Decision making under uncertainty is a cross-cutting challenge in science and engineering. Most approaches to this challenge employ probabilistic representations of uncertainty. In complicated systems accessible only via data or black-box models, however, these representations are rarely known. We discuss how to characterize and manipulate such representations using triangular transport maps, which approximate any complex probability distribution as a transformation of a simple, well-understood distribution. The particular structure of triangular transport guarantees many desirable mathematical and computational properties that translate well into solving practical problems. Triangular maps are actively used for density estimation, (conditional) generative modelling, Bayesian inference, data assimilation, optimal experimental design, and related tasks. While there is ample literature on the development and theory of triangular transport methods, this manuscript provides a detailed introduction for scientists interested in employing measure transport without assuming a formal mathematical background. We build intuition for the key foundations of triangular transport, discuss many aspects of its practical implementation, and outline the frontiers of this field.
We introduce an open-ended test grounded in algorithmic probability that can avoid benchmark contamination in the quantitative evaluation of frontier models in the context of their Artificial General Intelligence (AGI) and Superintelligence (ASI) claims. Unlike other tests, this test does not rely on statistical compression methods (such as GZIP or LZW), which are more closely related to Shannon entropy than to Kolmogorov complexity and are not able to test beyond simple pattern matching. The test challenges aspects of AI, in particular LLMs, related to features of intelligence of fundamental nature such as synthesis and model creation in the context of inverse problems (generating new knowledge from observation). We argue that metrics based on model abstraction and abduction (optimal Bayesian `inference') for predictive `planning' can provide a robust framework for testing intelligence, including natural intelligence (human and animal), narrow AI, AGI, and ASI. We found that LLM model versions tend to be fragile and incremental as a result of memorisation only with progress likely driven by the size of training data. The results were compared with a hybrid neurosymbolic approach that theoretically guarantees universal intelligence based on the principles of algorithmic probability and Kolmogorov complexity. The method outperforms LLMs in a proof-of-concept on short binary sequences. We prove that compression is equivalent and directly proportional to a system's predictive power and vice versa. That is, if a system can better predict it can better compress, and if it can better compress, then it can better predict. Our findings strengthen the suspicion regarding the fundamental limitations of LLMs, exposing them as systems optimised for the perception of mastery over human language.
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.
This focused review explores a range of neural operator architectures for approximating solutions to parametric partial differential equations (PDEs), emphasizing high-level concepts and practical implementation strategies. The study covers foundational models such as Deep Operator Networks (DeepONet), Principal Component Analysis-based Neural Networks (PCANet), and Fourier Neural Operators (FNO), providing comparative insights into their core methodologies and performance. These architectures are demonstrated on two classical linear parametric PDEs: the Poisson equation and linear elastic deformation. Beyond forward problem-solving, the review delves into applying neural operators as surrogates in Bayesian inference problems, showcasing their effectiveness in accelerating posterior inference while maintaining accuracy. The paper concludes by discussing current challenges, particularly in controlling prediction accuracy and generalization. It outlines emerging strategies to address these issues, such as residual-based error correction and multi-level training. This review can be seen as a comprehensive guide to implementing neural operators and integrating them into scientific computing workflows.
We propose a scalable inference algorithm for Bayes posteriors defined on a reproducing kernel Hilbert space (RKHS). Given a likelihood function and a Gaussian random element representing the prior, the corresponding Bayes posterior measure $\Pi_{\text{B}}$ can be obtained as the stationary distribution of an RKHS-valued Langevin diffusion. We approximate the infinite-dimensional Langevin diffusion via a projection onto the first $M$ components of the Kosambi-Karhunen-Lo\`eve expansion. Exploiting the thus obtained approximate posterior for these $M$ components, we perform inference for $\Pi_{\text{B}}$ by relying on the law of total probability and a sufficiency assumption. The resulting method scales as $O(M^3+JM^2)$, where $J$ is the number of samples produced from the posterior measure $\Pi_{\text{B}}$. Interestingly, the algorithm recovers the posterior arising from the sparse variational Gaussian process (SVGP) (see Titsias, 2009) as a special case, owed to the fact that the sufficiency assumption underlies both methods. However, whereas the SVGP is parametrically constrained to be a Gaussian process, our method is based on a non-parametric variational family $\mathcal{P}(\mathbb{R}^M)$ consisting of all probability measures on $\mathbb{R}^M$. As a result, our method is provably close to the optimal $M$-dimensional variational approximation of the Bayes posterior $\Pi_{\text{B}}$ in $\mathcal{P}(\mathbb{R}^M)$ for convex and Lipschitz continuous negative log likelihoods, and coincides with SVGP for the special case of a Gaussian error likelihood.
Neural population activity exhibits complex, nonlinear dynamics, varying in time, over trials, and across experimental conditions. Here, we develop Conditionally Linear Dynamical System (CLDS) models as a general-purpose method to characterize these dynamics. These models use Gaussian Process (GP) priors to capture the nonlinear dependence of circuit dynamics on task and behavioral variables. Conditioned on these covariates, the data is modeled with linear dynamics. This allows for transparent interpretation and tractable Bayesian inference. We find that CLDS models can perform well even in severely data-limited regimes (e.g. one trial per condition) due to their Bayesian formulation and ability to share statistical power across nearby task conditions. In example applications, we apply CLDS to model thalamic neurons that nonlinearly encode heading direction and to model motor cortical neurons during a cued reaching task
The diversity of time series applications and scarcity of domain-specific data highlight the need for time-series models with strong few-shot learning capabilities. In this work, we propose a novel training scheme and a transformer-based architecture, collectively referred to as TimePFN, for multivariate time-series (MTS) forecasting. TimePFN is based on the concept of Prior-data Fitted Networks (PFN), which aims to approximate Bayesian inference. Our approach consists of (1) generating synthetic MTS data through diverse Gaussian process kernels and the linear coregionalization method, and (2) a novel MTS architecture capable of utilizing both temporal and cross-channel dependencies across all input patches. We evaluate TimePFN on several benchmark datasets and demonstrate that it outperforms the existing state-of-the-art models for MTS forecasting in both zero-shot and few-shot settings. Notably, fine-tuning TimePFN with as few as 500 data points nearly matches full dataset training error, and even 50 data points yield competitive results. We also find that TimePFN exhibits strong univariate forecasting performance, attesting to its generalization ability. Overall, this work unlocks the power of synthetic data priors for MTS forecasting and facilitates strong zero- and few-shot forecasting performance.
Tuberculosis (TB) remains a formidable global health challenge, driven by complex spatiotemporal transmission dynamics and influenced by factors such as population mobility and behavioral changes. We propose an Epidemic-Guided Deep Learning (EGDL) approach that fuses mechanistic epidemiological principles with advanced deep learning techniques to enhance early warning systems and intervention strategies for TB outbreaks. Our framework is built upon a modified networked Susceptible-Infectious-Recovered (MN-SIR) model augmented with a saturated incidence rate and graph Laplacian diffusion, capturing both long-term transmission dynamics and region-specific population mobility patterns. Compartmental model parameters are rigorously estimated using Bayesian inference via the Markov Chain Monte Carlo approach. Theoretical analysis leveraging the comparison principle and Green's formula establishes global stability properties of the disease-free and endemic equilibria. Building on these epidemiological insights, we design two forecasting architectures, EGDL-Parallel and EGDL-Series, that integrate the mechanistic outputs of the MN-SIR model within deep neural networks. This integration mitigates the overfitting risks commonly encountered in data-driven methods and filters out noise inherent in surveillance data, resulting in reliable forecasts of real-world epidemic trends. Experiments conducted on TB incidence data from 47 prefectures in Japan and 31 provinces in mainland China demonstrate that our approach delivers robust and accurate predictions across multiple time horizons (short to medium-term forecasts), supporting its generalizability across regions with different population dynamics.
Reverberant speech, denoting the speech signal degraded by the process of reverberation, contains crucial knowledge of both anechoic source speech and room impulse response (RIR). This work proposes a variational Bayesian inference (VBI) framework with neural speech prior (VINP) for joint speech dereverberation and blind RIR identification. In VINP, a probabilistic signal model is constructed in the time-frequency (T-F) domain based on convolution transfer function (CTF) approximation. For the first time, we propose using an arbitrary discriminative dereverberation deep neural network (DNN) to predict the prior distribution of anechoic speech within a probabilistic model. By integrating both reverberant speech and the anechoic speech prior, VINP yields the maximum a posteriori (MAP) and maximum likelihood (ML) estimations of the anechoic speech spectrum and CTF filter, respectively. After simple transformations, the waveforms of anechoic speech and RIR are estimated. Moreover, VINP is effective for automatic speech recognition (ASR) systems, which sets it apart from most deep learning (DL)-based single-channel dereverberation approaches. Experiments on single-channel speech dereverberation demonstrate that VINP reaches an advanced level in most metrics related to human perception and displays unquestionable state-of-the-art (SOTA) performance in ASR-related metrics. For blind RIR identification, experiments indicate that VINP attains the SOTA level in blind estimation of reverberation time at 60 dB (RT60) and direct-to-reverberation ratio (DRR). Codes and audio samples are available online.
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient, but are rarely favoured due to their inferior performance. Here, we extend distance-based phylogenetics using an entropy-based likelihood of the evolution among pairs of taxa, allowing for fast Bayesian inference in genome-scale datasets. We provide evidence of a close link between the inference criteria used in distance methods and Felsenstein's likelihood, such that the methods are expected to have comparable performance in practice. Using the entropic likelihood, we perform Bayesian inference on three phylogenetic benchmark datasets and find that estimates closely correspond with previous inferences. We also apply this rapid inference approach to a 60-million-site alignment from 363 avian taxa, covering most avian families. The method has outstanding performance and reveals substantial uncertainty in the avian diversification events immediately after the K-Pg transition event. The entropic likelihood allows for efficient Bayesian phylogenetic inference, accommodating the analysis demands of the genomic era.
Simulation-based calibration checking (SBC) refers to the validation of an inference algorithm and model implementation through repeated inference on data simulated from a generative model. In the original and commonly used approach, the generative model uses parameters drawn from the prior, and thus the approach is testing whether the inference works for simulated data generated with parameter values plausible under that prior. This approach is natural and desirable when we want to test whether the inference works for a wide range of datasets we might observe. However, after observing data, we are interested in answering whether the inference works conditional on that particular data. In this paper, we propose posterior SBC and demonstrate how it can be used to validate the inference conditionally on observed data. We illustrate the utility of posterior SBC in three case studies: (1) A simple multilevel model; (2) a model that is governed by differential equations; and (3) a joint integrative neuroscience model which is approximated via amortized Bayesian inference with neural networks.
Subspace inference for neural networks assumes that a subspace of their parameter space suffices to produce a reliable uncertainty quantification. In this work, we mathematically derive the optimal subspace model to a Bayesian inference scenario based on the Laplace approximation. We demonstrate empirically that, in the optimal case, often a fraction of parameters less than 1% is sufficient to obtain a reliable estimate of the full Laplace approximation. Since the optimal solution is derived, we can evaluate all other subspace models against a baseline. In addition, we give an approximation of our method that is applicable to larger problem settings, in which the optimal solution is not computable, and compare it to existing subspace models from the literature. In general, our approximation scheme outperforms previous work. Furthermore, we present a metric to qualitatively compare different subspace models even if the exact Laplace approximation is unknown.
Graph representation learning has emerged as a cornerstone for tasks like node classification and link prediction, yet prevailing self-supervised learning (SSL) methods face challenges such as computational inefficiency, reliance on contrastive objectives, and representation collapse. Existing approaches often depend on feature reconstruction, negative sampling, or complex decoders, which introduce training overhead and hinder generalization. Further, current techniques which address such limitations fail to account for the contribution of node embeddings to a certain prediction in the absence of labeled nodes. To address these limitations, we propose a novel joint embedding predictive framework for graph SSL that eliminates contrastive objectives and negative sampling while preserving semantic and structural information. Additionally, we introduce a semantic-aware objective term that incorporates pseudo-labels derived from Gaussian Mixture Models (GMMs), enhancing node discriminability by evaluating latent feature contributions. Extensive experiments demonstrate that our framework outperforms state-of-the-art graph SSL methods across benchmarks, achieving superior performance without contrastive loss or complex decoders. Key innovations include (1) a non-contrastive, view-invariant joint embedding predictive architecture, (2) Leveraging single context and multiple targets relationship between subgraphs, and (3) GMM-based pseudo-label scoring to capture semantic contributions. This work advances graph SSL by offering a computationally efficient, collapse-resistant paradigm that bridges spatial and semantic graph features for downstream tasks. The code for our paper can be found at https://github.com/Deceptrax123/JPEB-GSSL
This paper addresses the challenges in learning-based monocular positioning by proposing VKFPos, a novel approach that integrates Absolute Pose Regression (APR) and Relative Pose Regression (RPR) via an Extended Kalman Filter (EKF) within a variational Bayesian inference framework. Our method shows that the essential posterior probability of the monocular positioning problem can be decomposed into APR and RPR components. This decomposition is embedded in the deep learning model by predicting covariances in both APR and RPR branches, allowing them to account for associated uncertainties. These covariances enhance the loss functions and facilitate EKF integration. Experimental evaluations on both indoor and outdoor datasets show that the single-shot APR branch achieves accuracy on par with state-of-the-art methods. Furthermore, for temporal positioning, where consecutive images allow for RPR and EKF integration, VKFPos outperforms temporal APR and model-based integration methods, achieving superior accuracy.
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.
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.
Contaminant observations and outliers often cause problems when estimating the parameters of cognitive models, which are statistical models representing cognitive processes. In this study, we test and improve the robustness of parameter estimation using amortized Bayesian inference (ABI) with neural networks. To this end, we conduct systematic analyses on a toy example and analyze both synthetic and real data using a popular cognitive model, the Drift Diffusion Models (DDM). First, we study the sensitivity of ABI to contaminants with tools from robust statistics: the empirical influence function and the breakdown point. Next, we propose a data augmentation or noise injection approach that incorporates a contamination distribution into the data-generating process during training. We examine several candidate distributions and evaluate their performance and cost in terms of accuracy and efficiency loss relative to a standard estimator. Introducing contaminants from a Cauchy distribution during training considerably increases the robustness of the neural density estimator as measured by bounded influence functions and a much higher breakdown point. Overall, the proposed method is straightforward and practical to implement and has a broad applicability in fields where outlier detection or removal is challenging.
Gene silencing via small interfering RNA (siRNA) represents a transformative tool in cancer therapy, offering specificity and reduced off-target effects compared to conventional treatments. A crucial step in siRNA-based therapies is endosomal escape, the release of siRNA from endosomes into the cytoplasm. Quantifying endosomal escape is challenging due to the dynamic nature of the process and limitations in imaging and analytical techniques. Traditional methods often rely on fluorescence intensity measurements or manual image processing, which are time-intensive and fail to capture continuous dynamics. This paper presents a novel computational framework that integrates automated image processing to analyze time-lapse fluorescent microscopy data of endosomal escape, hierarchical Bayesian inference, and stochastic simulations. Our method employs image segmentation techniques such as binary masks, Gaussian filters, and multichannel color quantification to extract precise spatial and temporal data from microscopy images. Using a hierarchical Bayesian approach, we estimate the parameters of a compartmental model that describes endosomal escape dynamics, accounting for variability over time. These parameters inform a Gillespie stochastic simulation algorithm, ensuring realistic simulations of siRNA release events over time. Our framework provides a scalable and reproducible method for quantifying endosomal escape. The model captures uncertainty and variability in parameter estimation, and endosomal escape dynamics. Additionally, synthetic data generation allows researchers to validate experimental findings and explore alternative conditions without extensive laboratory work. This integrated approach not only improves the accuracy of endosomal escape quantification but also provides predictive insights for optimizing siRNA delivery systems and advancing gene therapy research.
In two-player cooperative games, agents can play together effectively when they have accurate assumptions about how their teammate will behave, but may perform poorly when these assumptions are inaccurate. In language games, failure may be due to disagreement in the understanding of either the semantics or pragmatics of an utterance. We model coarse uncertainty in semantics using a prior distribution of language models and uncertainty in pragmatics using the cognitive hierarchy, combining the two aspects into a single prior distribution over possible partner types. Fine-grained uncertainty in semantics is modeled using noise that is added to the embeddings of words in the language. To handle all forms of uncertainty we construct agents that learn the behavior of their partner using Bayesian inference and use this information to maximize the expected value of a heuristic function. We test this approach by constructing Bayesian agents for the game of Codenames, and show that they perform better in experiments where semantics is uncertain
Parametric Bayesian modeling offers a powerful and flexible toolbox for scientific data analysis. Yet the model, however detailed, may still be wrong, and this can make inferences untrustworthy. In this paper we study nonparametrically perturbed parametric (NPP) Bayesian models, in which a parametric Bayesian model is relaxed via a distortion of its likelihood. We analyze the properties of NPP models when the target of inference is the true data distribution or some functional of it, such as in causal inference. We show that NPP models can offer the robustness of nonparametric models while retaining the data efficiency of parametric models, achieving fast convergence when the parametric model is close to true. To efficiently analyze data with an NPP model, we develop a generalized Bayes procedure to approximate its posterior. We demonstrate our method by estimating causal effects of gene expression from single cell RNA sequencing data. NPP modeling offers an efficient approach to robust Bayesian inference and can be used to robustify any parametric Bayesian model.