Amortized Inference

State-space models (SSMs) are powerful probabilistic tools for modeling time-varying systems with latent dynamics. Inference in SSMs involves the estimation of latent states and parameters. In this work, we focus on parameter inference, which for SSMs is in general a very challenging problem due to the intractability of the likelihood. Recently, neural estimation methods, such as sequential neural likelihood (SNL), have shown promising results in Bayesian inference problems. In this paper, we show that SNL, when applied to the SSM setting, suffers important limitations, such as requiring a large amount of simulated samples to achieve a moderate performance, scaling poorly with sequence length, while not being amortized. We then introduce a novel inference algorithm called truncated-SNL (T-SNL), which addresses the limitations of SNL. Our algorithm is more accurate, more stable and robust during training, more scalable to longer temporal sequences, and can be amortized when new observations become available. Our experiments show that T-SNL is sample-efficient, robust, and flexible algorithm which outperforms other approaches.

Neural processes amortize Gaussian process inference, replacing the exact $O(n^3)$ posterior with a learned $O(n)$ map from context sets to predictive distributions. For a class of latent neural processes, we bound the Kullback--Leibler (KL) divergence between the GP and LNP predictives, decomposing it into three interpretable sources, namely label contamination as the neural process uses label values to estimate a quantity that is label-independent in the exact GP, an information bottleneck because the finite-dimensional representation cannot resolve the full context geometry, and amortization error from a single encoder network shared across all contexts. The bottleneck truncation term decays in the representation dimension $d$ as $O(e^{-cd^{2/d_x}})$ for squared-exponential kernels on $\mathbb{R}^{d_x}$ where $c > 0$ is a kernel-dependent constant and as $O(d^{-2ν/d_x})$ for Matérn-$ν$ kernels, directly linking architecture sizing to kernel smoothness and input dimension. The label contamination term is $O(1)$ in general, with only the observation-noise component decaying as $O(1/n)$, identifying a persistent cost of routing uncertainty estimation through a label-dependent representation. These results characterize the costs of amortization within the analyzed class and yield architectural recommendations to predict variance from context locations alone in the GP-amortization regime, and replace mean aggregation with second-order pooling to close the dominant amortization gap.

Survival analysis provides a powerful statistical framework for modeling time-to-event outcomes in the presence of censoring. However, selecting an appropriate estimator from the many specialized survival approaches often requires substantial methodological and domain expertise. We introduce SurvivalPFN, a prior-data fitted network that amortizes Bayesian inference for censored observations through in-context learning. SurvivalPFN is pretrained on a diverse family of synthetic, identifiable, and right-censored data-generating processes, enabling it to amortize survival analysis in a single forward pass during inference. As a result, the model adapts to the effective complexity of each dataset without task-specific training or hyperparameter tuning, avoids restrictive parametric assumptions, and produces calibrated survival distributions. In a large-scale benchmark spanning 61 datasets, 21 methods, and 5 evaluation metrics, SurvivalPFN achieves strong predictive performance and often improves upon established survival models. These results suggest that SurvivalPFN offers a principled and practical foundation model for survival analysis, with potential applications in high-impact domains such as healthcare, finance, and engineering (https://github.com/rgklab/SurvivalPFN).

We consider amortized Bayesian inference for nonlinear inverse problems in settings where only samples from the joint distribution of parameters and observations are available. Classical methods such as Markov chain Monte Carlo require solving a new inference problem for each observation, which can be computationally prohibitive when inference must be repeated many times. We propose a transport-based approach that learns an observation-dependent map pushing forward a reference measure to approximate the posterior distribution. The map is trained by minimizing an averaged energy-distance objective between the true posterior and the learned pushforward. This formulation is likelihood-free, requiring only joint samples, and avoids density evaluation, invertibility constraints, and Jacobian determinant computations. For function-space inverse problems with Gaussian priors, we parameterize the transport map as the identity plus a perturbation in the Cameron-Martin space of the prior, preserving absolute continuity with respect to the prior. In infinite-dimensional settings, the map is represented using neural operators. We illustrate the method on a finite-dimensional nonlinear inverse problem and two PDE-constrained inverse problems arising in porous medium flow and seismic inversion. The results show that the learned transport captures posterior structure, including multimodality and dominant modes, while enabling fast posterior sampling for new observations.

This paper introduces an algorithm-agnostic approach to feature-based time series clustering via amortized neural inference. By training neural networks to approximate the optimal partitioning rule from simulated data, the proposed framework reduces reliance on conventional clustering methods, such as $K$-means, $K$-medoids, or hierarchical clustering, and their associated objective functions and heuristics. Leveraging statistical features, such as autocorrelations and quantile autocorrelations, the approach learns a data-driven affinity structure from which clustering partitions can be recovered, without requiring explicit prior specification of cluster shapes or structures. In addition, one version of the method can automatically determine the number of clusters, avoiding ad-hoc selection procedures. Comprehensive empirical studies show that the proposed framework achieves competitive or superior clustering accuracy relative to traditional methods, even in challenging scenarios where competing techniques are provided with the true number of clusters. An application to financial time series of stock returns illustrates its practical utility. By reducing the need for algorithm selection and calibration, the proposed framework opens new possibilities for automated, adaptive, and data-driven clustering of temporal data across scientific and industrial domains.

Nonlinear inverse problems often trade inexpensive but fragile first-order updates against curvature-aware methods such as Gauss-Newton and Levenberg-Marquardt, which obtain stronger directions by repeatedly solving Jacobian-based linearized systems. We propose a learned alternative: amortize local inverse geometry into a reusable reverse operator. Our framework learns a bidirectional surrogate, Deceptron, and deploys it through D-IPG (Deceptron Inverse-Preconditioned Gradient), an iterative solver that pulls residual-corrected measurement-space proposals back to latent space. The key mechanism is a Jacobian Composition Penalty (JCP), which trains the reverse Jacobian to act as a local left inverse of the forward Jacobian; its runtime counterpart, RJCP, measures the same inverse-consistency error along optimization trajectories. We prove that D-IPG is first-order equivalent to damped Gauss-Newton under local pseudoinverse consistency, with deviation controlled by composition error and conditioning. Across seven PDE inverse-problem benchmarks, D-IPG outperforms standard baselines, achieves 94.8% mean success across the six-problem reliability suite, and reaches comparable or better recovery quality at up to 77x lower inference-time solve cost on the main benchmarks.

The instrumental-variables (IV) setting is standard for partial identification of causal effects when unobserved confounding makes point identification impossible. Existing approaches face methodological bottlenecks: closed-form bound estimands are required -- e.g., Balke-Pearl equations in binary IV -- and even when available, designing accurate estimators requires manual effort tailored to each estimand. While direct Bayesian inference of the causal effects, instead of the bounds, circumvents these challenges, it is often computationally intensive and suffers from high prior sensitivity or under-dispersed posteriors. As a remedy, we introduce IV-ICL, an amortized Bayesian in-context learning method that learns the marginal posterior distribution of the causal effects directly and derives bounds as its quantiles. Unlike standard variational inference that optimizes exclusive KL divergence, amortized Bayesian inference minimizes the expected inclusive KL, a mass-covering objective. We empirically observe that optimizing inclusive KL can recover the entire identified set across diverse data-generating processes, while exclusive-KL (e.g. with variational inference) of the same Bayesian formulation collapses onto a single mode and fails to cover the identified set. We evaluate IV-ICL on synthetic and semi-synthetic IV benchmarks and show it produces intervals that are more reliably valid and more informative compared to efficient semi-parametric, Bayesian, and plug-in baselines, at 20-500x lower inference time. Beyond methodology, we propose a procedure to convert randomized controlled trials into IV benchmarks with provably preserved ground-truth causal effects that enables a more realistic evaluation of partial-identification methods.

Causal sensitivity analysis aims to provide bounds for causal effect estimates in the presence of unobserved confounding. However, existing methods for causal sensitivity analysis are per-instance procedures, meaning that changes to the dataset, causal query, sensitivity level, or treatment require new computation. Here, we instead present an in-context learning approach. Specifically, we propose an amortized approach to causal sensitivity analysis based on prior-data fitted networks. A key challenge is that the sensitivity bounds are not directly available when sampling training data. To address this, we develop a general prior-data construction that is applicable across the class of generalized treatment sensitivity models. Our construction involves a Lagrangian scalarization of the objective to generate training labels for the bounds through a tradeoff between causal effect min/max-imization and sensitivity model violation, which avoids model-specific analytical derivations. We further show that, under standard convexity and linearity conditions, our objective recovers the full Pareto frontier of solutions. Empirically, we demonstrate our amortized approach across various datasets, causal queries, and sensitivity levels, where our approach achieves a test-time computation that is orders of magnitude faster than per-instance methods. To the best of our knowledge, ours is the first foundation model for in-context learning for causal sensitivity analysis.

Neural posterior estimation has emerged as a powerful tool for amortized inference, with growing adoption across scientific and applied domains. In many of these applications, the conditioning variable is a set of observations whose elements depend not only on the target but also on unknown factors shared across the set. Optimal inference therefore requires treating the set jointly, which in turn requires training the estimator at the deployment set size -- a regime where memory and compute quickly become prohibitive. We introduce a simple, theoretically grounded strategy that decouples representation learning from posterior modeling. Our method trains a mean-pool Deep Set on sets of size at most two, producing an encoder that generalizes to arbitrary set sizes. The inference head is then finetuned on pre-aggregated embeddings, making training cost essentially independent of the deployment set size N. Across scalar, image, multi-view 3D, molecular, and high-dimensional conditional generation benchmarks with N in the thousands, our approach matches or outperforms standard baselines at a fraction of the compute.

Probabilistic conditioning is concerned with the identification of a distribution of a random variable $X$ given a random variable $Y$. It is a cornerstone of scientific and engineering applications where modeling uncertainty is key. This problem has traditionally been addressed in machine learning by directly learning the conditional distribution of a fixed joint distribution. This paper introduces a novel perspective: we propose to solve the conditioning problem by identifying a single operator that maps any joint density to its conditional, thus amortizing over joint-conditional pairs. We establish that the conditioning operator can be approximated to arbitrary accuracy by neural operators. Our proof relies on new results establishing continuity of the conditioning operator over suitable classes of densities. Finally, we learn the conditioning map for a class of Gaussian mixtures using neural operators, illustrating the promise of our framework. This work provides the theoretical underpinnings for general-purpose, amortized methods for probabilistic conditioning, such as foundation models for Bayesian inference.

Bayesian predictive inference propagates parameter uncertainty to quantities of interest through the posterior-predictive distribution. In practice, this is typically performed using a two-stage procedure: first approximating the posterior distribution of model parameters, and then propagating posterior samples through the predictive model via Monte Carlo simulation. This sequential workflow can be computationally demanding, particularly for high-fidelity models such as those governed by partial differential equations. We propose a variational Bayesian framework that directly targets the posterior-predictive distribution and jointly learns variational approximations of both the posterior and the corresponding predictive distribution. The formulation introduces a variational upper bound on the Kullback--Leibler divergence together with moment-based regularization terms. The variational distributions are trained in an amortized manner, shifting computational effort to an offline stage and enabling efficient online inference. Numerical experiments ranging from analytical benchmarks to a finite-element solid mechanics problem demonstrate that the proposed method achieves more accurate predictive distributions than conventional two-stage variational inference, while substantially reducing the cost of online predictive inference.

Accurate condition monitoring of industrial equipment requires inferring latent degradation parameters from indirect sensor measurements under uncertainty. While traditional Bayesian methods like Markov Chain Monte Carlo (MCMC) provide rigorous uncertainty quantification, their heavy computational bottlenecks render them impractical for real-time process control. To overcome this limitation, we propose an AI-driven framework utilizing Simulation-Based Inference (SBI) powered by amortized neural posterior estimation to diagnose complex failure modes in heat exchangers. By training neural density estimators on a simulated dataset, our approach learns a direct, likelihood-free mapping from thermal-fluid observations to the full posterior distribution of degradation parameters. We benchmark this framework against an MCMC baseline across various synthetic fouling and leakage scenarios, including challenging low-probability, sparse-event failures. The results show that SBI achieves comparable diagnostic accuracy and reliable uncertainty quantification, while accelerating inference time by a factor of82$\times$ compared to traditional sampling. The amortized nature of the neural network enables near-instantaneous inference, establishing SBI as a highly scalable, real-time alternative for probabilistic fault diagnosis and digital twin realization in complex engineering systems.

Modeling high-dimensional dependencies while keeping likelihoods tractable remains challenging. Classical vine-copula pipelines are interpretable but can be expensive, while many neural estimators are flexible but less structured. In this work, we propose Vine Denoising Copula (VDC), an amortized vine-copula pipeline for continuous-data, simplified-vine dependence modeling. VDC trains a single bivariate denoising model and reuses it across all vine edges. For each edge, given pseudo-observations, the model predicts a piecewise-constant density grid. We then apply an IPFP/Sinkhorn projection that normalizes mass and drives the marginals to uniformity. This preserves the tractable vine-likelihood structure and the usual copula interpretation while replacing repeated per-edge optimization with GPU inference. Across synthetic and real-data benchmarks, VDC delivers strong bivariate density accuracy, competitive MI/TC estimation, and faster high-dimensional vine fitting. These gains make explicit information estimation and dependence decomposition feasible when repeated vine fitting would otherwise be costly, while conditional downstream tasks remain a limitation.

Neural fields, also known as implicit neural representations (INRs), offer a powerful framework for modeling continuous geometry, but their effectiveness in high-dimensional scientific settings is limited by slow convergence and scaling challenges. In this study, we extend INR models to handle spatiotemporal and multivariate signals and show how INR features can be transferred across scientific signals to enable efficient and scalable representation across time and ensemble runs in an amortized fashion. Across controlled transformation regimes (e.g., geometric transformations and localized perturbations of synthetic fields) and high-fidelity scientific domains-including turbulent flows, fluid-material impact dynamics, and astrophysical systems-we show that transferable features improve not only signal fidelity but also the accuracy of derived geometric and physical quantities, including density gradients and vorticity. In particular, transferable features reduce iterations to reach target reconstruction quality by up to an order of magnitude, increase early-stage reconstruction quality by multiple dB (with gains exceeding 10 dB in some cases), and consistently improve gradient-based physical accuracy.

Selection bias arises when the probability that an observation enters a dataset depends on variables related to the quantities of interest, leading to systematic distortions in estimation and uncertainty quantification. For example, in epidemiological or survey settings, individuals with certain outcomes may be more likely to be included, resulting in biased prevalence estimates with potentially substantial downstream impact. Classical corrections, such as inverse-probability weighting or explicit likelihood-based models of the selection process, rely on tractable likelihoods, which limits their applicability in complex stochastic models with latent dynamics or high-dimensional structure. Simulation-based inference enables Bayesian analysis without tractable likelihoods but typically assumes missingness at random and thus fails when selection depends on unobserved outcomes or covariates. Here, we develop a bias-aware simulation-based inference framework that explicitly incorporates selection into neural posterior estimation. By embedding the selection mechanism directly into the generative simulator, the approach enables amortized Bayesian inference without requiring tractable likelihoods. This recasting of selection bias as part of the simulation process allows us to both obtain debiased estimates and explicitly test for the presence of bias. The framework integrates diagnostics to detect discrepancies between simulated and observed data and to assess posterior calibration. The method recovers well-calibrated posterior distributions across three statistical applications with diverse selection mechanisms, including settings in which likelihood-based approaches yield biased estimates. These results recast the correction of selection bias as a simulation problem and establish simulation-based inference as a practical and testable strategy for parameter estimation under selection bias.

Discrete choice models are fundamental tools in management science, economics, and marketing for understanding and predicting decision-making. Logit-based models are dominant in applied work, largely due to their convenient closed-form expressions for choice probabilities. However, they impose restrictive assumptions on the stochastic utility component, constraining our ability to capture realistic substitution patterns. We propose an amortized inference approach that relies on a neural network emulator to approximate choice probabilities for general error distributions, including those with correlated errors. We develop a specialized neural network architecture designed to respect the invariance properties of discrete choice models. We provide group-theoretic foundations for the architecture, including a proof of universal approximation given a minimal set of invariant features. Once trained, the emulator enables rapid likelihood evaluation and gradient computation. We use Sobolev training, augmenting the likelihood loss with a gradient-matching penalty, so that the emulator learns both choice probabilities and their derivatives. We show that emulator-based maximum likelihood estimators are consistent and asymptotically normal under mild approximation conditions, and we provide sandwich standard errors that remain valid for a psuedo-true parameter even with imperfect likelihood approximation. Simulations show significant gains over the GHK simulator in accuracy and speed.

Maximum inner product search (MIPS) is a crucial subroutine in machine learning, requiring the identification of a vector taken within a database (the keys) that best aligns with a given query. We propose amortized MIPS: a regression-based approach that trains neural networks to directly predict MIPS solutions, amortizing the cost of repeatedly solving MIPS for queries drawn from a known distribution over a fixed key database. Our key insight is that the MIPS value function is the \emph{support} function of the set of keys, a well-studied convex function whose gradient yields the optimal key. This motivates two complementary amortized models: SupportNet, an input-convex neural network trained to regress the support function, and KeyNet, a vector-valued network that directly regresses the optimal key. SupportNet can serve as a cluster router, steering queries toward relevant database partitions, while KeyNet can be used as a drop-in replacement for the original query, fed directly to off-the-shelf indexing pipelines. Our experiments on the BEIR benchmark show that, for document embeddings, learned \SupportNet{}s and \KeyNet{}s significantly improve IVF match rates when accounting for compute effort, whether measured in FLOPs, number of probes, or wall-clock time. Our code is available at: https://github.com/apple/ml-amips.

Since the turn of the century, approximate Bayesian inference has steadily evolved as new computational techniques have been incorporated to handle increasingly complex, large-scale predictive problems. The recent success of deep neural networks and foundation models has now given rise to a new paradigm in statistical modeling, in which Bayesian inference can be amortized through large-scale learned predictors. In amortized inference, substantial computation is required at the beginning to train a neural network, but it can subsequently produce approximate posteriors or predictions at much lower computational cost across a wide range of tasks. While the typical Bayesian inference procedures are computationally expensive due to repeated likelihood calculations and Monte Carlo steps for each new dataset, amortized inference provides a much lower computational cost at deployment. Despite the growing popularity of amortized inference, its statistical interpretation and position within Bayesian inference remain poorly explored. In this paper, we present a statistical perspective on several major neural architectures, including feedforward networks, Deep Sets, and Transformers, and examine how they naturally support amortized Bayesian inference. We explore how these models perform structured approximation and also probabilistic reasoning in ways that yield controlled generalization error throughout a wide range of deployment scenarios, and how these properties can be harnessed for Bayesian computation. Via simulation studies, we evaluate the accuracy, robustness, and uncertainty quantification of amortized inference across varying sample sizes, varying noise distributional families, varying sparsity levels, and multimodality, highlighting its strengths and limitations.

We consider problems of parameter estimation where design variables can be actively optimized to maximize information gain. To this end, we introduce JADAI, a framework that jointly amortizes Bayesian adaptive design and inference by training a policy, a history network, and an inference network end-to-end. The networks minimize a generic loss that aggregates incremental reductions in posterior error along experimental sequences. Inference networks are instantiated with diffusion-based posterior estimators that can approximate high-dimensional and multimodal posteriors at every experimental step. Across standard adaptive design benchmarks, JADAI achieves superior or competitive performance.

Amortized inference is the task of training a parametric model, such as a neural network, to approximate a distribution with a given unnormalized density where exact sampling is intractable. When sampling is implemented as a sequential decision-making process, reinforcement learning (RL) methods, such as generative flow networks, can be used to train the sampling policy. Off-policy RL training facilitates the discovery of diverse, high-reward candidates, but existing methods still face challenges in efficient exploration. We propose to use an adaptive training distribution (the \teacher) to guide the training of the primary amortized sampler (the \student). The \teacher, an auxiliary behavior model, is trained to sample high-loss regions of the \student and can generalize across unexplored modes, thereby enhancing mode coverage by providing an efficient training curriculum. We validate the effectiveness of this approach in a synthetic environment designed to present an exploration challenge, two diffusion-based sampling tasks, and four biochemical discovery tasks demonstrating its ability to improve sample efficiency and mode coverage. Source code is available at https://github.com/alstn12088/adaptive-teacher.

Autoregressive large language models (LLMs) compress knowledge from their training data through next-token conditional distributions. This limits tractable querying of this knowledge to start-to-end autoregressive sampling. However, many tasks of interest -- including sequence continuation, infilling, and other forms of constrained generation -- involve sampling from intractable posterior distributions. We address this limitation by using amortized Bayesian inference to sample from these intractable posteriors. Such amortization is algorithmically achieved by fine-tuning LLMs via diversity-seeking reinforcement learning algorithms: generative flow networks (GFlowNets). We empirically demonstrate that this distribution-matching paradigm of LLM fine-tuning can serve as an effective alternative to maximum-likelihood training and reward-maximizing policy optimization. As an important application, we interpret chain-of-thought reasoning as a latent variable modeling problem and demonstrate that our approach enables data-efficient adaptation of LLMs to tasks that require multi-step rationalization and tool use.

We present a new algorithm for amortized inference in sparse probabilistic graphical models (PGMs), which we call $Δ$-amortized inference ($Δ$-AI). Our approach is based on the observation that when the sampling of variables in a PGM is seen as a sequence of actions taken by an agent, sparsity of the PGM enables local credit assignment in the agent's policy learning objective. This yields a local constraint that can be turned into a local loss in the style of generative flow networks (GFlowNets) that enables off-policy training but avoids the need to instantiate all the random variables for each parameter update, thus speeding up training considerably. The $Δ$-AI objective matches the conditional distribution of a variable given its Markov blanket in a tractable learned sampler, which has the structure of a Bayesian network, with the same conditional distribution under the target PGM. As such, the trained sampler recovers marginals and conditional distributions of interest and enables inference of partial subsets of variables. We illustrate $Δ$-AI's effectiveness for sampling from synthetic PGMs and training latent variable models with sparse factor structure.