Tensor Network (TN) Kernel Machines speed up model learning by representing parameters as low-rank TNs, reducing computation and memory use. However, most TN-based Kernel methods are deterministic and ignore parameter uncertainty. Further, they require manual tuning of model complexity hyperparameters like tensor rank and feature dimensions, often through trial-and-error or computationally costly methods like cross-validation. We propose Bayesian Tensor Network Kernel Machines, a fully probabilistic framework that uses sparsity-inducing hierarchical priors on TN factors to automatically infer model complexity. This enables automatic inference of tensor rank and feature dimensions, while also identifying the most relevant features for prediction, thereby enhancing model interpretability. All the model parameters and hyperparameters are treated as latent variables with corresponding priors. Given the Bayesian approach and latent variable dependencies, we apply a mean-field variational inference to approximate their posteriors. We show that applying a mean-field approximation to TN factors yields a Bayesian ALS algorithm with the same computational complexity as its deterministic counterpart, enabling uncertainty quantification at no extra computational cost. Experiments on synthetic and real-world datasets demonstrate the superior performance of our model in prediction accuracy, uncertainty quantification, interpretability, and scalability.
Despite their widespread use, large language models (LLMs) are known to hallucinate incorrect information and be poorly calibrated. This makes the uncertainty quantification of these models of critical importance, especially in high-stakes domains, such as autonomy and healthcare. Prior work has made Bayesian deep learning-based approaches to this problem more tractable by performing inference over the low-rank adaptation (LoRA) parameters of a fine-tuned model. While effective, these approaches struggle to scale to larger LLMs due to requiring further additional parameters compared to LoRA. In this work we present $\textbf{Scala}$ble $\textbf{B}$ayesian $\textbf{L}$ow-Rank Adaptation via Stochastic Variational Subspace Inference (ScalaBL). We perform Bayesian inference in an $r$-dimensional subspace, for LoRA rank $r$. By repurposing the LoRA parameters as projection matrices, we are able to map samples from this subspace into the full weight space of the LLM. This allows us to learn all the parameters of our approach using stochastic variational inference. Despite the low dimensionality of our subspace, we are able to achieve competitive performance with state-of-the-art approaches while only requiring ${\sim}1000$ additional parameters. Furthermore, it allows us to scale up to the largest Bayesian LLM to date, with four times as a many base parameters as prior work.
Variational inference (VI) is a popular approach in Bayesian inference, that looks for the best approximation of the posterior distribution within a parametric family, minimizing a loss that is typically the (reverse) Kullback-Leibler (KL) divergence. In this paper, we focus on the following parametric family: mixtures of isotropic Gaussians (i.e., with diagonal covariance matrices proportional to the identity) and uniform weights. We develop a variational framework and provide efficient algorithms suited for this family. In contrast with mixtures of Gaussian with generic covariance matrices, this choice presents a balance between accurate approximations of multimodal Bayesian posteriors, while being memory and computationally efficient. Our algorithms implement gradient descent on the location of the mixture components (the modes of the Gaussians), and either (an entropic) Mirror or Bures descent on their variance parameters. We illustrate the performance of our algorithms on numerical experiments.
The expressiveness of flow-based models combined with stochastic variational inference (SVI) has, in recent years, expanded the application of optimization-based Bayesian inference to include problems with complex data relationships. However, until now, SVI using flow-based models has been limited to problems of fixed dimension. We introduce CoSMIC, normalizing flows (COntextually-Specified Masking for Identity-mapped Components), an extension to neural autoregressive conditional normalizing flow architectures that enables using a single amortized variational density for inference over a transdimensional target distribution. We propose a combined stochastic variational transdimensional inference (VTI) approach to training CoSMIC flows using techniques from Bayesian optimization and Monte Carlo gradient estimation. Numerical experiments demonstrate the performance of VTI on challenging problems that scale to high-cardinality model spaces.
Recent contributions of semantic information theory reveal the set-element relationship between semantic and syntactic information, represented as synonymous relationships. In this paper, we propose a synonymous variational inference (SVI) method based on this synonymity viewpoint to re-analyze the perceptual image compression problem. It takes perceptual similarity as a typical synonymous criterion to build an ideal synonymous set (Synset), and approximate the posterior of its latent synonymous representation with a parametric density by minimizing a partial semantic KL divergence. This analysis theoretically proves that the optimization direction of perception image compression follows a triple tradeoff that can cover the existing rate-distortion-perception schemes. Additionally, we introduce synonymous image compression (SIC), a new image compression scheme that corresponds to the analytical process of SVI, and implement a progressive SIC codec to fully leverage the model's capabilities. Experimental results demonstrate comparable rate-distortion-perception performance using a single progressive SIC codec, thus verifying the effectiveness of our proposed analysis method.
Diffusion models exhibit excellent sample quality, but existing guidance methods often require additional model training or are limited to specific tasks. We revisit guidance in diffusion models from the perspective of variational inference and control, introducing Diffusion Trajectory Matching (DTM) that enables guiding pretrained diffusion trajectories to satisfy a terminal cost. DTM unifies a broad class of guidance methods and enables novel instantiations. We introduce a new method within this framework that achieves state-of-the-art results on several linear, non-linear, and blind inverse problems without requiring additional model training or specificity to pixel or latent space diffusion models. Our code will be available at https://github.com/czi-ai/oc-guidance
Meta-reinforcement learning trains a single reinforcement learning agent on a distribution of tasks to quickly generalize to new tasks outside of the training set at test time. From a Bayesian perspective, one can interpret this as performing amortized variational inference on the posterior distribution over training tasks. Among the various meta-reinforcement learning approaches, a common method is to represent this distribution with a point-estimate using a recurrent neural network. We show how one can augment this point estimate to give full distributions through the Laplace approximation, either at the start of, during, or after learning, without modifying the base model architecture. With our approximation, we are able to estimate distribution statistics (e.g., the entropy) of non-Bayesian agents and observe that point-estimate based methods produce overconfident estimators while not satisfying consistency. Furthermore, when comparing our approach to full-distribution based learning of the task posterior, our method performs on par with variational baselines while having much fewer parameters.
Recent advances in self-supervised learning (SSL) have revolutionized computer vision through innovative architectures and learning objectives, yet they have not fully leveraged insights from biological visual processing systems. Recently, a brain-inspired SSL model named PhiNet was proposed; it is based on a ResNet backbone and operates on static image inputs with strong augmentation. In this paper, we introduce PhiNet v2, a novel Transformer-based architecture that processes temporal visual input (that is, sequences of images) without relying on strong augmentation. Our model leverages variational inference to learn robust visual representations from continuous input streams, similar to human visual processing. Through extensive experimentation, we demonstrate that PhiNet v2 achieves competitive performance compared to state-of-the-art vision foundation models, while maintaining the ability to learn from sequential input without strong data augmentation. This work represents a significant step toward more biologically plausible computer vision systems that process visual information in a manner more closely aligned with human cognitive processes.
Remote photoplethysmography (rPPG) technology infers heart rate by capturing subtle color changes in facial skin using a camera, demonstrating great potential in non-contact heart rate measurement. However, measurement accuracy significantly decreases in complex scenarios such as lighting changes and head movements compared to ideal laboratory conditions. Existing deep learning models often neglect the quantification of measurement uncertainty, limiting their credibility in dynamic scenes. To address the issue of insufficient rPPG measurement reliability in complex scenarios, this paper introduces Bayesian neural networks to the rPPG field for the first time, proposing the Robust Fusion Bayesian Physiological Network (RF-BayesPhysNet), which can model both aleatoric and epistemic uncertainty. It leverages variational inference to balance accuracy and computational efficiency. Due to the current lack of uncertainty estimation metrics in the rPPG field, this paper also proposes a new set of methods, using Spearman correlation coefficient, prediction interval coverage, and confidence interval width, to measure the effectiveness of uncertainty estimation methods under different noise conditions. Experiments show that the model, with only double the parameters compared to traditional network models, achieves a MAE of 2.56 on the UBFC-RPPG dataset, surpassing most models. It demonstrates good uncertainty estimation capability in no-noise and low-noise conditions, providing prediction confidence and significantly enhancing robustness in real-world applications. We have open-sourced the code at https://github.com/AIDC-rPPG/RF-Net
Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.
As modern neural networks get more complex, specifying a model with high predictive performance and sound uncertainty quantification becomes a more challenging task. Despite some promising theoretical results on the true posterior predictive distribution of Bayesian neural networks, the properties of even the most commonly used posterior approximations are often questioned. Computational burdens and intractable posteriors expose miscalibrated Bayesian neural networks to poor accuracy and unreliable uncertainty estimates. Approximate Bayesian inference aims to replace unknown and intractable posterior distributions with some simpler but feasible distributions. The dimensions of modern deep models, coupled with the lack of identifiability, make Markov chain Monte Carlo (MCMC) tremendously expensive and unable to fully explore the multimodal posterior. On the other hand, variational inference benefits from improved computational complexity but lacks the asymptotical guarantees of sampling-based inference and tends to concentrate around a single mode. The performance of both approaches heavily depends on architectural choices; this paper aims to shed some light on this by considering the computational costs, accuracy and uncertainty quantification in different scenarios including large width and out-of-sample data. To improve posterior exploration, different model averaging and ensembling techniques are studied, along with their benefits on predictive performance. In our experiments, variational inference overall provided better uncertainty quantification than MCMC; further, stacking and ensembles of variational approximations provided comparable accuracy to MCMC at a much-reduced cost.
Spatial transcriptomics (ST) is a novel technique that simultaneously captures pathological images and gene expression profiling with spatial coordinates. Since ST is closely related to pathological features such as disease subtypes, it may be valuable to augment image representation with pathological information. However, there are no attempts to leverage ST for image recognition ({\it i.e,} patch-level classification of subtypes of pathological image.). One of the big challenges is significant batch effects in spatial transcriptomics that make it difficult to extract pathological features of images from ST. In this paper, we propose a batch-agnostic contrastive learning framework that can extract consistent signals from gene expression of ST in multiple patients. To extract consistent signals from ST, we utilize the batch-agnostic gene encoder that is trained in a variational inference manner. Experiments demonstrated the effectiveness of our framework on a publicly available dataset. Code is publicly available at https://github.com/naivete5656/TPIRBAE
Continual learning is learning from a sequence of tasks with the aim of learning new tasks without forgetting old tasks. Sequential function-space variational inference (SFSVI) is a continual learning method based on variational inference which uses a Gaussian variational distribution to approximate the distribution of the outputs of a finite number of selected inducing points. Since the posterior distribution of a neural network is multi-modal, a Gaussian distribution could only match one mode of the posterior distribution, and a Gaussian mixture distribution could be used to better approximate the posterior distribution. We propose an SFSVI method which uses a Gaussian mixture variational distribution. We also compare different types of variational inference methods with and without a fixed pre-trained feature extractor. We find that in terms of final average accuracy, Gaussian mixture methods perform better than Gaussian methods and likelihood-focused methods perform better than prior-focused methods.
Topic models are widely used for discovering latent thematic structures in large text corpora, yet traditional unsupervised methods often struggle to align with predefined conceptual domains. This paper introduces Seeded Poisson Factorization (SPF), a novel approach that extends the Poisson Factorization framework by incorporating domain knowledge through seed words. SPF enables a more interpretable and structured topic discovery by modifying the prior distribution of topic-specific term intensities, assigning higher initial rates to predefined seed words. The model is estimated using variational inference with stochastic gradient optimization, ensuring scalability to large datasets. We apply SPF to an Amazon customer feedback dataset, leveraging predefined product categories as guiding structures. Our evaluation demonstrates that SPF achieves superior classification performance compared to alternative guided topic models, particularly in terms of computational efficiency and predictive performance. Furthermore, robustness checks highlight SPF's ability to adaptively balance domain knowledge and data-driven topic discovery, even in cases of imperfect seed word selection. These results establish SPF as a powerful and scalable alternative for integrating expert knowledge into topic modeling, enhancing both interpretability and efficiency in real-world applications.
Neural posterior estimation (NPE), a type of amortized variational inference, is a computationally efficient means of constructing probabilistic catalogs of light sources from astronomical images. To date, NPE has not been used to perform inference in models with spatially varying covariates. However, ground-based astronomical images have spatially varying sky backgrounds and point spread functions (PSFs), and accounting for this variation is essential for constructing accurate catalogs of imaged light sources. In this work, we introduce a method of performing NPE with spatially varying backgrounds and PSFs. In this method, we generate synthetic catalogs and semi-synthetic images for these catalogs using randomly sampled PSF and background estimates from existing surveys. Using this data, we train a neural network, which takes an astronomical image and representations of its background and PSF as input, to output a probabilistic catalog. Our experiments with Sloan Digital Sky Survey data demonstrate the effectiveness of NPE in the presence of spatially varying backgrounds and PSFs for light source detection, star/galaxy separation, and flux measurement.
In real-world applications, node features in graphs often contain noise from various sources, leading to significant performance degradation in GNNs. Although several methods have been developed to enhance robustness, they rely on the unrealistic assumption that noise in node features is independent of the graph structure and node labels, thereby limiting their applicability. To this end, we introduce a more realistic noise scenario, dependency-aware noise on graphs (DANG), where noise in node features create a chain of noise dependencies that propagates to the graph structure and node labels. We propose a novel robust GNN, DA-GNN, which captures the causal relationships among variables in the data generating process (DGP) of DANG using variational inference. In addition, we present new benchmark datasets that simulate DANG in real-world applications, enabling more practical research on robust GNNs. Extensive experiments demonstrate that DA-GNN consistently outperforms existing baselines across various noise scenarios, including both DANG and conventional noise models commonly considered in this field.
Time series domain adaptation aims to transfer the complex temporal dependence from the labeled source domain to the unlabeled target domain. Recent advances leverage the stable causal mechanism over observed variables to model the domain-invariant temporal dependence. However, modeling precise causal structures in high-dimensional data, such as videos, remains challenging. Additionally, direct causal edges may not exist among observed variables (e.g., pixels). These limitations hinder the applicability of existing approaches to real-world scenarios. To address these challenges, we find that the high-dimension time series data are generated from the low-dimension latent variables, which motivates us to model the causal mechanisms of the temporal latent process. Based on this intuition, we propose a latent causal mechanism identification framework that guarantees the uniqueness of the reconstructed latent causal structures. Specifically, we first identify latent variables by utilizing sufficient changes in historical information. Moreover, by enforcing the sparsity of the relationships of latent variables, we can achieve identifiable latent causal structures. Built on the theoretical results, we develop the Latent Causality Alignment (LCA) model that leverages variational inference, which incorporates an intra-domain latent sparsity constraint for latent structure reconstruction and an inter-domain latent sparsity constraint for domain-invariant structure reconstruction. Experiment results on eight benchmarks show a general improvement in the domain-adaptive time series classification and forecasting tasks, highlighting the effectiveness of our method in real-world scenarios. Codes are available at https://github.com/DMIRLAB-Group/LCA.
Integrated Gradients (IG), a widely used axiomatic path-based attribution method, assigns importance scores to input features by integrating model gradients along a straight path from a baseline to the input. While effective in some cases, we show that straight paths can lead to flawed attributions. In this paper, we identify the cause of these misattributions and propose an alternative approach that treats the input space as a Riemannian manifold, computing attributions by integrating gradients along geodesics. We call this method Geodesic Integrated Gradients (GIG). To approximate geodesic paths, we introduce two techniques: a k-Nearest Neighbours-based approach for smaller models and a Stochastic Variational Inference-based method for larger ones. Additionally, we propose a new axiom, Strong Completeness, extending the axioms satisfied by IG. We show that this property is desirable for attribution methods and that GIG is the only method that satisfies it. Through experiments on both synthetic and real-world data, we demonstrate that GIG outperforms existing explainability methods, including IG.
This paper provides a comprehensive analysis of variational inference in latent variable models for survival analysis, emphasizing the distinctive challenges associated with applying variational methods to survival data. We identify a critical weakness in the existing methodology, demonstrating how a poorly designed variational distribution may hinder the objective of survival analysis tasks--modeling time-to-event distributions. We prove that the optimal variational distribution, which perfectly bounds the log-likelihood, may depend on the censoring mechanism. To address this issue, we propose censor-dependent variational inference (CDVI), tailored for latent variable models in survival analysis. More practically, we introduce CD-CVAE, a V-structure Variational Autoencoder (VAE) designed for the scalable implementation of CDVI. Further discussion extends some existing theories and training techniques to survival analysis. Extensive experiments validate our analysis and demonstrate significant improvements in the estimation of individual survival distributions.
As AI models grow in power and generality, understanding how agents learn and make decisions in complex environments is critical to promoting ethical behavior. This study introduces the Odyssey, a lightweight, adaptive text based adventure game, providing a scalable framework for exploring AI ethics and safety. The Odyssey examines the ethical implications of implementing biological drives, specifically, self preservation, into three different agents. A Bayesian agent optimized with NEAT, a Bayesian agent optimized with stochastic variational inference, and a GPT 4o agent. The agents select actions at each scenario to survive, adapting to increasingly challenging scenarios. Post simulation analysis evaluates the ethical scores of the agent decisions, uncovering the tradeoffs it navigates to survive. Specifically, analysis finds that when danger increases, agents ethical behavior becomes unpredictable. Surprisingly, the GPT 4o agent outperformed the Bayesian models in both survival and ethical consistency, challenging assumptions about traditional probabilistic methods and raising a new challenge to understand the mechanisms of LLMs' probabilistic reasoning.