Amortized Inference

Probing the hypothesis space after seeing the data remains valid under possibilistic inferential models (IMs), provided the significance level stays fixed. The price is computation, as each plausibility is a supremum of the possibility contour over the hypothesis, and the contour itself is approximated at each queried parameter value. We propose a possibilistic radial transport, which hides the contour value of a parameter in the radius of its source point. When a transport that maximizes within-shell entropy is picked, sampling parameters covering a confidence cut becomes a matter of truncating the radius. We provide a deep learning algorithm that enforces the contour depth condition while maximizing the entropy within each shell. Our amortization makes coverage and power assessments of the learned approximation practical as well as predictive check of new datasets. We also use the sampler to construct a Bel-Pl spectrum for comparing and selecting interpretable hypotheses that satisfy a prescribed Bel-Pl decision criterion. In simulations the learned contours match or improve on ellipsoidal approximations to the cuts, while the coverage and power track the exact reference. Finally, we probe hypotheses about ovarian aging using synthetic AMH records, asking for each woman how many more years her median AMH level will remain above a specified reference value.

Standard causal identification methods often assume no unmeasured confounding and can fail when relevant confounders are unobserved. Proximal causal inference instead uses proxy variables to identify effects under hidden confounding. However, nonparametric proximal estimation can be challenging in practice: recovering causal estimands such as the conditional average treatment effect (CATE) requires solving an ill-posed integral equation that is data-hungry, hyperparameter-sensitive, and optimization-unstable. Bayesian inference for such models provides a desirable alternative, mitigating these difficulties by regularizing through the prior. However, computing a posterior is itself challenging, as a typical likelihood function will include latent variables. Following the recent success of tabular foundation models in backdoor, instrumental variable, and frontdoor settings, we propose that prior-data fitted networks (PFNs) are uniquely suited to resolve this bottleneck. Indeed, by training on synthetic data sampled from compliant structural causal models with access to oracle counterfactuals, we simplify the task substantially, amortizing the implied Bayesian operator inversion into a single transformer forward pass. Compared to prior literature that focuses primarily on point estimation, our model, ProximalFM, explicitly targets the Bayesian posterior distribution of the CATE. One unique aspect of this problem is that we need to provide Monte Carlo estimates of the oracle CATEs, leading to a novel variation of PFNs that accounts for the added stochastic error. Across a diverse suite of proximal regimes, ProximalFM achieves consistently strong CATE-estimation performance without dataset-specific tuning, with its largest advantage when latent confounding is substantial and the proxies are weakly informative; it also provides fast inference through a single amortized forward pass.

Many machine learning methods aim to approximate the lower-dimensional manifold on which the data lives. A desirable feature of such methods is that they should capture the epistemic uncertainty of this learned manifold. One model that achieves this is the Gaussian Process Latent Variable Model, in which a Gaussian Process (GP) mapping from the latent space provides an estimate of the uncertainty of the manifold. However, the effectiveness of this uncertainty estimation is limited by the mean-field variational approximation between the GP inducing points and the latent variables. In this work, we apply Amortized Structured Stochastic Variational Inference to allow the variational posterior for the latent space to be conditionally dependent on the value of the inducing points. We demonstrate that this more flexible variational posterior improves several metrics relating to the reconstruction of points on the data manifold.

We develop a general method for amortized Bayesian inference on multilevel models of arbitrary structure. Given a generative model specified as a directed acyclic graph, our method automatically derives valid factorizations of the joint posterior and matching neural network architectures. The key steps, graph expansion and graph inversion, yield an inverse graph that determines how inference networks are stacked and conditioned, producing factorizations that amortize over the number of groups and the number of observations within each group. Unlike approaches that simplify the dependency structure to speed up learning or inference, our method preserves all conditional independence and exchangeability assumptions of the generative model. Across three case studies, it closely matches gold-standard samplers on models with more than 6,500 parameters while reducing inference to a near-instant forward pass once trained.

Casting Bayesian inference as a neural network optimization problem targeting an amortized posterior is attractive, as it extends to otherwise intractable statistical models and offers near instantaneous inference for new datasets after prepaying the training cost. Although theory guarantees faithfulness under ideal convergence, practical amortized inference still requires iterating over architectures and optimization choices and ultimately ``satisficing'' under finite simulation, compute, and time budgets. Even the best-performing solution may thus retain avoidable representation gaps that typically require problem-specific fixes. Here, we propose a generic alternative which improves training dynamics with auxiliary guidance losses applied to internal representations. Specifically, we show how such guidance leads to faster convergence when training data is abundant and to better performance when it is scarce. We formalize representation gaps as getting stuck in a local optimum at the information bottleneck between the parts of the network tasked with feature learning and those tasked with conditional distribution learning, and offer a generic diagnostic to separate summary failures from inference failures. Finally, we demonstrate that auxiliary supervision improves convergence speed and accuracy on a range of challenging real-world inference problems.

Augmenting small concurrent studies with external or historical cohorts is attractive in drug development, where enrollment is slow, follow-up is expensive, and closely related trial or real-world data are often already available. Bayesian dynamic borrowing (BDB) provides a principled framework for adaptively controlling the influence of external data, but classical implementations often depend on hand-specified priors and MCMC-based inference, which can be computationally expensive and not generalizable. In this work, we study amortized neural posterior estimation (NPE) as a flexible alternative. A single network is pretrained on simulated current/external dataset pairs spanning covariate shift, outcome drift, and joint non-exchangeability, and then returns an approximate posterior for a scalar current-study target in a single forward pass. Through simulation studies, we find that NPE is most useful under outcome drift and joint mismatch: in the harder outcome-drift regimes, it gives up to about five-fold lower absolute bias than the best classical baseline and keeps Type I error close to nominal. After pretraining, posterior summaries are obtained in about 8 ms per dataset, roughly $10^3\times$ faster than MCMC-based borrowing baselines in our timing experiment. We further analyze Alzheimer's Disease Neuroimaging Initiative (ADNI) data and show that, when mild cognitive impairment outcomes differ across cohorts, the NPE formulation recovers the later-cohort risk level in this example without claiming greater precision. Code is available at https://github.com/ChinHungScott/NPE-for-Bayesian-Dynamic-Borrowing-MLHC-.

Many physical data assimilation (DA) workflows require smoothing methods that represent non-Gaussian posteriors over physical state variables, scale to high-dimensional simulators, train from observation windows alone, and remain compatible with calibration of the prescribed simulator. We introduce PR-Smoother, a simulator-preserving amortized smoother designed for this prescribed-simulator DA regime. Its key design principle is to keep the prescribed simulator explicit in both the evidence lower bound and the variational family: rather than learning replacement dynamics or a learned trajectory prior, PR-Smoother learns only future-conditioned corrections around the prescribed rollout. This yields an explicit non-Gaussian smoothing distribution over physical trajectories and supports joint state, parameter, and sensor-bias learning from observations alone. The variational family contains the exact smoother in deterministic and linear-Gaussian limits. Empirically, PR-Smoother captures multimodal posteriors in 4-dimensional Lorenz-96, remains accurate under ambiguous nonlinear observations and process noise in 40-dimensional Lorenz-96, and scales to joint state-parameter-bias inference in 16,384-dimensional Kolmogorov flow.

Hierarchical data is ubiquitous in the empirical sciences and is most commonly analyzed with generalized linear mixed-effects models (GLMMs). Bayesian inference for GLMMs yields calibrated uncertainty but requires MCMC; the No-U-Turn Sampler (NUTS) is the gold standard but is slow and must restart from scratch for every new dataset, model and prior. We introduce metabeta, a pretrained neural network for prior-amortized in-context Bayesian inference over GLMMs. Unlike previous neural posterior estimators that fix the prior at training time, metabeta accepts prior families and hyperparameters as inputs at test time, enabling zero-shot generalization. Two set transformers and conditional normalizing flows mirror the posterior's two-level structure (global parameters shared across groups, local parameters per group). The model is trained on millions of realistic simulated datasets spanning continuous, binary, and count outcomes. By default, the flow posterior is refined by Independence Metropolis-Hastings against the unnormalized posterior, so its correctness rests on the sampler rather than the network; this yields tuning-free inference two to three orders of magnitude faster than NUTS. Alternatively, the flow can warm-start NUTS, giving nearly identical inference with substantially increased speed and stability. On controlled benchmarks with ground-truth parameters, metabeta matches NUTS in parameter recovery, calibration and out-of-sample prediction. On out-of-distribution real datasets, its posteriors closely match those of NUTS across all parameter types, and they remain faithful under misspecified likelihoods and priors, out-of-distribution predictors, collinear designs, and data-poor regimes. The model is open-source and open-weights and thus immediately deployable.

Variational autoencoders (VAEs) offer an efficient approach to amortized Bayesian inference for inverse problems, but posterior accuracy can depend strongly on the choice of variational regularization, particularly when the inverse problem contains weakly identified parameter directions. This study investigates three objectives: a reverse Kullback--Leibler formulation (VAE-KL), an asymmetric Jensen--Shannon formulation (VAE-JS), and a Jensen--Shannon--Wasserstein formulation (VAE-JSWA), which replaces the reverse Kullback--Leibler regularizer with the squared 2-Wasserstein distance while retaining forward-Kullback--Leibler posterior supervision. A full-covariance Gaussian encoder and a pre-trained physics-based surrogate are used for amortized posterior inference. A local linear--Gaussian analysis in the generalized Fisher basis is developed to characterize the variance-dependent gradients of the three objectives. The formulations are first evaluated using linear--Gaussian benchmarks with known posterior solutions and subsequently tested on nonlinear physics-based inverse problems, including an inverse problem governed by a linear ODE and two PDE-constrained problems. VAE-KL performs slightly better than the other formulations in the well-conditioned benchmark, where all three approaches yield comparable posterior approximations, whereas VAE-JSWA provides substantially lower posterior errors in the strongly ill-conditioned benchmark. The nonlinear physics-based problems exhibit a similar conditioning-dependent trend, with JS-based formulations providing greater benefit as posterior ill-conditioning increases. These results indicate that posterior conditioning is an important factor in selecting variational objectives and motivate geometry-adaptive variational inference for Bayesian inverse problems.

Amortizing physics-informed neural networks (PINNs) across related PDEs requires describing each equation to a reusable solver. Coefficient vectors encode numerical parameters in predefined slots, leaving operator and cross-field assignments implicit. We make these relationships explicit in an operator graph, with nodes for fields, derivatives, terms, and residuals and coefficients retained as term attributes. A graph hypernetwork generates diagonal codes that initialize a meta-trained factorized PINN for each target equation. Meta-training and target-specific adaptation use governing equations and prescribed conditions without solution labels. We compare coefficient-vector, DeepSets-based term-set, and graph conditioning by solution accuracy within a fixed adaptation budget. In scalar convection-diffusion-reaction problems, both term-based descriptors improve high-reaction accuracy, with similar performance. In two-field Fisher-KPP, meta-training sees uncoupled and one-way systems; after 3,000 adaptation steps on unseen two-way coupling, the graph's mean final error is 35.7% below the term set and 67.7% below the coefficient vector. In a fixed-structure capacitively coupled plasma model, the coefficient vector performs best. These results support extending coefficient conditioning with explicit equation relationships for physics-based solver adaptation.

We consider the problem of sampling compositional and discrete objects from a given unnormalized posterior distribution. Notably, recent studies have shown that this problem can be efficiently solved by learning a deterministic Markov Decision Process (MDP) that progressively builds each object in proportion to the posterior. In this work, however, we demonstrate that the Markovian assumption can both hamper signal propagation during training and catastrophically reduce the learned sampler's expressivity due to state aliasing. To address these issues, we propose lifting the MDP with a learnable latent dynamical system that allows the underlying policy to depend on the entire past trajectory---and not only on the current state. In view of this, we refer to the resulting method as path-dependent discrete amortized inference. Importantly, we provably extend existing learning algorithms for discrete amortized samplers to our setting. In experiments on standard benchmark problems, we also show that our approach often leads to faster learning convergence and improved state space exploration relatively to prior techniques.

Mean-reverting dynamics are pervasive in finance, and the Cox--Ingersoll--Ross (CIR) process is a standard model for the time series they produce, from short rates to credit default swap (CDS) spreads. Yet CIR models capture only \emph{correlated} co-movement, not \emph{causal} influence between series, so they cannot answer the system's response when one series is externally shocked, which observational conditionals confound with historical co-movement. We make two contributions. First, an amortized model for distributional causal effect estimation that frames trajectories as time-stamped observations and predicts the calibrated multi-horizon shock response without retraining per scenario. Second, a causal multivariate CIR data-generating process that supplies the paired observational and interventional ground truth that real markets cannot. We instantiate and calibrate the framework on CDS spreads as a testbed. CIR-ACTIVA's validity is established on synthetic ground truth, independent of how well the simulator matches reality, while practical grounding is assessed by backtesting the generated traces against real CDS data. Against observational and amortized causal-inference baselines, CIR-ACTIVA leads on both causal selectivity in the joint distribution and horizon-resolved calibration, retaining its selectivity once the interventional law varies over the horizon, with gains concentrating at short horizons. This opens up a class of what-if queries on coupled spread systems, CDS stress testing among them, that observational forecasters cannot answer.

The drift diffusion model (DDM) is a cornerstone of cognitive decision-making research. Although numerous estimation methods exist, researchers continue to seek inference approaches that are both fast and flexible across diverse study designs. Amortized Bayesian inference (ABI) can provide nearly instantaneous inference for complex stochastic models like the DDM, but neural networks trained for one study design cannot generalize to others. In this paper, we propose a divide-and-conquer framework that address this limitation. The core idea is that the DDM's independence assumption allows the full dataset to be decomposed into pairwise shards, each sharing a common structure that a single neural network can learn. Inference is performed on each shard separately and the resulting posteriors are combined via consensus MCMC to approximate the full posterior. Using simulated datasets, we evaluate the accuracy and uncertainty of this method. Our results show that the proposed divide-and-conquer approach achieves accuracy and uncertainty comparable to MCMC while reducing computational cost by several orders of magnitude. This work not only advances DDM estimation but also demonstrates a general strategy for improving the scalability and generalizability of ABI methods across diverse applications.

A central aim of unsupervised learning is to uncover latent factors that explain dependencies among observations. Probabilistic models typically achieve this by introducing multiple latent variables linked through a graph of conditional relationships, with distributional parameters and their dependence learnt from data. Learning relies either on distributional choices that allow tractable belief propagation, or on approximations that scale poorly with model size and complexity. We build on the recently developed recognition-parametrised modelling paradigm to propose an alternative approach: RAMP, a method that implicitly defines latent structure by learning a flexible, nonlinear, amortised message-passing framework. We show that RAMP enables efficient likelihood-based recovery of latent-variable distributions within expressive nonlinear models acting on complex high-dimensional data.

We introduce Deep Adaptive Bayesian Screening (DABS), a method for performing adaptive factorial screening in high-dimensional discrete design spaces. DABS learns a policy network offline to sequentially select informative experiments, amortizing Bayesian Optimal Experimental Design. It handles binary designs, incorporates sparsity and interactions via a spike-and-slab prior with strong heredity. The model is trained using a contrastive lower bound on information about factor activity with nuisance effect sizes and noise variance analytically integrated out. Unlike prior amortized Bayesian design approaches, DABS also integrates Gibbs posterior inference at deployment, yielding posterior probabilities of factor activity and credible intervals on effect sizes. We demonstrate DABS on screening problems calibrated to real-world benchmarks and show it achieves superior accuracy and scalability over classical and Bayesian baselines under tight experimental budgets.

Quantum state tomography is sample-starved, and the states one prepares live on a narrow, learnable manifold. A $k{=}0$ prior-only control shows that on concentrated families a prior estimate is already near-optimal, so ``high fidelity at few measurements'' can be family memorization rather than tomography; genuine measurement-efficiency needs a model that conditions on the measurements and demonstrably uses them. On a shared matrix-product-state (MPS) core parameterization we study two routes. ApproachA learns a generative prior over MPS cores with measurement-guided posterior inference (gold-standard-validated, but whose few-measurement accuracy the control shows is largely the prior). ApproachB, our main proposal, is a \emph{fixed-protocol amortized} MPS estimator trained once with a gauge-invariant fidelity loss; we deliberately do not rest it on a permutation-invariant set encoder (a plain MLP matches it). The decisive lever is the measurement design: motivated by the fact that local reduced density matrices determine a $χ$-MPS, conditioning on an \emph{informative local} Pauli set rather than random strings turns a modest, memorization-prone estimator into a high-fidelity one ($\approx\!0.95$, up to $+0.59$ over prior-only, decisively passing a shuffled-measurement control). A dropout ensemble, conformally recalibrated, gives $\approx\!90\%$-coverage intervals -- including for observables never measured, where a shot-based interval does not exist. Quality holds as the system grows (fidelity $0.90$ at $n{=}10$, gain \emph{growing} in $n$; $0.88$ at bond dimension $χ{=}4$), the parameterization is polynomial (native contraction to $20$ qubits), and we close the loop on IBM hardware ($5$ states at $0.97$ from hardware-measured Paulis).

Large language models (LLMs) exhibit strong reasoning and world-knowledge capabilities, yet often struggle to gather information effectively across the multi-turn interactions required in sequential decision-making settings. We introduce Amortised Sequential Information Gathering (ASIG), a fine-tuning approach that amortises Bayesian Experimental Design (BED) into LLM policies via a multi-turn extension of Group Relative Policy Optimisation with an Expected Information Gain reward. Evaluated on the 20 Questions task, ASIG more than doubles the success rate of the 7B base model and reduces inference cost by over $25\times$ relative to BED-LLM, a competitive inference-time baseline. Applied to MediQ, a medical diagnosis benchmark unseen during training, ASIG improves information-seeking performance at the 7B scale, suggesting that the learned strategies can transfer out of distribution. Our findings show that amortising BED into LLM policies provides an effective and computationally efficient approach to sequential information gathering.

Adaptive experiments for average treatment effects (ATE) require randomized allocations balancing valid inference with statistical efficiency. The oracle design is a covariate-dependent Neyman rule governed by unknown arm-conditional outcome variances. We investigate whether this sequential variance-estimation and allocation process can be amortized via in-context learning. We introduce Bayesian in-context experimenters: transformer policies trained to imitate a Bayesian posterior Neyman teacher. The teacher updates nonparametric beliefs over potential outcomes using experimental history to assign posterior Neyman treatment probabilities. This design converges to the oracle rule, supporting efficient ATE inference. Transformers constructively implement this mapping through attention-based sufficient statistics and projected gradient descent, imitating Bayesian updating for Gaussian-series priors. To address unknown outcome smoothness, we combine smoothness-indexed experimenters using a mixture-of-experts transformer. The gate acts as a hierarchical posterior over smoothness classes, concentrating on near-oracle experts. By bounding the complexity of the transformer class, we prove this amortized policy can be learned via empirical risk minimization using supervised pretraining. Experiments confirm accurate teacher imitation, adaptive allocation, and improved ATE precision over baselines.

Hierarchical predictive coding provides an interpretable framework for perception as error-driven inference in multi-layer generative models, while sparse coding imposes parsimonious latent representations through explicit sparsity constraints. Their combination yields hierarchical sparse predictive coding models with appealing computational and neuroscientific properties, but practical use is often limited by the cost of iterative latent inference. In such models, each input may require many recurrent refinement steps before a useful sparse representation is obtained, and this burden becomes more severe as the hierarchy deepens. We study this bottleneck by holding the hierarchical sparse energy fixed and varying the inference procedure. The comparison includes four schemes: classical iterative inference based on ISTA, an accelerated MFISTA reference, structurally informed amortized inference using a LISTA-style bottom-up encoder adapted to the hierarchical model, and a hybrid method in which this fast amortized initialization is followed by a small number of corrective energy-based refinement steps. Under this shared objective, we measure reconstruction quality, sparsity, latency, and stability on static image benchmarks. The results show that a shallow LISTA-style initializer plus short corrective recurrence improves over pure amortization while remaining much faster than long iterative inference.

Gaussian Processes (GPs) are a powerful tool for Bayesian time-series modeling, yet their cubic computational cost remains a severe barrier for application to long, high-cadence datasets in astronomy. While specialized scalable solvers like Celerite elegantly reduce this scaling to linear time, repeatedly evaluating the exact likelihood during iterative Bayesian sampling is a bottleneck for developing more complex models, like hierarchical or additive models in which Celerite is only one component. To make this inference computationally tractable, we introduce a generative surrogate framework. By utilizing a Variational Autoencoder (VAE) to learn a compressed representation of the Celerite prior, we map highly correlated stochastic dependencies into a low-dimensional, isotropic manifold. This transition completely bypasses exact covariance operations, shifting the computational burden to a rapid neural network forward pass. Through an extensive simulation study, we show that the generative surrogate accurately reproduces the structural fidelity of exact physical kernels like Celerite. Finally, we demonstrate embedding our VAE approximation into an additive model that combines Celerite and a hidden Markov model (HMM) for stellar flare detection in time series data of stars. We evaluate the joint VAE+HMM architecture against the exact Celerite+HMM framework on empirical astrophysical time series and demonstrate that the proposed methodology achieves significant reductions in computational time, enabling the rigorous, large-scale characterization of stellar flares across massive data archives.

Bayesian predictive inference provides a principled framework for uncertainty quantification, data efficiency, and robust generalization. However, exact inference is often intractable, and scalable approximations may remain computationally expensive or require restrictive modeling assumptions that degrade predictive performance. Prior-Data Fitted and in-context models have recently emerged as an amortized alternative by learning to map datasets directly to predictive distributions, but existing approaches are tightly coupled to the support of the training prior and lack explicit mechanisms for adapting to new priors at test time, resulting in limited robustness under distribution shift. We introduce a multi-task in-context learning framework for amortized hierarchical Bayesian predictive inference that explicitly represents prior information as a prefix of in-context datasets. A transformer trained on sequences of prior and target tasks learns to adapt its predictions across families of priors. On a suite of evaluations with increasing difficulty, including out-of-meta-distribution priors and priors with high-dimensional latent structures, our method matches oracle Bayesian predictors while being orders of magnitude faster. We further demonstrate its practical relevance on a real-world spatiotemporal temperature prediction benchmark. Code is available at https://github.com/martianmartina/multi-task-bayesian-icl/.

Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in $F_1$, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.

Space-based monitoring of atmospheric carbon dioxide (CO$_2$) constrains the global carbon budget. NASA's Orbiting Carbon Observatory-2 (OCO-2) estimates column-averaged dry-air mole fractions of CO$_2$ (XCO$_2$) from high-resolution spectra, but operational retrievals are computationally expensive and impose stringent Gaussianity assumptions on the retrieved posterior. We present a deep learning framework that addresses both through amortized probabilistic inference. Lacking ground truth for real observations, we train and evaluate on a high-fidelity OCO-2 simulation ensemble with calibrated forward-model errors, comparing against the version-10 ACOS full-physics retrieval on the same radiances. Our architecture encodes each spectral band separately and estimates posteriors of the full CO$_2$ column, or summaries thereof, with Laplace approximations and conditional normalizing flows. Once trained, inference costs milliseconds per sounding rather than minutes, and calibrated posteriors are attainable at that cost. Trained on simulations that explicitly include forward-model discrepancy, our retrievals are more accurate than the operational one for XCO$_2$ on both data partitions we consider, and competitive on profiles. The flow represents asymmetric posteriors that a Gaussian cannot, a gain attributable to shape rather than scale, and its advantage in predictive density persists where its accuracy advantage does not. These results are established on a land-only ensemble against one configuration of the operational algorithm. On reference soundings withheld from training and on two unseen months the XCO$_2$ and density advantages persist while calibration degrades under sparsely sampled observing conditions, pointing to the diversity of the simulated scene population rather than the method as the main obstacle.

Bayesian inference for inverse problems is run to evaluate integrals -- posterior expectations, tail probabilities, and risks -- across a stream of observations. The standard estimate averages the integrand over posterior samples, a Monte-Carlo average whose error decays only as the square root of the sample size, so accuracy demands many samples -- prohibitive when each one calls a partial-differential-equation forward model. Mean-shift interacting particles need far fewer: they return a small set of signed-weight nodes -- a deterministic quadrature whose weighted averages estimate those integrals. Finding the nodes, however, is a per-observation optimization that, in its most accurate form, reads the posterior score at every step -- returning the cost it meant to save. We introduce amortized mean-shift interacting particles, a learned map that emits the weighted nodes from an observation and a few posterior samples in a single forward pass. Training asks only for joint parameter-observation samples and a posterior to draw from -- a conditional normalizing flow, an empirical conditional, or any reference the user can sample -- and the map learns to integrate that posterior from samples alone, evaluating neither its density nor its score. Once trained, it generalizes to unseen observations and integrands at any node budget and improves on independent samples in two ways: by reweighting them, provably no worse than the equal weights of Monte-Carlo; and by moving them, which empirically lowers it further. Across closed-form, sampled, learned, and physics-based posteriors -- up to a thousand-coefficient groundwater field -- it integrates more accurately than the same number of samples at every budget, and a posterior-whitened, dimension-aware kernel removes the high-dimensional wall. The result is a Pareto improvement on Monte-Carlo integration, not a competitor to drawing more samples.

Marginal inference in discrete graphical models forces a choice between exactness and scalability: exact algorithms are intractable for high-treewidth graphs, while iterative approximations (Belief Propagation, variational methods) sacrifice convergence guarantees on frustrated topologies. We argue that this dichotomy stems from a mismatched inductive bias: iterative methods abandon the sequential elimination structure that makes exact inference correct. We introduce In-Context Graphical Inference (ICG-I), an autoregressive Graph Transformer that restores this structure by mimicking Variable Elimination with learned, Tensor- Train-compressed intermediate factors, paired with a Dirichlet output layer and Weighted Conformal Prediction for calibrated, distribution-free coverage guarantees under topological shift. We prove that TT compression errors propagate at most lincarly through the autoregressive chain, that the Dirichlet-Multinomial loss is a proper scoring rule, and that WCP maintains coverage with a quantifiable degradation under estimated density ratios. We conducted intensive experiments to evaluate ICG-I and achieved state-of-the-art performance across all benchmarks. ICG-I reduces MAE from 0.041 (best baseline) to 0.020 on standard instances and achieves 0.048 on N=500 frustrated spin glasses where BP diverges entirely.

Physics models are inherently imperfect due to misspecified or missing mechanisms, resulting in systematic discrepancies between model predictions and real-world observations. The Kennedy-O'Hagan (KOH) framework addresses this issue through explicit discrepancy modeling. However, its non-amortized, per-instance formulation limits scalability across families of related systems. We introduce Amortized Physics-Informed Calibration (APIC), a population-level extension of KOH that leverages Neural Processes to perform scalable Bayesian inference across realizations. Our framework employs a two-branch latent architecture to disentangle instance-specific physical parameters from shared, state-dependent structural discrepancies. By integrating differentiable physics into an amortized inference backbone, APIC enables rapid calibration of unseen realizations from sparse observations while quantifying uncertainty. Experiments on the damped spring oscillator, the Lotka-Volterra system, and the advection-diffusion PDE with misspecified physics demonstrate improved parameter recovery and consistent identification of the systemic discrepancy structure compared to other calibration approaches.

Measuring statistical dependency between high-dimensional random variables is a fundamental task in data science and machine learning. Neural mutual information (MI) estimators offer a promising avenue, but they typically require costly iterative optimization for each new dataset, making them impractical for real-time applications. We present InfoAtlas, a foundation model-like architecture that eliminates this bottleneck by directly inferring MI in a single forward pass. Pretrained on large-scale synthetic data with rich dependence patterns, InfoAtlas learns to identify diverse dependence structures and predict MI directly from the dataset. Comprehensive experiments demonstrate that InfoAtlas matches state-of-the-art neural estimators in accuracy while achieving $100\times$ speedup, can flexibly handle varying dimensions and sample sizes through a single unified model, and generalizes effectively to complex, real-world scenarios. By reformulating MI estimation as an inference task, InfoAtlas establishes a foundation for real-time dependency analysis.

Symbolic regression (SR) seeks closed-form mathematical expressions that fit observed data. Neural SR methods amortize the search by training an encoder to map observations directly to expressions in a single pass, but this amortized inference leaves a residual amortization gap between its one-shot prediction and the true posterior. We propose Latent Equation Embedding (LEE), a framework that closes this gap through iterative amortized inference in a functionally grounded latent space. LEE learns a shared latent space Z equipped with three components: an encoder f_theta that jointly embeds symbolic tokens and numerical observations into a single latent vector z; an expression decoder g_expr that reconstructs formulas from z; and an evaluation decoder g_eval that predicts function values from z, explicitly grounding the latent space in functional behavior. At inference, LEE performs iterative refinement by re-encoding decoded expressions jointly with observations, progressively improving the latent estimate. LEE uses the encoder itself as a learned inference optimizer: each re-encoding step implicitly computes the mismatch between the candidate and the data. Because g_eval is differentiable in z, we additionally interleave continuous gradient descent with discrete re-encoding, yielding a hybrid iterative and gradient refinement procedure. On SRBench across three noise levels, against 19 baselines spanning genetic programming, symbolic-neural hybrids, and pre-trained Transformers, LEE produces expressions 2--10x simpler than the strongest accuracy-oriented baselines, including Operon, GP-GOMEA, TPSR, RAG-SR, and GenSR, with complexity 8--11 versus 20--90. These results advance the low-complexity region of the accuracy-complexity Pareto frontier and show graceful degradation as noise increases.

Amortized inference promises fast test-time Bayesian inference, but existing methods are inherently tied to fixed models. Extending amortization to unseen models typically requires retraining or costly test-time finetuning. In this paper, we ask: is it possible to build a single inference network capable of generalizing across varying priors, likelihoods, and dimensionality? We introduce Amortized Factor Inference Networks (AFINs), a family of encode-merge-decode inference networks built on dimension-independent modules that map a model specification and its observations to the parameters of a variational posterior. Experimentally, a single trained AFIN achieves posterior accuracy comparable to NUTS and several variational inference methods, while requiring 2 to 4 orders of magnitude less test-time compute. Code is available at https://github.com/joohwanko/AFINs.

Discrete diffusion models have emerged as powerful frameworks for generating structured categorical data. However, efficiently sampling from reward-tilted distributions remains a fundamental challenge. While Twisted Sequential Monte Carlo (SMC) offers asymptotic exactness for this task, estimating the optimal twist function in discrete state spaces necessitates costly Monte Carlo approximations, resulting a severe computational bottleneck at inference. To overcome this limitation, we introduce Contrastive Distribution Matching (CDM), a novel framework that amortizes the cost of SMC inference by learning a parameterized twist function via positive and negative samples. For efficient training, we reformulate the gradient estimator to leverage the closed-form forward kernels of discrete diffusion models. In practice, evaluating our learned twist function incurs less than 5% additional computational overhead compared to a single forward pass of the base model. Through extensive empirical evaluations, we demonstrate that CDM consistently outperforms existing baselines under matched wall-clock time. We validate the effectiveness and versatility of our approach across a diverse range of applications, including toxic text generation, regulatory DNA sequence design, protein designability, and diffusion large language model alignment.