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Probabilistic Methods · Bayesian Models and Methods

Dario Coscia, Max Welling, Nicola Demo, Gianluigi Rozza

Autoregressive and recurrent networks have achieved remarkable progress across various fields, from weather forecasting to molecular generation and Large Language Models. Despite their strong predictive capabilities, these models lack a rigorous framework for addressing uncertainty, which is key in scientific applications such as PDE solving, molecular generation and machine l earning Force Fields.To address this shortcoming we present BARNN: a variational Bayesian Autoregressive and Recurrent Neural Network. BARNNs aim to provide a principled way to turn any autoregressive or recurrent model into its Bayesian version. BARNN is based on the variational dropout method, allowing to apply it to large recurrent neural networks as well. We also introduce a temporal version of the“Variational Mixtures of Posteriors” prior (tVAMP-prior) to make Bayesian inference efficient and well-calibrated. Extensive experiments on PDE modelling and molecular generation demonstrate that BARNN not only achieves comparable or superior accuracy compared to existing methods, but also excels in uncertainty quantification and modelling long-range dependencies.

Applications · Health / Medicine

Alexander Capstick, Rahul G. Krishnan, Payam Barnaghi

Large language models (LLMs) acquire a breadth of information across various domains. However, their computational complexity, cost, and lack of transparency often hinder their direct application for predictive tasks where privacy and interpretability are paramount. In fields such as healthcare, biology, and finance, specialised and interpretable linear models still hold considerable value. In such domains, labelled data may be scarce or expensive to obtain. Well-specified prior distributions over model parameters can reduce the sample complexity of learning through Bayesian inference; however, eliciting expert priors can be time-consuming. We therefore introduce AutoElicit to extract knowledge from LLMs and construct priors for predictive models. We show these priors are informative and can be refined using natural language. We perform a careful study contrasting AutoElicit with in-context learning and demonstrate how to perform model selection between the two methods. We find that AutoElicit yields priors that can substantially reduce error over uninformative priors, using fewer labels, and consistently outperform in-context learning. We show that AutoElicit saves over 6 months of labelling effort when building a new predictive model for urinary tract infections from sensor recordings of people living with dementia.

Probabilistic Methods · Bayesian Models and Methods

Alan Amin, Andres Potapczynski, Andrew Wilson

To understand how genetic variants in human genomes manifest in phenotypes - traits like height or diseases like asthma - geneticists have sequenced and measured hundreds of thousands of individuals. Geneticists use this data to build models that predict how a genetic variant impacts phenotype given genomic features of the variant, like DNA accessibility or the presence of nearby DNA-bound proteins. As more data and features become available, one might expect predictive models to improve. Unfortunately, training these models is bottlenecked by the need to solve expensive linear algebra problems because variants in the genome are correlated with nearby variants, requiring inversion of large matrices. Previous methods have therefore been restricted to fitting small models, and fitting simplified summary statistics, rather than the full likelihood of the statistical model. In this paper, we leverage modern fast linear algebra techniques to develop DeepWAS (Deep genome Wide Association Studies), a method to train large and flexible neural network predictive models to optimize likelihood. Surprisingly, we find that larger models only improve performance when using our full likelihood approach; when trained by fitting traditional summary statistics, larger models perform no better than small ones. We find larger models trained on more features make better predictions, potentially improving disease predictions and therapeutic target identification.

Applications · Time Series

Abdelhakim Benechehab, Vasilii Feofanov, Giuseppe Paolo, Albert Thomas, Maurizio Filippone, Balázs Kégl

Pre-trained foundation models (FMs) have shown exceptional performance in univariate time series forecasting tasks. However, several practical challenges persist, including managing intricate dependencies among features and quantifying uncertainty in predictions. This study aims to tackle these critical limitations by introducing **adapters**—feature-space transformations that facilitate the effective use of pre-trained univariate time series FMs for multivariate tasks. Adapters operate by projecting multivariate inputs into a suitable latent space and applying the FM independently to each dimension. Inspired by the literature on representation learning and partially stochastic Bayesian neural networks, we present a range of adapters and optimization/inference strategies. Experiments conducted on both synthetic and real-world datasets confirm the efficacy of adapters, demonstrating substantial enhancements in forecasting accuracy and uncertainty quantification compared to baseline methods. Our framework, **AdaPTS**, positions adapters as a modular, scalable, and effective solution for leveraging time series FMs in multivariate contexts, thereby promoting their wider adoption in real-world applications. We release the code at https://github.com/abenechehab/AdaPTS.

Probabilistic Methods · Bayesian Models and Methods

Jake Snell, Thomas Griffiths

As machine learning-based prediction systems are increasingly used in high-stakes situations, it is important to understand how such predictive models will perform upon deployment. Distribution-free uncertainty quantification techniques such as conformal prediction provide guarantees about the loss black-box models will incur even when the details of the models are hidden. However, such methods are based on frequentist probability, which unduly limits their applicability. We revisit the central aspects of conformal prediction from a Bayesian perspective and thereby illuminate the shortcomings of frequentist guarantees. We propose a practical alternative based on Bayesian quadrature that provides interpretable guarantees and offers a richer representation of the likely range of losses to be observed at test time.

Probabilistic Methods · Bayesian Models and Methods

Stefano Cortinovis, Francois Caron

Prediction-powered inference (PPI) enables valid statistical inference by combining experimental data with machine learning predictions. When a sufficient number of high-quality predictions is available, PPI results in more accurate estimates and tighter confidence intervals than traditional methods. In this paper, we propose to inform the PPI framework with prior knowledge on the quality of the predictions. The resulting method, which we call frequentist, assisted by Bayes, PPI (FAB-PPI), improves over PPI when the observed prediction quality is likely under the prior, while maintaining its frequentist guarantees. Furthermore, when using heavy-tailed priors, FAB-PPI adaptively reverts to standard PPI in low prior probability regions. We demonstrate the benefits of FAB-PPI in real and synthetic examples.

Probabilistic Methods · Variational Inference

Ngoc Quan Pham, Tuan Truong, Quyen Tran, Tan Nguyen, Dinh Phung, Trung Le

We introduce Interactive Bayesian Distributional Robustness (IBDR), a novel Bayesian inference framework that allows modeling the interactions between particles, thereby enhancing ensemble quality through increased particle diversity. IBDR is grounded in a generalized theoretical framework that connects the distributional population loss with the approximate posterior, motivating a practical dual optimization procedure that enforces distributional robustness while fostering particle diversity. We evaluate IBDR's performance against various baseline methods using the VTAB-1K benchmark and the common reasoning language task. The results consistently show that IBDR outperforms these baselines, underscoring its effectiveness in real-world applications.

General Machine Learning · Clustering

Arhit Chakrabarti, Yang Ni, Debdeep Pati, Bani Mallick

We consider the problem of clustering grouped data for which the observations may include group-specific variables in addition to the variables that are shared across groups. This type of data is quite common; for example, in cancer genomic studies, molecular information is available for all cancers whereas cancer-specific clinical information may only be available for certain cancers. Existing grouped clustering methods only consider the shared variables but ignore valuable information from the group-specific variables. To allow for these group-specific variables to aid in the clustering, we propose a novel Bayesian nonparametric approach, termed global-local (GLocal) Dirichlet process, that models the "global-local" structure of the observations across groups. We characterize the GLocal Dirichlet process using the stick-breaking representation and the representation as a limit of a finite mixture model. We theoretically quantify the approximation errors of the truncated prior, the corresponding finite mixture model, and the associated posterior distribution. We develop a fast variational Bayes algorithm for scalable posterior inference, which we illustrate with extensive simulations and a TCGA pan-gastrointestinal cancer dataset.

Probabilistic Methods · Bayesian Models and Methods

Siddarth Venkatraman, Mohsin Hasan, Minsu Kim, Luca Scimeca, Marcin Sendera, Yoshua Bengio, Glen Berseth, Nikolay Malkin

Any well-behaved generative model over a variable $\mathbf{x}$ can be expressed as a deterministic transformation of an exogenous (‘*outsourced'*) Gaussian noise variable $\mathbf{z}$: $\mathbf{x}=f_\theta(\mathbf{z})$. In such a model (*eg*, a VAE, GAN, or continuous-time flow-based model), sampling of the target variable $\mathbf{x} \sim p_\theta(\mathbf{x})$ is straightforward, but sampling from a posterior distribution of the form $p(\mathbf{x}\mid\mathbf{y}) \propto p_\theta(\mathbf{x})r(\mathbf{x},\mathbf{y})$, where $r$ is a constraint function depending on an auxiliary variable $\mathbf{y}$, is generally intractable.We propose to amortize the cost of sampling from such posterior distributions with diffusion models that sample a distribution in the noise space ($\mathbf{z}$). These diffusion samplers are trained by reinforcement learning algorithms to enforce that the transformed samples $f_\theta(\mathbf{z})$ are distributed according to the posterior in the data space ($\mathbf{x}$). For many models and constraints, the posterior in noise space is smoother than in data space, making it more suitable for amortized inference. Our method enables conditional sampling under unconditional GAN, (H)VAE, and flow-based priors, comparing favorably with other inference methods. We demonstrate the proposed ___outsourced diffusion sampling___ in several experiments with large pretrained prior models: conditional image generation, reinforcement learning with human feedback, and protein structure generation.

Probabilistic Methods · Bayesian Models and Methods

Jacopo Talpini, Marco Savi, Giovanni Neglia

One-Shot Federated Learning (FL) is a recent paradigm that enables multiple clients to cooperatively learn a global model in a single round of communication with a central server. In this paper, we analyze the One-Shot FL problem through the lens of Bayesian inference and propose FedBEns, an algorithm that leverages the inherent multimodality of local loss functions to find better global models.Our algorithm leverages a mixture of Laplace approximations for the clients' local posteriors, which the server then aggregates to infer the global model. We conduct extensive experiments on various datasets, demonstrating that the proposed method outperforms competing baselines that typically rely on unimodal approximations of the local losses.

Deep Learning · Large Language Models

Xinyue Zeng, Haohui Wang, Junhong Lin, Jun Wu, Tyler Cody, Dawei Zhou

The proliferation of open-sourced Large Language Models (LLMs) and diverse downstream tasks necessitates efficient model selection, given the impracticality of fine-tuning all candidates due to computational constraints. Despite the recent advances in LLM selection, a fundamental research question largely remains nascent: *how can we model the dynamic behaviors of LLMs during fine-tuning, thereby enhancing our understanding of their generalization performance across diverse downstream tasks?* In this work, we propose a novel theoretical framework that provides a proper lens to assess the generalization capabilities of LLMs, thereby enabling accurate and efficient LLM selection for downstream applications. In particular, we first derive a *PAC-Bayesian Generalization Bound* that unveils fine-tuning dynamics of LLMs and then introduce *LensLLM*, a Neural Tangent Kernel (NTK)-based Rectified Scaling Model that enables accurate performance predictions across diverse tasks while maintaining computational efficiency. Extensive empirical results on 3 large-scale benchmarks demonstrate that our model achieves up to 91.1% accuracy and reduces up to 88.5% computational cost in LLM selection, outperforming 5 state-of-the-art methods. We open-source our proposed *LensLLM* model and corresponding results at [LensLLM.io](https://github.com/Susan571/LENSLLM.git).

Applications · Chemistry, Physics, and Earth Sciences

Rohit Sonker, Alexandre Capone, Andrew Rothstein, Hiro Kaga, Egemen Kolemen, Jeff Schneider

Machine learning algorithms often struggle to control complex real-world systems. In the case of nuclear fusion, these challenges are exacerbated, as the dynamics are notoriously complex, data is poor, hardware is subject to failures, and experiments often affect dynamics beyond the experiment's duration. Existing tools like reinforcement learning, supervised learning, and Bayesian optimization address some of these challenges but fail to provide a comprehensive solution. To overcome these limitations, we present a multi-scale Bayesian optimization approach that integrates a high-frequency data-driven dynamics model with a low-frequency Gaussian process. By updating the Gaussian process between experiments, the method rapidly adapts to new data, refining the predictions of the less reliable dynamical model. We validate our approach by controlling tearing instabilities in the DIII-D nuclear fusion plant. Offline testing on historical data shows that our method significantly outperforms several baselines. Results on live experiments on the DIII-D tokamak, conducted under high-performance plasma scenarios prone to instabilities, shows a 50\% success rate — marking a 117\% improvement over historical outcomes.

Deep Learning · Sequential Models, Time series

Mehmet Yiğit Balık, Maksim Sinelnikov, Priscilla Ong, Harri Lähdesmäki

High-dimensional time-series datasets are common in domains such as healthcare and economics. Variational autoencoder (VAE) models, where latent variables are modeled with a Gaussian process (GP) prior, have become a prominent model class to analyze such correlated datasets. However, their applications are challenged by the inherent cubic time complexity that requires specific GP approximation techniques, as well as the general challenge of modeling both shared and individual-specific correlations across time. Though inducing points enhance GP prior VAE scalability, optimizing them remains challenging, especially since discrete covariates resist gradient‑based methods. In this work, we propose a scalable basis function approximation technique for GP prior VAEs that mitigates these challenges and results in linear time complexity, with a global parametrization that eliminates the need for amortized variational inference and the associated amortization gap, making it well-suited for conditional generation tasks where accuracy and efficiency are crucial. Empirical evaluations on synthetic and real-world benchmark datasets demonstrate that our approach not only improves scalability and interpretability but also drastically enhances predictive performance.

Position · Methodology

Samuel Gabriel Müller, Arik Reuter, Noah Hollmann, David Rügamer, Frank Hutter

Training neural networks on randomly generated artificial datasets yields Bayesian models that capture the prior defined by the dataset-generating distribution.Prior-data Fitted Networks (PFNs) are a class of methods designed to leverage this insight.In an era of rapidly increasing computational resources for pre-training and a near stagnation in the generation of new real-world data in many applications, PFNs are poised to play a more important role across a wide range of applications.They enable the efficient allocation of pre-training compute to low-data scenarios.Originally applied to small Bayesian modeling tasks, the field of PFNs has significantly expanded to address more complex domains and larger datasets. This position paper argues that PFNs and other amortized inference approaches represent the future of Bayesian inference, leveraging amortized learning to tackle data-scarce problems. We thus believe they are a fruitful area of research. In this position paper, we explore their potential and directions to address their current limitations.

Probabilistic Methods

Arik Reuter, Tim G. J. Rudner, Vincent Fortuin, David Rügamer

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 and enables us to infer complex posterior distributions for models 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 that do not operate in context. The source code for this paper is available at https://github.com/ArikReuter/ICL_for_Full_Bayesian_Inference

Probabilistic Methods · Bayesian Models and Methods

Pankaj Bhagwat, Linglong Kong, Bei Jiang

Conformal prediction has emerged as a popular technique for facilitating valid predictive inference across a spectrum of machine learning models, under minimal assumption of exchangeability. Recently, Hoff (2023) showed that full conformal Bayes provides the most efficient prediction sets (smallest by expected volume) among all prediction sets that are valid at the $(1 - \alpha)$ level if the model is correctly specified. However, a critical issue arises when the Bayesian model itself may be mis-specified, resulting in prediction interval that might be suboptimal, even though it still enjoys the frequentist coverage guarantee. To address this limitation, we propose an innovative solution that combines Bayesian model averaging (BMA) with conformal prediction. This hybrid not only leverages the strengths of Bayesian conformal prediction but also introduces a layer of robustness through model averaging. Theoretically, we prove that the resulting prediction interval will converge to the optimal level of efficiency, if the true model is included among the candidate models. This assurance of optimality, even under potential model uncertainty, provides a significant improvement over existing methods, ensuring more reliable and precise uncertainty quantification.

Applications · Chemistry and Drug Discovery

Hanlin Wu, Yuxuan Song, Jingjing Gong, Ziyao Cao, Yawen Ouyang, Jianbing Zhang, Hao Zhou, Wei-Ying Ma, Jingjing Liu

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song, et al.,2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., 200x speedup (10 v.s. 2000 steps network forwards) compared with previous Diffusion-based methods on MP-20 dataset.

Applications · Robotics

Guanxing Lu, Ziwei Wang, Changliu Liu, Jiwen Lu, Yansong Tang

Embodied Instruction Following (EIF) requires agents to complete human instruction by interacting objects in complicated surrounding environments. Conventional methods directly consider the sparse human instruction to generate action plans for agents, which usually fail to achieve human goals because of the instruction incoherence in action descriptions. On the contrary, we propose ThinkBot that reasons the thought chain in human instruction to recover the missing action descriptions, so that the agent can successfully complete human goals by following the coherent instruction. Specifically, we first design an instruction completer based on large language models to recover the missing actions with interacted objects between consecutive human instruction, where the perceived surrounding environments and the completed sub-goals are considered for instruction completion. Based on the partially observed scene semantic maps, we present an object localizer to infer the position of interacted objects and the related Bayesian uncertainty for close-loop planning. Extensive experiments in the simulated environment show that our ThinkBot outperforms the state-of-the-art EIF methods by a sizable margin in both success rate and execution efficiency. Project page: https://guanxinglu.github.io/thinkbot/.

Deep Learning · Generative Models and Autoencoders

Siddharth Ramchandran, Manuel Haussmann, Harri Lähdesmäki

Bayesian optimisation (BO) using a Gaussian process (GP)-based surrogate model is a powerful tool for solving black-box optimisation problems but does not scale well to high-dimensional data. Previous works have proposed to use variational autoencoders (VAEs) to project high-dimensional data onto a low-dimensional latent space and to implement BO in the inferred latent space. In this work, we propose a conditional generative model for efficient high-dimensional BO that uses a GP surrogate model together with GP prior VAEs. A GP prior VAE extends the standard VAE by conditioning the generative and inference model on auxiliary covariates, capturing complex correlations across samples with a GP. Our model incorporates the observed target quantity values as auxiliary covariates learning a structured latent space that is better suited for the GP-based BO surrogate model. It handles partially observed auxiliary covariates using a unifying probabilistic framework and can also incorporate additional auxiliary covariates that may be available in real-world applications. We demonstrate that our method improves upon existing latent space BO methods on simulated datasets as well as on commonly used benchmarks.

Deep Learning · Generative Models and Autoencoders

Ye Yuan, Can Chen, Christopher Pal, Xue Liu

In offline multi-objective optimization (MOO), we leverage an offline dataset of designs and their associated labels to simultaneously minimize multiple objectives. This setting more closely mirrors complex real-world problems compared to single-objective optimization. Recent works mainly employ evolutionary algorithms and Bayesian optimization, with limited attention given to the generative modeling capabilities inherent in such data. In this study, we explore generative modeling in offline MOO through flow matching, noted for its effectiveness and efficiency. We introduce \textit{ParetoFlow}, specifically designed to guide flow sampling to approximate the Pareto front. Traditional predictor~(classifier) guidance is inadequate for this purpose because it models only a single objective. In response, we propose a \textit{multi-objective predictor guidance} module that assigns each sample a weight vector, representing a weighted distribution across multiple objective predictions. A local filtering scheme is introduced to address non-convex Pareto fronts. These weights uniformly cover the entire objective space, effectively directing sample generation towards the Pareto front. Since distributions with similar weights tend to generate similar samples, we introduce a \textit{neighboring evolution} module to foster knowledge sharing among neighboring distributions. This module generates offspring from these distributions, and selects the most promising one for the next iteration. Our method achieves state-of-the-art performance across various tasks. Our code is available.