked in the manner of Cho & Saul (2009), even though marginally the process exhibits stable behavior, and hence covariances are not even necessarily defined. We also provide useful generalizations of the recent results of Loría & Bhadra (2024) on shallow networks to multi-layer networks, and remedy the prohibitive computational burden of their approach. The computational and statistical benefits over competing approaches stand out in simulations and in demonstrations on benchmark data sets.

Meta-learning aims to train models that can generalize to new tasks with limited labeled data by extracting shared features across diverse task datasets. Additionally, it accounts for prediction uncertainty during both training and evaluation, a concept known as uncertainty-aware meta-learning. Neural Process (NP) is a well-known uncertainty-aware meta-learning method that constructs implicit stochastic processes using parametric neural networks, enabling rapid adaptation to new tasks. However, existing NP methods face challenges in accommodating diverse input dimensions and learned features, limiting their broad applicability across regression tasks. To address these limitations and advance the utility of NP models as general regressors, we introduce Dimension Agnostic Neural Process (DANP). DANP incorporates Dimension Aggregator Block (DAB) to transform input features into a fixed-dimensional space, enhancing the model's ability to handle diverse datasets. Furthermore, leveraging the Transformer architecture and latent encoding layers, DANP learns a wider range of features that are generalizable across various tasks. Through comprehensive experimentation on various synthetic and practical regression tasks, we empirically show that DANP outperforms previous NP variations, showcasing its effectiveness in overcoming the limitations of traditional NP models and its potential for broader applicability in diverse regression scenarios.

In the analysis of brain functional MRI (fMRI) data using regression models, Bayesian methods are highly valued for their flexibility and ability to quantify uncertainty. However, these methods face computational challenges in high-dimensional settings typical of brain imaging, and the often pre-specified correlation structures may not accurately capture the true spatial relationships within the brain. To address these issues, we develop a general prior specifically designed for regression models with large-scale imaging data. We introduce the Soft-Thresholded Conditional AutoRegressive (ST-CAR) prior, which reduces instability to pre-fixed correlation structures and provides inclusion probabilities to account for the uncertainty in choosing active voxels in the brain. We apply the ST-CAR prior to scalar-on-image (SonI) and image-on-scalar (IonS) regression models—both critical in brain imaging studies—and develop efficient computational algorithms using variational inference (VI) and stochastic subsampling techniques. Simulation studies demonstrate that the ST-CAR prior outperforms existing methods in identifying active brain regions with complex correlation patterns, while our VI algorithms offer superior computational performance. We further validate our approach by applying the ST-CAR to working memory fMRI data from the Adolescent Brain Cognitive Development (ABCD) study, highlighting its effectiveness in practical brain imaging applications.

Accurately estimating the informativeness of individual samples in a dataset is an important objective in deep learning, as it can guide sample selection, which can improve model efficiency and accuracy by removing redundant or potentially harmful samples. We propose $\text{\textit{Laplace Sample Information}}$ ($\mathsf{LSI}$) measure of sample informativeness grounded in information theory widely applicable across model architectures and learning settings. $\mathsf{LSI}$ leverages a Bayesian approximation to the weight posterior and the KL divergence to measure the change in the parameter distribution induced by a sample of interest from the dataset. We experimentally show that $\mathsf{LSI}$ is effective in ordering the data with respect to typicality, detecting mislabeled samples, measuring class-wise informativeness, and assessing dataset difficulty. We demonstrate these capabilities of $\mathsf{LSI}$ on image and text data in supervised and unsupervised settings. Moreover, we show that $\mathsf{LSI}$ can be computed efficiently through probes and transfers well to the training of large models.

Machine learning is increasingly deployed in safety-critical domains where erroneous predictions may lead to potentially catastrophic consequences, highlighting the need for learning systems to be aware of how confident they are in their own predictions: in other words, 'to know when they do not know’. In this paper, we propose a novel Random-Set Neural Network (RS-NN) approach to classification which predicts *belief functions* (rather than classical probability vectors) over the class list using the mathematics of *random sets*, i.e., distributions over the collection of *sets* of classes. RS-NN encodes the 'epistemic' uncertainty induced by training sets that are insufficiently representative or limited in size via the size of the convex set of probability vectors associated with a predicted belief function. Our approach outperforms state-of-the-art Bayesian and Ensemble methods in terms of accuracy, uncertainty estimation and out-of-distribution (OoD) detection on multiple benchmarks (CIFAR-10 vs SVHN/Intel-Image, MNIST vs FMNIST/KMNIST, ImageNet vs ImageNet-O). RS-NN also scales up effectively to large-scale architectures (e.g. WideResNet-28-10, VGG16, Inception V3, EfficientNetB2 and ViT-Base-16), exhibits remarkable robustness to adversarial attacks and can provide statistical guarantees in a conformal learning setting.

The rising interest in Bayesian deep learning (BDL) has led to a plethora of methods for estimating the posterior distribution. However, efficient computation of inferences, such as predictions, has been largely overlooked with Monte Carlo integration remaining the standard. In this work we examine streamlining prediction in BDL through a single forward pass without sampling. For this, we use local linearisation of activation functions and local Gaussian approximations at linear layers. Thus allowing us to analytically compute an approximation of the posterior predictive distribution. We showcase our approach for both MLP and transformers, such as ViT and GPT-2, and assess its performance on regression and classification tasks. Open-source library: https://github.com/AaltoML/SUQ.

Quantifying uncertainty is an essential part of predictive modeling, especially in the context of high-stakes decision-making. While classification output includes data uncertainty by design in the form of class probabilities, the regression task generally aims only to predict the expected value of the target variable. Probabilistic extensions often assume parametric distributions around the expected value, optimizing the likelihood over the resulting explicit densities. However, using parametric distributions can limit practical applicability, making it difficult for models to capture skewed, multi-modal, or otherwise complex distributions. In this paper, we propose optimizing a novel nondeterministic neural network regression architecture for loss functions derived from a sample-based approximation of the continuous ranked probability score (CRPS), enabling a truly distribution-free approach by learning to sample from the target's aleatoric distribution, rather than predicting explicit densities. Our approach allows the model to learn well-calibrated, arbitrary uni- and multivariate output distributions. We evaluate the method on a variety of synthetic and real-world tasks, including uni- and multivariate problems, function inverse approximation, and standard regression uncertainty benchmarks. Finally, we make all experiment code publicly available.

Conformal prediction (CP) converts any model's output to prediction sets with a guarantee to cover the true label with (adjustable) high probability. Robust CP extends this guarantee to worst-case (adversarial) inputs. Existing baselines achieve robustness by bounding randomly smoothed conformity scores. In practice, they need expensive Monte-Carlo (MC) sampling (e.g. $\sim10^4$ samples per point) to maintain an acceptable set size. We propose a robust conformal prediction that produces smaller sets even with significantly lower MC samples (e.g. 150 for CIFAR10). Our approach binarizes samples with an adjustable (or automatically adjusted) threshold selected to preserve the coverage guarantee. Remarkably, we prove that robustness can be achieved by computing only one binary certificate, unlike previous methods that certify each calibration (or test) point. Thus, our method is faster and returns smaller robust sets. We also eliminate a previous limitation that requires a bounded score function.

Recently, Ainsworth et al. (2023) showed that using weight matching (WM) to minimize the $L^2$ distance in a permutation search of model parameters effectively identifies permutations that satisfy linear mode connectivity (LMC), where the loss along a linear path between two independently trained models with different seeds remains nearly constant. This paper analyzes LMC using WM, which is useful for understanding stochastic gradient descent's effectiveness and its application in areas like model merging. We first empirically show that permutations found by WM do not significantly reduce the $L^2$ distance between two models, and the occurrence of LMC is not merely due to distance reduction by WM itself. We then demonstrate that permutations can change the directions of the singular vectors, but not the singular values, of the weight matrices in each layer. This finding shows that permutations found by WM primarily align the directions of singular vectors associated with large singular values across models. This alignment brings the singular vectors with large singular values, which determine the model's functionality, closer between the original and merged models, allowing the merged model to retain functionality similar to the original models, thereby satisfying LMC. This paper also analyzes activation matching (AM) in terms of singular vectors and finds that the principle of AM is likely the same as that of WM. Finally, we analyze the difference between WM and the straight-through estimator (STE), a dataset-dependent permutation search method, and show that WM can be more advantageous than STE in achieving LMC among three or more models.

Although theoretically compelling, Bayesian learning with modern machine learning models is computationally challenging since it requires approximating a high dimensional posterior distribution. In this work, we (i) introduce **_posteriors_**, an easily extensible PyTorch library hosting general-purpose implementations making Bayesian learning accessible and scalable to large data and parameter regimes; (ii) present a tempered framing of stochastic gradient Markov chain Monte Carlo, as implemented in posteriors, that transitions seamlessly into optimization and unveils a minor modification to deep ensembles to ensure they are asymptotically unbiased for the Bayesian posterior, and (iii) demonstrate and compare the utility of Bayesian approximations through experiments including an investigation into the cold posterior effect and applications with large language models. _**posteriors**_ repository: https://github.com/normal-computing/posteriors

Bayesian Neural Networks (BNNs) provide a promising framework for modeling predictive uncertainty and enhancing out-of-distribution robustness (OOD) by estimating the posterior distribution of network parameters. Stochastic Gradient Markov Chain Monte Carlo (SGMCMC) is one of the most powerful methods for scalable posterior sampling in BNNs, achieving efficiency by combining stochastic gradient descent with second-order Langevin dynamics. However, SGMCMC often suffers from limited sample diversity in practice, which affects uncertainty estimation and model performance. We propose a simple yet effective approach to enhance sample diversity in SGMCMC without the need for tempering or running multiple chains. Our approach reparameterizes the neural network by decomposing each of its weight matrices into a product of matrices, resulting in a sampling trajectory that better explores the target parameter space. This approach produces a more diverse set of samples, allowing faster mixing within the same computational budget. Notably, our sampler achieves these improvements without increasing the inference cost compared to the standard SGMCMC. Extensive experiments on image classification tasks, including OOD robustness, diversity, loss surface analyses, and a comparative study with Hamiltonian Monte Carlo, demonstrate the superiority of the proposed approach.

Discovering a unique causal structure is difficult due to both inherent identifiability issues, and the consequences of finite data. As such, uncertainty over causal structures, such as those obtained from a Bayesian posterior, are often necessary for downstream tasks. Finding an accurate approximation to this posterior is challenging, due to the large number of possible causal graphs, as well as the difficulty in the subproblem of finding posteriors over the functional relationships of the causal edges. Recent works have used Bayesian meta learning to view the problem of posterior estimation as a supervised learning task. Yet, these methods are limited as they cannot reliably sample from the posterior over causal structures and fail to encode key properties of the posterior, such as correlation between edges and permutation equivariance with respect to nodes. To address these limitations, we propose a Bayesian meta learning model that allows for sampling causal structures from the posterior and encodes these key properties. We compare our meta-Bayesian causal discovery against existing Bayesian causal discovery methods, demonstrating the advantages of directly learning a posterior over causal structure.

We present a novel approach to calibrating linguistic expressions of certainty, e.g., "Maybe" and "Likely". Unlike prior work that assigns a single score to each certainty phrase, we model uncertainty as distributions over the simplex to capture their semantics more accurately. To accommodate this new representation of certainty, we generalize existing measures of miscalibration and introduce a novel post-hoc calibration method. Leveraging these tools, we analyze the calibration of both humans (e.g., radiologists) and computational models (e.g., language models) and provide interpretable suggestions to improve their calibration.

This paper presents an innovative approach, called credal wrapper, to formulating a credal set representation of model averaging for Bayesian neural networks (BNNs) and deep ensembles (DEs), capable of improving uncertainty estimation in classification tasks. Given a finite collection of single predictive distributions derived from BNNs or DEs, the proposed credal wrapper approach extracts an upper and a lower probability bound per class, acknowledging the epistemic uncertainty due to the availability of a limited amount of distributions. Such probability intervals over classes can be mapped on a convex set of probabilities (a credal set) from which, in turn, a unique prediction can be obtained using a transformation called intersection probability transformation. In this article, we conduct extensive experiments on several out-of-distribution (OOD) detection benchmarks, encompassing various dataset pairs (CIFAR10/100 vs SVHN/Tiny-ImageNet, CIFAR10 vs CIFAR10-C, CIFAR100 vs CIFAR100-C and ImageNet vs ImageNet-O) and using different network architectures (such as VGG16, ResNet-18/50, EfficientNet B2, and ViT Base). Compared to the BNN and DE baselines, the proposed credal wrapper method exhibits superior performance in uncertainty estimation and achieves a lower expected calibration error on corrupted data.

There are various measures of predictive uncertainty in the literature, but their relationships to each other remain unclear. This paper uses a decomposition of statistical pointwise risk into components associated with different sources of predictive uncertainty: namely, aleatoric uncertainty (inherent data variability) and epistemic uncertainty (model-related uncertainty). Together with Bayesian methods applied as approximations, we build a framework that allows one to generate different predictive uncertainty measures. We validate measures, derived from our framework on image datasets by evaluating its performance in detecting out-of-distribution and misclassified instances using the AUROC metric. The experimental results confirm that the measures derived from our framework are useful for the considered downstream tasks.

Scaling test-time compute to search for optimal solutions is an important step towards building generally-capable language models that can reason. Recent work, however, shows that tasks of varying complexity require distinct search strategies to solve optimally, thus making it challenging to design a one-size-fits-all approach. Prior solutions either attempt to predict task difficulty to select the optimal search strategy, often infeasible in practice, or use a static, pre-defined strategy, e.g., repeated parallel sampling or greedy sequential search, which is sub-optimal. In this work, we argue for an alternative view using the probabilistic framework of Bayesian optimization (BO), where the search strategy is adapted dynamically based on the evolving uncertainty estimates of solutions as search progresses. To this end, we introduce Bayesian-OPRO (BOPRO)––a generalization of a recent method for in-context optimization, which iteratively samples from new proposal distributions by modifying the prompt to the LLM with a subset of its previous generations selected to explore or exploit different parts of the search space. We evaluate our method on word search, molecule optimization, and a joint hypothesis+program search task using a 1-D version of the challenging Abstraction and Reasoning Corpus (1D-ARC). Our results show that BOPRO outperforms all baselines in word search (≥10 points) and molecule optimization (higher quality and 17% fewer invalid molecules), but trails a best-k prompting strategy in program search. Our analysis reveals that despite the ability to balance exploration and exploitation using BOPRO, failure is likely due to the inability of code representation models in distinguishing sequences with low edit-distances.

We propose a novel Stochastic Differential Equation (SDE) framework to address the problem of learning uncertainty-aware representations for graph-structured data. While Graph Neural Ordinary Differential Equations (GNODEs) have shown promise in learning node representations, they lack the ability to quantify uncertainty. To address this, we introduce Latent Graph Neural Stochastic Differential Equations (LGNSDE), which enhance GNODE by embedding randomness through a Bayesian prior-posterior mechanism for epistemic uncertainty and Brownian motion for aleatoric uncertainty. By leveraging the existence and uniqueness of solutions to graph-based SDEs, we prove that the variance of the latent space bounds the variance of model outputs, thereby providing theoretically sensible guarantees for the uncertainty estimates. Furthermore, we show mathematically that LGNSDEs are robust to small perturbations in the input, maintaining stability over time. Empirical results across several benchmarks demonstrate that our framework is competitive in out-of-distribution detection, robustness to noise perturbations, and active learning, underscoring the ability of LGNSDEs to quantify uncertainty reliably.

We give a principled method for decomposing the predictive uncertainty of a model into aleatoric and epistemic components with explicit semantics relating them to the real-world data distribution. While many works in the literature have proposed such decompositions, they lack the type of formal guarantees we provide. Our method is based on the new notion of higher-order calibration, which generalizes ordinary calibration to the setting of higher-order predictors that predict _mixtures_ over label distributions at every point. We show how to measure as well as achieve higher-order calibration using access to $k$-snapshots, namely examples where each point has $k$ independent conditional labels. Under higher-order calibration, the estimated aleatoric uncertainty at a point is guaranteed to match the real-world aleatoric uncertainty averaged over all points where the prediction is made. To our knowledge, this is the first formal guarantee of this type that places no assumptions whatsoever on the real-world data distribution. Importantly, higher-order calibration is also applicable to existing higher-order predictors such as Bayesian and ensemble models and provides a natural evaluation metric for such models. We demonstrate through experiments that our method produces meaningful uncertainty decompositions in tasks such as image classification.