BlackJAX is a library implementing sampling and variational inference algorithms commonly used in Bayesian computation. It is designed for ease of use, speed, and modularity by taking a functional approach to the algorithms' implementation. BlackJAX is written in Python, using JAX to compile and run NumpPy-like samplers and variational methods on CPUs, GPUs, and TPUs. The library integrates well with probabilistic programming languages by working directly with the (un-normalized) target log density function. BlackJAX is intended as a collection of low-level, composable implementations of basic statistical 'atoms' that can be combined to perform well-defined Bayesian inference, but also provides high-level routines for ease of use. It is designed for users who need cutting-edge methods, researchers who want to create complex sampling methods, and people who want to learn how these work.
As machine learning becomes more prominent there is a growing demand to perform several inference tasks in parallel. Running a dedicated model for each task is computationally expensive and therefore there is a great interest in multi-task learning (MTL). MTL aims at learning a single model that solves several tasks efficiently. Optimizing MTL models is often achieved by computing a single gradient per task and aggregating them for obtaining a combined update direction. However, these approaches do not consider an important aspect, the sensitivity in the gradient dimensions. Here, we introduce a novel gradient aggregation approach using Bayesian inference. We place a probability distribution over the task-specific parameters, which in turn induce a distribution over the gradients of the tasks. This additional valuable information allows us to quantify the uncertainty in each of the gradients dimensions, which can then be factored in when aggregating them. We empirically demonstrate the benefits of our approach in a variety of datasets, achieving state-of-the-art performance.
The inadequate mixing of conventional Markov Chain Monte Carlo (MCMC) methods for multi-modal distributions presents a significant challenge in practical applications such as Bayesian inference and molecular dynamics. Addressing this, we propose Diffusive Gibbs Sampling (DiGS), an innovative family of sampling methods designed for effective sampling from distributions characterized by distant and disconnected modes. DiGS integrates recent developments in diffusion models, leveraging Gaussian convolution to create an auxiliary noisy distribution that bridges isolated modes in the original space and applying Gibbs sampling to alternately draw samples from both spaces. A novel Metropolis-within-Gibbs scheme is proposed to enhance mixing in the denoising sampling step. DiGS exhibits a better mixing property for sampling multi-modal distributions than state-of-the-art methods such as parallel tempering, attaining substantially improved performance across various tasks, including mixtures of Gaussians, Bayesian neural networks and molecular dynamics.
Many machine learning applications require operating on a spatially distributed dataset. Despite technological advances, privacy considerations and communication constraints may prevent gathering the entire dataset in a central unit. In this paper, we propose a distributed sampling scheme based on the alternating direction method of multipliers, which is commonly used in the optimization literature due to its fast convergence. In contrast to distributed optimization, distributed sampling allows for uncertainty quantification in Bayesian inference tasks. We provide both theoretical guarantees of our algorithm's convergence and experimental evidence of its superiority to the state-of-the-art. For our theoretical results, we use convex optimization tools to establish a fundamental inequality on the generated local sample iterates. This inequality enables us to show convergence of the distribution associated with these iterates to the underlying target distribution in Wasserstein distance. In simulation, we deploy our algorithm on linear and logistic regression tasks and illustrate its fast convergence compared to existing gradient-based methods.
State-of-the-art methods for Bayesian inference in state-space models are (a) conditional sequential Monte Carlo (CSMC) algorithms; (b) sophisticated 'classical' MCMC algorithms like MALA, or mGRAD from Titsias and Papaspiliopoulos (2018, arXiv:1610.09641v3 [stat.ML]). The former propose $N$ particles at each time step to exploit the model's 'decorrelation-over-time' property and thus scale favourably with the time horizon, $T$ , but break down if the dimension of the latent states, $D$, is large. The latter leverage gradient-/prior-informed local proposals to scale favourably with $D$ but exhibit sub-optimal scalability with $T$ due to a lack of model-structure exploitation. We introduce methods which combine the strengths of both approaches. The first, Particle-MALA, spreads $N$ particles locally around the current state using gradient information, thus extending MALA to $T > 1$ time steps and $N > 1$ proposals. The second, Particle-mGRAD, additionally incorporates (conditionally) Gaussian prior dynamics into the proposal, thus extending the mGRAD algorithm to $T > 1$ time steps and $N > 1$ proposals. We prove that Particle-mGRAD interpolates between CSMC and Particle-MALA, resolving the 'tuning problem' of choosing between CSMC (superior for highly informative prior dynamics) and Particle-MALA (superior for weakly informative prior dynamics). We similarly extend other 'classical' MCMC approaches like auxiliary MALA, aGRAD, and preconditioned Crank-Nicolson-Langevin (PCNL) to $T > 1$ time steps and $N > 1$ proposals. In experiments, for both highly and weakly informative prior dynamics, our methods substantially improve upon both CSMC and sophisticated 'classical' MCMC approaches.
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do not fully understand how cell proliferation regulation impacts cell migration phenomena. Here, we present a minimal continuum model of cell migration with cell cycle dynamics, which includes density-dependent effects and hence can account for cell proliferation regulation. By combining minimal mathematical modelling, Bayesian inference, and recent experimental data, we quantify the impact of tissue crowding across different cell cycle stages in epithelial tissue expansion experiments. Our model suggests that cells sense local density and adapt cell cycle progression in response, during G1 and the combined S/G2/M phases, providing an explicit relationship between each cell cycle stage duration and local tissue density, which is consistent with several experimental observations. Finally, we compare our mathematical model predictions to different experiments studying cell cycle regulation and present a quantitative analysis on the impact of density-dependent regulation on cell migration patterns. Our work presents a systematic approach for investigating and analysing cell cycle data, providing mechanistic insights into how individual cells regulate proliferation, based on population-based experimental measurements.
Bayesian neural networks (BNNs) are a principled approach to modeling predictive uncertainties in deep learning, which are important in safety-critical applications. Since exact Bayesian inference over the weights in a BNN is intractable, various approximate inference methods exist, among which sampling methods such as Hamiltonian Monte Carlo (HMC) are often considered the gold standard. While HMC provides high-quality samples, it lacks interpretable summary statistics because its sample mean and variance is meaningless in neural networks due to permutation symmetry. In this paper, we first show that the role of permutations can be meaningfully quantified by a number of transpositions metric. We then show that the recently proposed rebasin method allows us to summarize HMC samples into a compact representation that provides a meaningful explicit uncertainty estimate for each weight in a neural network, thus unifying sampling methods with variational inference. We show that this compact representation allows us to compare trained BNNs directly in weight space across sampling methods and variational inference, and to efficiently prune neural networks trained without explicit Bayesian frameworks by exploiting uncertainty estimates from HMC.
Sequential Bayesian inference over predictive functions is a natural framework for continual learning from streams of data. However, applying it to neural networks has proved challenging in practice. Addressing the drawbacks of existing techniques, we propose an optimization objective derived by formulating continual learning as sequential function-space variational inference. In contrast to existing methods that regularize neural network parameters directly, this objective allows parameters to vary widely during training, enabling better adaptation to new tasks. Compared to objectives that directly regularize neural network predictions, the proposed objective allows for more flexible variational distributions and more effective regularization. We demonstrate that, across a range of task sequences, neural networks trained via sequential function-space variational inference achieve better predictive accuracy than networks trained with related methods while depending less on maintaining a set of representative points from previous tasks.
Reliable predictive uncertainty estimation plays an important role in enabling the deployment of neural networks to safety-critical settings. A popular approach for estimating the predictive uncertainty of neural networks is to define a prior distribution over the network parameters, infer an approximate posterior distribution, and use it to make stochastic predictions. However, explicit inference over neural network parameters makes it difficult to incorporate meaningful prior information about the data-generating process into the model. In this paper, we pursue an alternative approach. Recognizing that the primary object of interest in most settings is the distribution over functions induced by the posterior distribution over neural network parameters, we frame Bayesian inference in neural networks explicitly as inferring a posterior distribution over functions and propose a scalable function-space variational inference method that allows incorporating prior information and results in reliable predictive uncertainty estimates. We show that the proposed method leads to state-of-the-art uncertainty estimation and predictive performance on a range of prediction tasks and demonstrate that it performs well on a challenging safety-critical medical diagnosis task in which reliable uncertainty estimation is essential.
One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise, so for typical sample sizes there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over DAGs, but not both. In this paper we leverage the fact that it is possible to estimate the "velocity" of gene expression with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. Since our objective is to model uncertainty over discrete structures, we leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches.
Diffusion models have gained traction as powerful algorithms for synthesizing high-quality images. Central to these algorithms is the diffusion process, a set of equations which maps data to noise in a way that can significantly affect performance. In this paper, we explore whether the diffusion process can be learned from data. Our work is grounded in Bayesian inference and seeks to improve log-likelihood estimation by casting the learned diffusion process as an approximate variational posterior that yields a tighter lower bound (ELBO) on the likelihood. A widely held assumption is that the ELBO is invariant to the noise process: our work dispels this assumption and proposes multivariate learned adaptive noise (MULAN), a learned diffusion process that applies noise at different rates across an image. Specifically, our method relies on a multivariate noise schedule that is a function of the data to ensure that the ELBO is no longer invariant to the choice of the noise schedule as in previous works. Empirically, MULAN sets a new state-of-the-art in density estimation on CIFAR-10 and ImageNet and reduces the number of training steps by 50%. We provide the code, along with a blog post and video tutorial on the project page: https://s-sahoo.com/MuLAN
One of the pivotal tasks in scientific machine learning is to represent underlying dynamical systems from time series data. Many methods for such dynamics learning explicitly require the derivatives of state data, which are not directly available and can be approximated conventionally by finite differences. However, the discrete approximations of time derivatives may result in poor estimations when state data are scarce and/or corrupted by noise, thus compromising the predictiveness of the learned dynamical models. To overcome this technical hurdle, we propose a new method that learns nonlinear dynamics through a Bayesian inference of characterizing model parameters. This method leverages a Gaussian process representation of states, and constructs a likelihood function using the correlation between state data and their derivatives, yet prevents explicit evaluations of time derivatives. Through a Bayesian scheme, a probabilistic estimate of the model parameters is given by the posterior distribution, and thus a quantification is facilitated for uncertainties from noisy state data and the learning process. Specifically, we will discuss the applicability of the proposed method to several typical scenarios for dynamical systems: identification and estimation with an affine parametrization, nonlinear parametric approximation without prior knowledge, and general parameter estimation for a given dynamical system.
Estimating heterogeneous treatment effects across individuals has attracted growing attention as a statistical tool for performing critical decision-making. We propose a Bayesian inference framework that quantifies the uncertainty in treatment effect estimation to support decision-making in a relatively small sample size setting. Our proposed model places Gaussian process priors on the nonparametric components of a semiparametric model called a partially linear model. This model formulation has three advantages. First, we can analytically compute the posterior distribution of a treatment effect without relying on the computationally demanding posterior approximation. Second, we can guarantee that the posterior distribution concentrates around the true one as the sample size goes to infinity. Third, we can incorporate prior knowledge about a treatment effect into the prior distribution, improving the estimation efficiency. Our experimental results show that even in the small sample size setting, our method can accurately estimate the heterogeneous treatment effects and effectively quantify its estimation uncertainty.
Exact Bayesian inference on state-space models~(SSM) is in general untractable, and unfortunately, basic Sequential Monte Carlo~(SMC) methods do not yield correct approximations for complex models. In this paper, we propose a mixed inference algorithm that computes closed-form solutions using belief propagation as much as possible, and falls back to sampling-based SMC methods when exact computations fail. This algorithm thus implements automatic Rao-Blackwellization and is even exact for Gaussian tree models.
Federated Learning (FL) involves training a model over a dataset distributed among clients, with the constraint that each client's dataset is localized and possibly heterogeneous. In FL, small and noisy datasets are common, highlighting the need for well-calibrated models that represent the uncertainty of predictions. The closest FL techniques to achieving such goals are the Bayesian FL methods which collect parameter samples from local posteriors, and aggregate them to approximate the global posterior. To improve scalability for larger models, one common Bayesian approach is to approximate the global predictive posterior by multiplying local predictive posteriors. In this work, we demonstrate that this method gives systematically overconfident predictions, and we remedy this by proposing $\beta$-Predictive Bayes, a Bayesian FL algorithm that interpolates between a mixture and product of the predictive posteriors, using a tunable parameter $\beta$. This parameter is tuned to improve the global ensemble's calibration, before it is distilled to a single model. Our method is evaluated on a variety of regression and classification datasets to demonstrate its superiority in calibration to other baselines, even as data heterogeneity increases. Code available at https://github.com/hasanmohsin/betaPredBayesFL
The vast majority of time-series forecasting approaches require a substantial training dataset. However, many real-life forecasting applications have very little initial observations, sometimes just 40 or fewer. Thus, the applicability of most forecasting methods is restricted in data-sparse commercial applications. While there is recent work in the setting of very limited initial data (so-called `zero-shot' forecasting), its performance is inconsistent depending on the data used for pretraining. In this work, we take a different approach and devise ForecastPFN, the first zero-shot forecasting model trained purely on a novel synthetic data distribution. ForecastPFN is a prior-data fitted network, trained to approximate Bayesian inference, which can make predictions on a new time series dataset in a single forward pass. Through extensive experiments, we show that zero-shot predictions made by ForecastPFN are more accurate and faster compared to state-of-the-art forecasting methods, even when the other methods are allowed to train on hundreds of additional in-distribution data points.
Semi-implicit variational inference (SIVI) has been introduced to expand the analytical variational families by defining expressive semi-implicit distributions in a hierarchical manner. However, the single-layer architecture commonly used in current SIVI methods can be insufficient when the target posterior has complicated structures. In this paper, we propose hierarchical semi-implicit variational inference, called HSIVI, which generalizes SIVI to allow more expressive multi-layer construction of semi-implicit distributions. By introducing auxiliary distributions that interpolate between a simple base distribution and the target distribution, the conditional layers can be trained by progressively matching these auxiliary distributions one layer after another. Moreover, given pre-trained score networks, HSIVI can be used to accelerate the sampling process of diffusion models with the score matching objective. We show that HSIVI significantly enhances the expressiveness of SIVI on several Bayesian inference problems with complicated target distributions. When used for diffusion model acceleration, we show that HSIVI can produce high quality samples comparable to or better than the existing fast diffusion model based samplers with a small number of function evaluations on various datasets.
Differentiable particle filters are an emerging class of sequential Bayesian inference techniques that use neural networks to construct components in state space models. Existing approaches are mostly based on offline supervised training strategies. This leads to the delay of the model deployment and the obtained filters are susceptible to distribution shift of test-time data. In this paper, we propose an online learning framework for differentiable particle filters so that model parameters can be updated as data arrive. The technical constraint is that there is no known ground truth state information in the online inference setting. We address this by adopting an unsupervised loss to construct the online model updating procedure, which involves a sequence of filtering operations for online maximum likelihood-based parameter estimation. We empirically evaluate the effectiveness of the proposed method, and compare it with supervised learning methods in simulation settings including a multivariate linear Gaussian state-space model and a simulated object tracking experiment.
Bayesian inference allows expressing the uncertainty of posterior belief under a probabilistic model given prior information and the likelihood of the evidence. Predominantly, the likelihood function is only implicitly established by a simulator posing the need for simulation-based inference (SBI). However, the existing algorithms can yield overconfident posteriors (Hermans *et al.*, 2022) defeating the whole purpose of credibility if the uncertainty quantification is inaccurate. We propose to include a calibration term directly into the training objective of the neural model in selected amortized SBI techniques. By introducing a relaxation of the classical formulation of calibration error we enable end-to-end backpropagation. The proposed method is not tied to any particular neural model and brings moderate computational overhead compared to the profits it introduces. It is directly applicable to existing computational pipelines allowing reliable black-box posterior inference. We empirically show on six benchmark problems that the proposed method achieves competitive or better results in terms of coverage and expected posterior density than the previously existing approaches.
Surrogate models are statistical or conceptual approximations for more complex simulation models. In this context, it is crucial to propagate the uncertainty induced by limited simulation budget and surrogate approximation error to predictions, inference, and subsequent decision-relevant quantities. However, quantifying and then propagating the uncertainty of surrogates is usually limited to special analytic cases or is otherwise computationally very expensive. In this paper, we propose a framework enabling a scalable, Bayesian approach to surrogate modeling with thorough uncertainty quantification, propagation, and validation. Specifically, we present three methods for Bayesian inference with surrogate models given measurement data. This is a task where the propagation of surrogate uncertainty is especially relevant, because failing to account for it may lead to biased and/or overconfident estimates of the parameters of interest. We showcase our approach in three detailed case studies for linear and nonlinear real-world modeling scenarios. Uncertainty propagation in surrogate models enables more reliable and safe approximation of expensive simulators and will therefore be useful in various fields of applications.