Latent Variable

Uncovering latent variables and their causal relations from observed data is a fundamental yet challenging problem. Existing methods often rely on restrictive assumptions, such as linear relations or invertible mixing functions. To better address this problem under general nonlinear mixing procedures, we propose a condition called the cross-Hessian Rank Constraint (HRC), which serves as a primitive rank-based tool for nonlinear latent causal discovery. In particular, we show that a rank-based property arises from the cross-Hessian of the observed-data log-density in the nonlinear case, revealing information about the latent variables, and reduces to the Tetrad constraints in the linear Gaussian case. More specifically, when two groups of observed variables are d-separated by a set of lower-dimensional latent variables, the rank of this cross-Hessian is equal to the dimension of the latent variables, under a mild affine derivative assumption on the conditional log-density derivatives. This assumption can be naturally satisfied when the noise level is low or the relevant nonlinearity is moderate. As a downstream application, we instantiate HRC in the pure one-factor measurement setting for locating latent variables and recovering their causal structure up to Markov equivalence. Experimental results on synthetic and real-world datasets support the theoretical claims.

We propose a new probabilistic model for general-purpose medical image registration that builds upon the mutual information registration criterion. It centers around a spatial interpolation technique that assumes latent voxel-wise correspondences between the images being registered. By exploiting these latent variables, we derive dedicated optimization and MCMC sampling techniques that only involve closed-form iterative updates. When applied to nonlinear registration, an efficient demons-like optimization algorithm is obtained that shows robust out-of-the-box performance across a variety of monomodal and multimodal registration tasks. We also demonstrate a corresponding sampler that can quantify, for the first time, uncertainty in multimodal registration scenarios with very high-dimensional 3D deformations. Our code, which we call BINDER (Bayesian INference for DEformable Registration), is freely available at https://github.com/ste93ste/BINDER.

Causal discovery aims to recover causal relationships from observed data. In various fields, exploring causal relationships among variables remains an important topic, but this task becomes challenging due to the existence of latent confounders. Ignoring such confounders can lead to false associations and incorrect edge directions. In this paper, we study the linear structural equation model with latent confounders. We propose an algorithm that iteratively identifies terminal (observed) nodes and reconstructs the directed acyclic graph of the observed variables. To do this, we recover the precision matrix of the observed variables as a sparse plus low-rank matrix: a sparse matrix captures the conditional dependencies among observed variables, while a low-rank matrix captures the combined influence of a few latent confounders. We establish that for $p$ observed variables, $r$ latent confounders and $s$ edges, our procedure correctly identifies the directed causal relationship among observed variables, for $n \gtrsim \max\{s\log p,\ r p\}$ samples. Experimental results validate our theoretical contributions.

Missing data, measurement error, and population heterogeneity are pervasive challenges in analyzing data arising from modern observational studies and machine learning applications. Although these problems frequently coexist and interact, they are often treated separately in existing works. We propose a unified probabilistic framework that jointly addresses these issues utilizing deep latent variable representation. The proposed method integrates a novel hierarchical tree-routed variational autoencoder with pattern-aware latent representations and calibration-based denoising. The framework accommodates missing data mechanisms, including MCAR, MAR, and MNAR, while simultaneously learning subgroup-specific and globally shared latent structure. The introduced reconvergent routing mechanism enables selective parameters to be shared across related subpopulations, which offers flexibility as well as improved statistical efficiency. Simulation studies demonstrate substantial improvements over existing deep generative imputation approaches under complex heterogeneous missingness and measurement-error settings. The proposed framework provides a principled approach for learning from noisy and incomplete data in modern healthcare and other high-dimensional applications.

The robust treatment of environmental and operational variability (EOV) is an open challenge in population-based structural health monitoring (PBSHM). The difficulty is compounded in the case that the EOV signals are unmeasured. A common approach in conventional SHM is to apply \emph{projection-based} methods that discard subspaces of healthy feature data, reasoning that the EOV signal dominates the variance of the measured features. However, a common pitfall of projection-based approaches is that when damage acts close to the same variance-dominant direction, damage sensitivity is removed along with the EOV. An alternative identifying assumption for the removal of particular unmeasured EOVs is slowness; the latent EOV process is characterised by its long temporal correlation. In this paper, the latent EOV is cast as a state-space Gaussian process, enabling tractable $\mathcal{O}(T)$ inference via a Kalman filter. A robust hierarchical Bayesian identification framework is developed that enables population-level identification of latent EOVs and EOV-free residual features, using a Laplace approximation. The approach is first validated on a single laboratory-scale benchmark structure from the literature, subject to thermal EOVs, demonstrating robust damage detection and EOV recovery. The method is then applied to a simulated nine-turbine offshore wind farm with staggered deployment and damage, where it delivers a substantial true-positive uplift over projection and cointegration-based baselines at matched false-positive rates.

The problem of learning from pairwise comparisons has been widely studied across many domains such as recommendation systems, social choice, and more recently, fine-tuning large language models. In this problem, the goal is to learn item rewards based on pairwise comparisons between them. In many scenarios, these comparisons are elicited from crowdworkers using platforms such as Amazon Mechanical Turk, Scale AI, etc. However, crowdworkers are often unreliable due to limited domain knowledge or revenue-maximizing (spamming) behavior. In this work, our goal is to understand whether worker reliability (competency) can be learned jointly with item rewards. To this end, we adopt the Boltzmann-rational model for pairwise comparisons, which extends the Bradley-Terry-Luce model by incorporating worker competencies. We derive an EM-based algorithm for learning under this model by introducing Polya-Gamma latent variables to transform the logistic likelihood into a conditionally Gaussian form, enabling tractable optimization and leading to a simplified $Q$ function in the E-step of the algorithm. This technique allows us to reduce our formulation to a matrix sensing problem, using which we establish theoretical convergence guarantees for our algorithm. We conduct extensive experiments on real-world and synthetic datasets. These experiments demonstrate the advantages of using our algorithm over several baselines and confirm its strong robustness to both spammers and adversarial workers, highlighting its practical effectiveness in realistic crowdsourcing and reward learning settings. The code and data is publicly available at https://github.com/KaustubhShejole/BoRa_EM.

We introduce the Unified Neural Variational Measurement of Proficiency (UNVaMP) architecture, a knowledge tracing method that integrates observed student-item interactions with internal memory to produce evolving latent representations of student knowledge. These representations support accurate predictions of future responses while enabling explicit control over the smoothness of estimated learning trajectories. UNVaMP can be configured as either a purely neural model or a hybrid model that predicts responses through an interpretable measurement function over the latent space. We show that a pure neural configuration (UNVaMP-MLP) achieves the strongest predictive performance among compared models on three out of four datasets. Meanwhile, a hybrid configuration (UNVaMP-MIRT, using a 1PL MIRT measurement function) lags only slightly behind UNVaMP-MLP, indicating that the predictive cost of interpretability is modest. Beyond predictive accuracy, UNVaMP provides the following: a principled mechanism for controlling volatility when estimating student latent variables, quantification of uncertainty over student knowledge state estimates, and flexible input specification that supports heterogeneous student-item interaction features. In addition, the hybrid UNVaMP-MIRT configuration generates interpretable moment-in-time student knowledge state estimates. Using an experimental dataset, we show that auxiliary inputs induce structured changes in the predictive behavior of UNVaMP-MIRT, consistent with sensitivity to underlying structure beyond response correctness. Furthermore, through a simulation study, we show that UNVaMP yields well-behaved knowledge state estimates under controlled measurement conditions. In total, these results indicate that UNVaMP is both useful for real-world education systems and capable of recovering underlying structure from student-item interactions.

Out-of-distribution (OOD) recommendation is vulnerable to preference shifts induced by a latent environment. Existing methods can infer latent states from logged interactions, yet the statistical meaning of the latent environment and its effect on preference remain underdetermined. We formulate this task as conditionally identifiable risk-aware recommendation (CI-RR) and propose Conditionally Identifiable Latent-Environment Recommendation (CILER). CILER uses a user-conditioned exponential family to model the latent environment and a feature-indexed polynomial to specify how it changes preference. It predicts by marginalizing item probabilities over the inferred environment distribution. Under sufficient variation, correct specification, and decoder regularity, CILER identifies the environment-sensitive representation up to the stated equivalence class. We further bound excess deployment log-risk by environment-inference error. Controlled studies test the observable consequences of sufficient variation and model specification. Experiments on three datasets show that CILER improves all twelve OOD ranking metrics under feature, temporal, and geographical shifts within shared support.

Flow matching assumes fully observed training data, which many real-world applications rarely provide. We propose Missing-Data Flow Matching, which treats the missing coordinates of training samples as latent variables and averages the flow matching loss over the values they could take. We first prove the correction is exact rather than approximate. Under missing completely at random with true completions, the incomplete-data objective equals the complete-data objective, so missingness changes nothing about what flow matching learns and the entire difficulty relocates to the completion model. Our finite-sample analysis then answers design questions that the algorithm leaves open, and the answers are not the ones intuition suggests. Missingness transfers estimator variance rather than adding it, one completion per example already matches complete-data variance exactly, and under a fixed evaluation budget one completion is optimal. A learned completion model contributes a single irreducible bias, which we bound by its expected conditional Wasserstein distance to the true completion law. Experiments numerically validate the theoretical predictions, show that deterministic rather than frozen imputation is what collapses the generated distribution, and place our method alongside strong classical and deep imputation baselines on real tabular data.

Discovering the direct causes and effects of a target variable from observational data is a fundamental problem in causal discovery, with broad applications in domains such as gene regulatory analysis and biomedical research. Existing causal discovery methods either learn a global causal structure, which incurs substantial computational cost, or assume the absence of latent variables and selection bias, assumptions that are often violated in real-world settings. Motivated by these challenges, we study local causal structure learning in the presence of latent variables and selection bias. Specifically, we first characterize a local region that enables target-specific causal discovery without recovering the entire global structure. We then establish a theoretical bridge between causal information learned from the observed distribution induced on this local region and the corresponding information in the global causal structure. Building on these foundations, we propose LoCaLS, a local causal structure learning algorithm that is sound and complete under standard assumptions and identifies the same direct causes and effects of a target variable as those identifiable by global causal discovery methods, while allowing for latent variables and selection bias. Extensive experiments on random and real-world structures demonstrate that the proposed method consistently achieves higher structural accuracy than existing local methods while requiring substantially less computational effort than state-of-the-art global methods. Furthermore, applications to two real-world gene expression datasets reveal biologically plausible target-specific causal structures, demonstrating its practical applicability in large-scale biological data analysis.

Modern ASR models trained on heterogeneously annotated data treat transcription style (verbatim vs. intended) as an uncontrolled latent variable, causing measurable decoding instability, evaluation confounding (up to 60% of reported WER attributable to style mismatch), and unreliable word-level timing. We show that models already encode both styles; the challenge is controlled activation. Using coverage-aware decoder task tokens trained on parallel verbatim/intended transcript pairs, we raise German disfluency F1 from 10% to 79% zero-shot, despite English-only training. Full English-only fine-tuning surpasses all baselines in verbatim accuracy, disfluency detection, and intended-mode quality across both languages. We further introduce supervised cross-attention fine-tuning that improves word-level timestamps on disfluent speech beyond forced-alignment baselines. Finally, we propose verbatimize, a new task enabling scalable creation and enrichment of speech corpora with high-quality canonical verbatim transcriptions.

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.

This paper considers a multi-environment factor model in which high-dimensional covariates are collected from heterogeneous environments, with auxiliary labels available in a subset of these environments. The joint distribution of the covariates may vary across environments, whereas the latent structure is decomposed into invariant factors with shared loadings and heterogeneous factors with environment-specific loadings. Such a model is motivated by transfer learning and latent factor regression, where one seeks stable low-dimensional representations for both interpretation and robust out-of-sample prediction of the response $Y$. Leveraging the invariance principle, we show that the invariant and heterogeneous factors are disentangled under a minimal structural condition. Based on this, we propose ATLAS, an Auxiliary-label and invariance-guided Transfer via Latent Alignment across heterogeneous environmentS. ATLAS is a unified procedure that leverages the invariance principle to separate aligned invariant and unaligned heterogeneous factors, and further exploits supervision from auxiliary labels to extract prediction-invariant and transferable factors from those unaligned heterogeneous factors. ATLAS yields near-oracle performance for downstream latent factor regression, enables transferable prediction in new environments through the full latent signal when auxiliary labels are available, and reduces to robust invariant-factor-only prediction otherwise. We establish sharp non-asymptotic error bounds for recovering invariant and heterogeneous factors, identifying all the response-invariant factors, and estimating the invariant signal in $Y$.

Residential short-term load forecasting (STLF) is challenging because household demand is heterogeneous, temporally variable, and shaped by diverse behavioural routines. This work investigates whether inferred behavioural structure can be embedded within the forecasting mechanism of a Neural Process-based probabilistic model, rather than used only as an external grouping signal, for context-conditioned residential STLF. We propose a behaviour-conditioned Attentive Neural Process framework that treats each load profile as a forecasting task. Behavioural structure is represented by a discrete latent variable inferred from the available context and used for behaviour-conditioned decoder conditioning, while a continuous latent variable captures shared functional uncertainty across heterogeneous profiles. To enable conditioning without ground-truth behavioural labels, clustering-derived information provides weak supervision during training, whereas test-time conditioning relies only on context-inferred class distributions. Experiments on the Smart Grid, Smart City (SGSC) dataset use user-disjoint train/validation/test splits, variable context lengths, and multi-step forecast horizons, with comparisons against a label-agnostic ANP baseline and fixed-window deterministic STLF baselines. The proposed variants improve MAE and CRPS over ANP across horizons and context settings, with the largest gains under limited context. The best-performing variant achieves average reductions of 7.9% in MAE and 6.9% in CRPS relative to ANP. Compared with fixed-window baselines, this variant achieves lower RMSE across all evaluated horizons while maintaining competitive MAE, suggesting fewer large prediction deviations under heterogeneous consumption patterns. These results support single-model, uncertainty-aware forecasting across heterogeneous households, contexts, and horizons.

We describe a model of perceptual inference in primary visual cortex (V1) equivalent to a minimal diffusion model whose function can be readily understood from its parameters. The model is based on sparse coding with a non-factorial prior over latent variables in the form of an unconstrained, pairwise interaction matrix, extending standard sparse coding inference to a general recurrent dynamical system. We efficiently train these recurrent dynamics using a denoising score-matching objective and implicit differentiation. After training on natural images, the learned interaction matrix mirrors the structure of horizontal connections in superficial layers of V1 that link neurons of similar orientation tuning. This model exhibits exceptionally good denoising performance, restoring image features such as extended contours amid extreme visual ambiguity, nearly matching the behavior of standard, black-box diffusion architectures in generalization regime. Owing to the model's simplicity, the network's Jacobian can be decomposed directly in terms of the interaction matrix between latent variables, revealing mechanistically how the recurrent dynamics assign high probability over a continuous family of natural structural deformations. Intriguingly, within this circuit, a large fraction of latent variables learn to disconnect from visual input altogether, essentially forming a hierarchical representation that appears to enforce global consistency among image features. Together, the model and results bridge two distinct domains: for neuroscience, it generates concrete, testable hypotheses regarding functional connectivity in recurrent neural circuits during perceptual inference tasks; for machine learning, it elucidates the internal mechanisms learned by diffusion models that allow them to generate infinitely many novel images from a finite training set.

In multi-party dialogues between a dialogue system and multiple users, identifying to whom an utterance is addressed is a key challenge. Prior work has typically treated addressee detection as a multi-class classification task, selecting a single label representing an individual participant or the group. This formulation assumes that address is inherently discrete and has primarily been used for predicting turn-taking. In this paper, we revisit this assumption by analyzing address as a continuous phenomenon. Using a multi-party human dialogue corpus annotated by multiple annotators, we construct both binary address labels derived from majority-vote addressee labels and continuous address levels inferred from annotator judgments using a latent-variable model. We then examine how these representations relate to turn-taking as well as listener behaviors, including gaze and backchannels. Our results show that, in addition to turn-taking, both gaze and backchannels are associated with address. Furthermore, models using continuous address levels achieve better predictive fit than those using discrete labels, suggesting that address may exhibit graded structure. Finally, we discuss the future directions of addressee detection research based on the findings of this study.

We study linear regression when the regressor is latent and observed only through multiple noisy measurements, each a smooth but possibly nonlinear function of the latent variable. The problem is acute in the measurement of occupational exposure to artificial intelligence, where competing scores yield downstream estimates that differ by a factor of eleven. A regression on any single measurement recovers a source-specific coefficient rather than the structural one. We fix the latent scale by requiring the consensus measurement function to be linear and bound the remaining curvature heterogeneity across sources relative to slope. Under this bound, the structural coefficient lies in a closed-form interval centered at a symmetric cross-source estimator. The interval is invariant to unknown source loadings, and its half-width is second order in the curvature bound and sharp to the same order. With at least four measurements, the bound is estimable from the joint distribution of the sources through a split-instrument auxiliary regression, and Imbens-Manski confidence intervals with the Stoye critical value attain uniform coverage over the curvature class, including at the point-identified boundary. The application matches six exposure measures to an American Community Survey panel of 8.88 million person-year observations for 2015 to 2024. The post-2022 employment coefficient changes sign between the language-model measures and the Webb patent-text measure, and an ex ante factor-analytic rule separates the Webb measure as a distinct construct. The five retained sources yield a loading-invariant consensus coefficient of -0.239, with a partial-identification half-width of 1.23 percent of the point estimate, or 1.88 percent at the one-sided 95 percent upper bound on the curvature. We read the application as measurement reconciliation rather than as a causal estimate of AI displacement.

Identifying heterogeneous treatment effects under unobserved confounding is central in observational causal inference. In proxy models with a discrete latent confounder, prior Synthetic Potential Outcomes (SPO) [Mazaheri-Squires-Uhler '25] recover the mixture of treatment effects through recursively constructed scalar moments. We show that this sequence is one projection of a more fundamental object. Under the same population factorization assumptions, there is an exact compressed observable operator: after projecting onto the shared proxy signal subspace, the difference of two treatment-arm quotient operators is similar to the diagonal matrix of latent treatment effects. Its eigenvalues are the latent effects; its lifted left eigenvectors, after anchor normalization, recover the target-proxy feature matrix and then the latent mixture proportions. Every scalar SPO moment is a bilinear functional of a power of this operator. The resulting estimator handles overcomplete proxy systems, replaces high-order scalar inversion with finite-dimensional spectral analysis, and admits high-probability first-order perturbation bounds for treatment effects, feature rows, and simplex-projected mixture weights.

Quantifying variability in a target population relative to a reference population is central to many scientific and clinical problems (e.g., diseased vs. healthy). Yet, without paired data and in the presence of heterogeneous target variation, existing methods struggle to separate multiple modes of target-specific variation. We propose \textit{CASL-VAE}, a deep contrastive latent variable model that learns structured latent generative factors from unpaired data. CASL-VAE factorizes variation into continuous common latent factors shared across populations and hierarchical salient latent factors that model target-specific heterogeneity as discrete subtypes and continuous within-subtype variation. Using variational inference, we show how approximate joint likelihood optimization over reference and target domains can be performed using unpaired data, providing a principled basis for paired-sample generation and cross-domain analysis. We validate CASL-VAE on semi-synthetic neuroimaging data, demonstrating improved subtype recovery and paired-sample generation compared to baseline clustering and generative models. We also validate its ability to reveal biologically plausible heterogeneity in Alzheimer's disease.

In partially exploratory factor analysis (PEFA), the loading structure and factor numbers are weakly specified. The regularized variational approximation for partially confirmatory factor analysis (PCFA VA) recovers this structure via Bayesian variable selection, using spike and slab priors to assign inclusion probabilities to unspecified loadings. This research introduces a post selection assessment framework for this approach. We convert converged solutions into covariance models using either hard selection (thresholding probabilities into a sparse pattern) or soft selection (retaining them as weights for effective parameter counts). We derive the resulting degrees of freedom, absolute fit diagnostics (RMSEA, SRMR, CFI, TLI), and relative criteria (AIC, BIC, ELBO). To determine factor numbers, we propose a scale free gain rule with a sustained drop guard. Simulations show absolute indices successfully track loading recovery and flag under factoring. While raw criteria over factor, our gain rule accurately recovers true dimensionality, with the ELBO variant proving most robust. Finally, a 100 item PID 5 example demonstrates that our model fits better than a confirmatory 25 facet model and concordantly recovers major structures across disjoint specifications.

Although LLMs have made significant progress in mathematical reasoning, determining whether a mathematical problem is solvable remains a fundamental yet challenging capability. While recent studies have probed internal representations of model solvability beliefs, verbalization has primarily been studied behaviorally rather than as an internal representation, limiting its analysis and manipulation. We address this gap by separately probing representations of solvability knowledge and verbalization, allowing us to disentangle the two within model hidden states. Across multiple LLMs, we show that knowledge and verbalization are encoded as distinct, linearly decodable representations and that fabrication is primarily associated with changes in verbalization rather than the underlying knowledge. Prompting with unsolvability cues reduces fabrication primarily by shifting verbalization, while activation steering demonstrates that these representations can be echanistically manipulated to improve model abstention.

Chart-to-code generation is commonly trained through supervised fine-tuning on reference plotting scripts, implicitly treating the gold code as a fully observable target. However, many chart programs contain latent variables that cannot be uniquely recovered from the rendered image. We identify this latent-observation mismatch in four forms across five chart types: aggregation-induced mismatch, where raw samples are reduced to box statistics or histogram bin masses; normalization-induced mismatch, where absolute scale is removed in pie charts; projection-induced mismatch, where 3D information is lost through 2D rendering; and level-set-induced mismatch, where a scalar field is observable only through selected contour lines. These mismatches introduce target ambiguity and require models to generate information unsupported by the image. We propose Observation-Aligned Supervision, which replaces latent variables with visually constrained quantities. We instantiate it using box statistics, bin weights, and wedge proportions, and study 3D scatter and contour charts through controlled experiments. Across multiple VLMs, observation-aligned supervision generally improves observable-value recovery in both-executable evaluations and mostly improves end-to-end recovery, while the contour study reveals a trade off between observation alignment and representational compactness.

Causal discovery with nonlinear mechanisms and latent confounders remains challenging. Existing methods often rely on either linear assumptions or causal sufficiency, limiting their applicability. We propose an MDL-based causal discovery framework that explicitly accounts for latent confounders while allowing flexible nonlinear mechanisms by minimizing the luckiness normalized maximum likelihood (LNML) code-length. The causal relationship between each variable pair is determined by selecting the shortest code-length of the causal model, and we introduce the notion of $Δ$-pseudo-collinearity to identify dependencies induced by latent confounders. Based on these ideas, we develop a greedy algorithm, termed Pseudo-Collinearity Guided Causal Discovery (PCG-CD). Experiments on synthetic and real-world datasets demonstrate that the proposed method accurately recovers directed causal relationships and effectively detects latent confounders.

Large Language Models (LLMs) have demonstrated the ability to simulate human-like OCEAN personality traits in generated text. Previous efforts have focused on prompt engineering or fine-tuning to shape LLM personality. In this work, we propose a mechanistic interpretability approach that directly intervenes on the model's latent features. Our method identifies latent directions in the residual stream corresponding to a target OCEAN trait using sparse autoencoders (SAEs) and contrastive activation analysis. We formalize an additive steering vector in activation space and demonstrate how applying a small additive shift to the hidden states enhances the target trait while preserving overall language modeling performance. To determine the optimal combination of feature shifts, we explore a linear weighting heuristic with grid search optimization that balances personality expression with task performance. Our approach shows promise in controllably steering personality traits at the mechanistic level while maintaining high performance on standard benchmarks.

Event-based Temporal Graph Neural Networks (ETGNNs) have demonstrated strong performance across a wide range of applications, including social network analysis, epidemic tracing, recommender systems, and political event forecasting. However, their increasing complexity poses significant challenges for explainability. Existing explanation methods focus only on a subset of the information flow within ETGNNs, typically tracing contributions from the event-related embeddings to the output. Consequently, they overlook the important pathways through event-induced variables, which mediate interactions between nodes and thereby play a central role in capturing long-range temporal dependencies. To overcome this limitation, we propose a novel attribution method that analyzes the entire information flow through all event-associated variables. Our method is built upon the recent Normalized Relevance Measure (NRM) framework, which enables explicit quantification of information flow originating from event embeddings as well as information flow passing through event-induced variables. It also ensures comparability of latent variables across layers, and supports higher-order analysis of interactions between events. To handle the architectural complexity of ETGNNs, we extend the NRM framework with a modular decomposition procedure that facilitates the systematic construction of relevance structure for complex neural architectures. We evaluate our approach on two synthetic datasets for epidemic tracing and social dynamics, as well as a real-world dataset of political event networks. Our qualitative and quantitative experiments show that our method consistently outperforms existing explanation approaches while producing more human-interpretable explanations.

Variable-order Markov models preserve local symbolic syntax by adapting context length, but long continuations can enter recurring high-order "tunnels": repeated suffixes, locally periodic passages, or copied fragments longer than the formal Markov order. This paper introduces signed pattern control for variable-order Markov generation with BP-Regular sampling. A weighted recurrence automaton computes an activation R for a chosen family of target patterns, and belief propagation samples exactly from P_beta(x) proportional to P_0(x) exp(beta R(x)). Negative coupling makes the target patterns costly during sampling; positive coupling rewards the same patterns and turns them into controlled attractors. The target family may be mined online from overactive generated material, supplied by a score or style vocabulary, or designed as an experimental probe. The main experiments use the online homeostatic case, choosing patterns that become overactive in the sampling history. On six duration-bearing monophonic sources, including Bach and Telemann material, the negative branch reduces generated 8-gram self-reuse, increases the effective number of generated 8-grams, and increases coverage of training-supported 4-gram contexts while preserving substantial lower-order support. A pitch-sequence replication on five Weimar Jazz Database solos gives the same anti-reuse signature outside Baroque material. The same signed mechanism also provides a positive branch for probing attractor basins, phase transitions, and hysteresis in the underlying variable-order model.

IVF pregnancy rates are routinely modeled using patient-level variables, while high-resolution laboratory environmental data remain underutilized. We show that this is a missed opportunity. Rather than relying on raw sensor averages, we engineer 55 context-aware temporal features, including rolling thermal stability, simultaneous temperature-humidity adherence, peak stress duration, and post-stress recovery speed, that capture the dynamics of incubator microenvironments. On 61 weeks of data from an Asian IVF clinic, these features reduce cross-validated prediction error to 1.27%, compared to 3-5% for raw averages. We then train a hierarchical Bayesian Beta regression model that shares environmental effects across an Asian and a Northern European clinic via partial pooling, while preserving site-specific baselines. On held-out data from the Northern European clinic, the model achieves R2 = 0.86 and a 64% error reduction for the 35-39 age group over a naive baseline, demonstrating that structured environmental monitoring contains clinically meaningful, transferable signal.

Causal abstractions formalize when a high-level structural causal model (SCM) captures the interventional behavior of a lower-level SCM. Existing applications of this notion largely follow a hypothesis-testing paradigm: an expert proposes a candidate high-level model and then evaluates if the low-level system implements it. We study the complementary problem of learning a high-level model directly from low-level measurements. Our contributions leverage hypotheses from low-rank causal discovery, and can be summarized as follows: (1) we show that observations generated by a low-rank graph induce latents that form a causal abstraction, (2) we provide identifiability results about these latents, and (3) we propose a practical objective to learn this high-level SCM.

Learning unsupervised representations of medical imaging cohorts can reveal anatomically meaningful prototypes without expert labels, which are often noisy and fail to capture true pathological heterogeneity. However, existing deep latent-variable models estimate Gaussian mixture priors via Euclidean averaging, producing prototypes that drift off the curved data manifold and degenerate as the number of sub-populations grows. We propose a manifold-anchored variational framework built on a geometry-aware Expectation-Maximization (EM) algorithm, whose M-step selects each sub-population prototype as the graph medoid with the highest diffusion centrality on a heat-kernel-weighted latent graph, ensuring that every prototype remains on-manifold. A Dirichlet energy regularizer enforces geometric smoothness of the latent space, and a per-sub-population uncertainty score enables label-free quality assessment. The manifold-anchored EM is a general-purpose geometric tool that extends standard EM and applies readily to other latent-variable models beyond this setting. On cardiac scar and brain MRI benchmarks, our framework attains the highest accuracy among all compared methods, produces the sharpest prototypes reported to date, and remains stable at large sub-population counts where all baselines degenerate. Code and implementation details are available at https://github.com/jr-xing/On-Manifold-Variational-Learning-with-Heat-Kernel-Priors.

Reliable generalization in conditional latent variable models requires understanding both identifiability and extrapolation: how observed variation across attributes determines latent structure, and how that structure determines distributions at unseen attributes. However, existing identifiability and extrapolation guarantees are largely model-specific, with separate analyses in nonlinear ICA, causal representation learning, perturbation modeling, and related conditional latent variable models. We introduce concept modulation models (CMMs), an attribute-indexed class of conditional generative models with structure $A\to Λ\to C\to X$, where attributes select modulators, modulators induce latent concept laws, and concepts generate observed features. CMMs lift transition-based identifiability to conditional settings by showing that feature agreement on observed attributes induces a latent concept transition constrained by the CMM class. We express these constraints through attribute potentials, log-density ratios between attribute-conditioned concept laws, separating the generic lifting step from model-specific rigidity arguments. The same potentials control extrapolation: agreement at unseen attributes holds exactly when the transported attribute-potential identities extend to those attributes. This yields algebraic extrapolation criteria, identifies the common potential-based proof objects behind several existing identifiability and extrapolation results, and, when combined with the model-specific rigidity arguments in those works, recovers their stated conclusions.

Variational inference (VI) is a core engine of modern AI, enabling scalable approximate Bayesian learning and uncertainty-aware training of large probabilistic and generative models. In this paper, we propose Structured Nonparametric Variational Inference (SN-VI), a novel framework for modeling complex dependencies among latent variables in posterior approximation, leveraging multivariate spline techniques. Unlike traditional methods that rely on the mean-field assumption, SN-VI preserves intricate latent variable dependencies, providing a flexible and accurate approximation of posteriors with arbitrary shapes. We establish rigorous theoretical guarantees, including the derivation of the lower bound for the variational objective and proof of asymptotic consistency in posterior estimation. To facilitate practical implementation, we develop an algorithm that automatically identifies dependent latent variables and their underlying dependence structure, without requiring manual specification. Simulation studies validate the effectiveness of SN-VI in approximating posterior distributions with bounded support and complex dependencies. The proposed method has been successfully applied to high-dimensional structured data, including computer vision datasets and spatial transcriptomics. In these applications, SN-VI demonstrates improved generative model performance and effectively uncovers coupled biological signals through the learned dependency structure.

Information lattice learning (ILL) learns interpretable rules of a signal by alternately projecting the signal onto a partition lattice that encodes a hierarchy of abstractions and lifting selected rules back to the signal domain. When the signal is a probability mass function, we show the probabilistic rules learned by ILL admit a natural probabilistic graphical model (PGM) interpretation and develop this interpretation in detail. A partition in ILL induces a deterministic quotient variable, and a rule is the marginal law of that quotient variable. A rule set is therefore a collection of marginal constraints over interpretable abstractions. General lifting is the feasible family of all joint distributions satisfying those constraints, while special lifting chooses a maximum-ignorance reconstruction, implemented in ILL by an L2 uniformity principle closely related to maximum entropy. Under a Shannon-entropy lifting, the same constraints yield a log-linear factor graph whose factors are indexed by learned abstractions. The information lattice itself, however, is not a Bayesian network: its edges encode refinement and coarsening of abstractions, not conditional dependence. Thus ILL is best viewed as structure learning for interpretable constraint-based factor graphs over quotient variables. This view clarifies how ILL relates to graphical models and maximum entropy models, while suggesting new directions for inference, identifiability, and hybrid symbolic-probabilistic learning.

When a neural time-series model reports that one variable modulates another's effect on a target, is the discovered interaction a property of the data or an artifact of model flexibility? We argue that this is fundamentally a question of identifiability, governed by the geometry of the observed input support rather than by the specific neural architecture. We study the problem in a multiplicative-gating extension of neural additive vector autoregression (GNAVAR), in which source contributions are modulated by other lagged variables. We show that representational capacity is not identifiability: dependent inputs induce leakage between edge-specific interaction terms, and low-dimensional support permits distinct interaction decompositions that agree on the observed data while differing elsewhere. We then prove a population identifiability theorem for normalized minimal GNAVAR decompositions under explicit support conditions, including settings with shared modulators. The theory yields a simple practitioner-facing diagnostic: the effective rank of the joint lag-block covariance predicts, before fitting, whether interaction recovery is feasible for a given candidate set. When the candidate set is unknown, a two-seed stability check provides a practical operational test. The same support condition organizes empirical outcomes into the three states predicted by the theory. Our results show that interaction recoverability depends on support geometry, that effective rank provides a practical pre-fit diagnostic, and that instability across independent fits is a characteristic signature of non-identifiable interaction discovery. The identifiability phenomenon, the support condition, and the instability signature are model-agnostic; GNAVAR is the vehicle that makes them provable.

Self-supervised methods that learn representations and predict dynamics fully in the latent space, such as JEPA, have been shown to confuse slowly varying noise with the dynamical signals they aim to capture. Specifically, when noise features remain approximately constant within each trajectory, contrastive predictive objectives preferentially encode these features instead of the true latent variables governing the system. The learned representation then becomes dominated by trajectory-specific noise, so downstream performance degrades with noise strength and does not improve even as the number and duration of training trajectories increase. We argue that this failure is a property of the objective itself, shared by a long line of contrastive predictive objectives that sample negatives across trajectories. To illustrate this generality, we study the failure mode and its remedy in two settings: a standard SimCLR-style JEPA on a synthetic moving-dot dataset, and DySIB, a recently introduced method designed for extracting physically interpretable representations of dynamics, on movies of a rigid-body pendulum. When negatives are instead sampled within a single trajectory, the slow noise can no longer distinguish frames within that trajectory, removing the predictive shortcut. Training one encoder simultaneously on many such trajectories then forces it to encode the variables relevant for the dynamics, with longer trajectories yielding better representations even for strong slow noise. Our results point toward principles for designing contrastive predictive objectives in dynamical representation learning, especially for physical systems with noisy experimental observations.

Causal mediation analysis decomposes a treatment effect into indirect pathways through mediators and direct pathways not operating through them. Modern biomedical studies often involve high-dimensional covariates and mediators that are noisy proxies for lower-dimensional latent biological processes. Existing methods typically rely on sparsity, linear factor models, or ignore the connection among variables in the learned representations, which can be restrictive when measurements are nonlinear and covariate and mediator factors are structurally dependent. We propose MediEncoder, a representation-learning framework for nonlinear high-dimensional mediation analysis. MediEncoder jointly learns low-dimensional covariate and mediator representations using a coupled encoder-decoder architecture with a cross-factor network that links treatment and covariate representations to mediator representations. The learned features are then used in a cross-fitted efficient influence function-based estimator of natural direct and indirect effects. The resulting estimator is multiply robust and asymptotically normal under suitable regularity conditions. Simulations show that MediEncoder improves estimation accuracy over competing dimension-reduction approaches, and an application to Alzheimer's Disease Neuroimaging Initiative data illustrates its utility in high-dimensional biomedical causal mediation analysis.

Digital learning environments record learners' responses to individual items, making it possible to study the development of specific skills rather than overall scores. Drawing conclusions about learning from these data requires a model that links responses to latent skills and tracks how mastery changes over time. When the skills measured by each item are unknown, the analyst must decide whether to estimate this structure, the Q-matrix, jointly with the learning process, or to establish it first and study learning afterwards. We show that this decision can change substantive conclusions about how learners develop. Using dynamic cognitive diagnostic models, we analyse data from two reading games measuring vocabulary and comprehension from Grade 2 to Grade 3, with item-text embeddings providing prior information for the unknown Q-matrix. A joint analysis and a bias-corrected stepwise analysis agree that most learners move toward mastering both skills, but disagree about how many remain only partially proficient at Grade 3, changing how reading progress would be reported. A simulation study identifies when the two analyses diverge and shows that joint analysis is more reliable when the item-skill structure is uncertain and the item pool changes between grades. We provide R code for both analyses.

Causal representation learning aims to infer the high-level latent causal concepts that give rise to observed low-level measurements. This is particularly relevant for heterogeneous data from different environments or domains since distribution shifts often arise through sparse, localized changes in some of the underlying causal mechanisms, while other parts of the generative process remain unchanged. Whereas identifiability of causal representations has been studied extensively, practical uncertainty-aware methods and real-world use cases remain less explored. In this work, we propose a Bayesian approach to learning causal representations from multi-environment data, focusing on the case of discrete causal concepts and unknown multi-node soft interventions. To this end, we translate causal assumptions and interpretability desiderata into suitable priors and parametric choices within a hierarchical model. We then devise an inference scheme based on sequential Monte Carlo sampling to approximate the resulting multimodal posterior. We showcase our approach through case studies on social survey data, where latent causal concepts correspond to cultural values or political opinions, measurements to survey responses, and environments to different countries or states. Our model infers meaningful high-level concepts and plausible causal relations among them, demonstrating its utility for learning causal representations of complex real-world data.

Latent visual reasoning (LVR) inserts supervised latent tokens between perception and answer generation in vision-language models (VLMs). The field uses alignment between these latents and their visual targets, i.e., cosine similarity or mean squared error (MSE), as both the training loss and the quality metric, assuming that better alignment yields a better answer. We test this with a designed matrix of five LVR variants and find the assumption inverted: cosine alignment is negatively correlated with accuracy across all five (r=-0.94). To explain this, we introduce PRISM, a pair of inference-time diagnostics: a linear probe that asks where the answer is decodable, and a corruption test that asks whether the latent is load-bearing. The supervised latents are largely bypassed. Corrupting them shifts accuracy by at most four points. The answer is decodable downstream of the latent but not at it, and the size of this decodability gap predicts how much each variant relies on its latent under perturbation. Consistent with an Information Bottleneck reading of the loss, the auxiliary objective reshapes the language model via shared parameters rather than via the latent variable it nominally optimizes.

We consider multi-environment prediction problems. We assume the environments change the distribution of a latent variable, while the mechanisms generating observed covariates and targets remain stable conditional on that variable. For example, hospitals or clinical cohorts may differ in the prevalence of latent patient states, even though the relationships between those states, physiological measurements, and outcomes remain unchanged. Given a dataset from multiple environments, we formulate a Bayesian model for such problems and derive the corresponding variational objective. We show that this objective decomposes into per-environment terms and an additional cross-environment balancing term induced by the model's structure. We use an empirical Bayes method to set the prior and incorporate it into the objective. Based on this objective, we develop an amortized variational algorithm for posterior approximation, and use the resulting learned latent variables to form predictions in new environments.We study our approach through simulations and real-world studies of astronomical source identification, microbiome-based disease detection, and ICU sepsis prediction. Across these settings, our method outperforms previous approaches for prediction in new environments.

This paper studies the problem of inverting the DDIM image generation process to recover latent variables, particularly the initial noise map, from a generated image. Existing methods often struggle with accuracy in this task. We propose a novel hybrid approach that combines direct inversion via gradient descent for the first step, followed by a fixed-point method for subsequent steps. Empirical evaluations across three datasets demonstrate that our method significantly improves the prediction of initial latent variables while achieving superior reconstruction accuracy. Additionally, we introduce a new evaluation, called the self-interpolation test, which assesses the quality of images generated from interpolated points between the true and predicted latent maps, offering deeper insights into performance. Our results reveal that while existing methods perform reasonably well in reconstruction, they consistently fail to accurately predict the initial latent variables, resulting in poor performance on the self-interpolation test. In contrast, our method outperforms all others across all metrics, providing valuable insights into diffusion models and enhancing their applications in image generation and editing.

Temporal systems often exhibit non-stationary behaviour, such as seasonal climate variation or glucose fluctuations in patients with type-1 diabetes. One way to model non-stationarity is through discrete latent regimes, i.e., stationary segments of time. Such systems induce a Markov Switching Model (MSM), a class of Hidden Markov Models with autoregressive dependencies among latent regimes and observed variables. Identifying latent regimes is challenging in the presence of frequent regime switches and nonlinear and non-Gaussian dynamics, particularly when there are instantaneous effects between the variables, e.g., due to slow rates of measurements. In this work, we establish the identifiability of both latent regimes and regime-dependent causal structures under temporal regime dependencies, nonlinear lagged and instantaneous effects, and independent noise from the exponential family. Our identifiability theory subsumes non-temporal mixtures of causal models. Furthermore, we introduce FlowMSM, a regime detection framework that can be paired with any stationary causal discovery method to recover regime-dependent causal structures. Experiments on synthetic benchmarks and a financial economics dataset demonstrate the effectiveness of our approach to detect latent regimes and discover causal structures from non-stationary time series.

Stochastic gradient Langevin dynamics combined with Gibbs updates (SGLD--Gibbs) provides a highly scalable approach to approximate Bayesian inference in latent variable models. However, it remains unclear how to tune the algorithm's hyperparameters in a principled manner to ensure the uncertainty estimates are statistically meaningful. In this work, we address this gap in tuning guidance by developing a statistical scaling limit theory for SGLD--Gibbs. We derive a joint asymptotic limit for the global parameters and latent variables under appropriate space-time rescaling. We show that global parameters converge to a diffusion-type limit, while each latent variable converges to a jump process, reflecting the use of intermittent Gibbs updates. This joint jump-diffusion structure reveals how latent-variable randomness contributes to the stationary distribution of the global parameters. We leverage our results to propose explicit guidance on hyperparameter tuning for SGLD--Gibbs that ensures meaningful uncertainty quantification. Numerical experiments show that SGLD--Gibbs with our tuning guidance leads to better parameter estimates, uncertainty quantification, and predictive performance than stochastic variational inference.

Recent speech language models rely on encoders that are optimized separately from autoregressive models. Since these encoders are unaware of the downstream objectives, the extracted representations may not be optimal for downstream tasks. To address this limitation, we introduce a discrete latent variable model on mel spectrograms that jointly optimizes the encoder and the speech language model. Joint optimization not only brings improvements over codec-based and other mel-spectrogram-based baselines on zero-shot Text-to-Speech (TTS) and Speech-to-Text (STT) tasks, but also effectively alleviates common issues in autoregressive mel spectrogram modeling, such as prolonged silence generation and word omissions.

We consider the problem of learning a counterfactually fair regressor. We adopt a causal uncertainty view in which counterfactual fairness is defined with resampled noise. We focus on obtaining theoretical fairness guarantees for a new post-processing estimator. We begin by showing that counterfactual fairness is equivalent to satisfying demographic parity conditional on the latent variable. This allows us to provide a closed-form expression of the optimal fair regressor via a barycentric quantile map. In order to handle continuous latent variables, we propose a discretized post-processing method. Then, under mild regularity assumptions, we prove high-probability finite-sample fairness guarantees for our estimator, providing an unfairness decay at rate $\tilde O(n^{-1/3})$, and establishing a matching risk bound of order $\tilde O(n^{-1/3})$. We provide a matching lower bound on the excess risk of almost fair predictions. Finally, we extend our results to the setting of relaxed counterfactual fairness. We validate our approach on real-world and synthetic data.

Deep generative models offer powerful tools for multivariate data analysis, but their black-box architectures are often unidentified and difficult to interpret. We introduce the Deep Discrete Encoder (DDE) Copula, an identifiable and interpretable generative model for multivariate data with arbitrary marginal distributions. The model places a hierarchical directed network of binary latent variables inside a copula framework, enabling flexible dependence modeling for mixed discrete and continuous data. Estimation is based on rank likelihoods, which decouple marginal modeling from posterior inference on the DDE parameters and avoid specifying the marginal distributions. We establish conditions for identification of the DDE copula parameters, ensuring that layer-specific parameters provide meaningful summaries of multivariate dependence. We also prove quotient-space posterior consistency for continuous margins under the exact rank likelihood and treat the extended rank likelihood for tied or mixed margins as a generalized likelihood, with concentration under an additional contrast condition. For computation, we propose a stochastic expectation-maximization algorithm for \emph{maximum a posteriori} estimation, together with initialization strategies that improve convergence. To learn network dimension adaptively, we extend Bayesian rank-selection priors to infer layer-specific widths. Simulations show strong finite-sample performance, and a personality-survey analysis reveals interpretable hierarchical latent structure in complex multivariate data.

In this paper, we introduce a model of evolution and learning in robots that co-optimizes a distribution of latent design vectors (genotypes) and a mixture of control experts (neural modules), which are gated by the latent coordinates of each decoded design (phenotype). This provides a scalable alternative to co-design algorithms that either train an individual policy for every robot, which is inefficient, or a monolithic universal controller for all robots, which results in overly conservative structures and behaviors. Our approach lies somewhere between these two extremes, preserving ancestral knowledge in a unified yet modular framework in which different body plans activate and deactivate different combinations of learned sensorimotor circuits for goal-directed behavior. This allows one part of the controller to be overhauled to better suit new species of designs as they emerge without disrupting the hard-earned knowledge contained within other expert modules. It also allows pretrained expert policies to be directly plugged into the mixture, which can steer evolution into otherwise unexplored areas of latent space containing desired morphological traits. We refer to this process as "evo by demo" and explore how it may be used to guide freeform evolution toward canonical structures defined by the pretrained model. Videos and code can be found at: https://eco-moe.github.io.

Causal discovery from multivariate time series is challenging when causal effects may occur both across time and within the same sampling interval. This issue is especially important in applications such as neuroscience, where the sampling rate may be coarse relative to the underlying dynamics and contemporaneous effects need not form an acyclic graph. We study causal discovery in linear Gaussian structural VAR models under an equal noise variance assumption, meaning that the structural noise terms have a common variance. Unlike the DAG-based cross-sectional equal noise variance setting, the time-series setting considered here does not generally yield point identification of a unique causal graph. Instead, multiple structural VAR parameterizations can induce the same stationary observed process law. We introduce a notion of observational equivalence tailored to this setting and show that the corresponding equivalence class is characterized by orthogonal transformations of the structural equations together with a global positive scale. This characterization leads to an equivalence-aware model discrepancy, the observational alignment discrepancy, which compares structural models modulo transformations that preserve the observed law. Building on this theory, we propose ENVAR, a sparsity-based procedure that searches over the induced observational equivalence class for a sparse normalized structural representative. We evaluate the proposed methodology on synthetic structural VAR data and on an fMRI dataset.

Many recent flow-matching and diffusion-style generative models rely on auxiliary stochastic dynamics during training: a richer process is simulated to define conditional targets, but the auxiliary state is either intractable to sample at generation time or simply not part of the desired output. Existing Generator Matching theory formalises conditioning on static latent random variables, and several recent papers prove special cases of projection results for particular augmented-state constructions. We introduce latent process generator matching, a general framework that treats the observed generative state as a deterministic image $X_t=Φ(Y_t)$ of a tractable Markov process $Y_t$. We show that in this setting one may learn the generator of a stochastic process on the image space which has the same one-time marginal distributions as the projected process. This generalizes and subsumes the discrete latent process results from the literature, and extends Generator Matching from static latent variables to a rich family of time-dependent latent conditional processes.

We study whether multimodal large language models (MLLMs) can leverage crystallographic plane indices (Miller indices) as a structured latent representation for reasoning about fracture geometry. We formulate Miller indices $z = (h,k,l)$ as a latent variable governing idealized planar fracture and evaluate two complementary capabilities: (i) latent inference, where the model maps visual observations to plane hypotheses under physically valid conditions, and (ii) latent applicability assessment, where the model determines whether such a representation is meaningful for a given fracture image. Through extensive experiments spanning synthetic data, controlled 2D--3D geometric pairs, and real-world fracture images across multiple material classes -- including ceramics, glass, metals, and concrete -- we show that MLLMs can reliably perform latent inference in idealized settings and, critically, can reject the latent representation when the underlying physics does not support it. As an exploratory extension, we further examine AI-generated fracture sequences and observe qualitatively plausible brittle-fracture progression behaviors, suggesting that multimodal generative models may encode partial implicit physical priors related to material failure dynamics. These results suggest that MLLMs can act as physics-aware reasoning systems conditioned on structured latent priors, provided that the domain of validity is explicitly modeled.

Identifying latent variables and the causal structure involving them is essential across various scientific fields. While many existing works fall under the category of constraint-based methods (with e.g. conditional independence or rank deficiency tests), they may face empirical challenges such as testing-order dependency, error propagation, and choosing an appropriate significance level. These issues can potentially be mitigated by properly designed score-based methods, such as Greedy Equivalence Search (GES) (Chickering, 2002) in the specific setting without latent variables. Yet, formulating score-based methods with latent variables is highly challenging. In this work, we develop score-based methods that are capable of identifying causal structures containing causally-related latent variables with identifiability guarantees. Specifically, we show that a properly formulated scoring function can achieve score equivalence and consistency for structure learning of latent variable causal models. We further provide a characterization of the degrees of freedom for the marginal over the observed variables under multiple structural assumptions considered in the literature, and accordingly develop both exact and continuous score-based methods. This offers a unified view of several existing constraint-based methods with different structural assumptions. Experimental results validate the effectiveness of the proposed methods.

Causal representation learning (CRL) seeks to uncover meaningful latent variables and their corresponding causal structure from high-dimensional observational data. Although its significance, CRL identifiability remains a crucial property, as it ensures the recovery of the mechanisms behind the data generation process, and hence the interpretability and robustness of the representation. Proving identifiability in CRL is intrinsically difficult, and we address in this work an even more challenging setting: multimodality. We consider multimodal observed data with a latent partially shared structure. Each modality is generated, through non linear mixing functions, from a specific subset of causal latent variables. Under flexible assumptions and without imposing any parametric distribution on the latent variables, we establish component-wise identifiability guarantees for the causal latent representation. Our identifiability results, furthermore, apply to the undercomplete scenario where we have, for each modality, more observed than latent variables. To instantiate our theoretical analysis, we introduce a Wasserstein-based module to recover the partially shared latent structure. Due to its differentiability, the latter can be easily integrated into all types of architecture, only requiring minimal changes. Extensive experiments on synthetic and realistic datasets validate the superiority of our approach over SOTA methods.

Despite their ubiquity, variational autoencoders (VAEs) inherently suffer from posterior collapse, a failure mode in which latent variables are effectively ignored. This failure arises because explicit prior imposition drives optimization toward loss landscape regions corresponding to uninformative latent representations. Here, we introduce Entropic Autoencoders (EAEs), a framework in which reconstruction loss is the only explicit objective, and entropy generates the latent variables' prior implicitly through a free energy-minimizing ensemble of encoders. This ensemble biases learning toward high-volume regions of near-optimal solutions, while decoder updates direct the search trajectories toward informative latent representations. We demonstrate that EAEs mitigate posterior collapse by learning non-Gaussian, multimodal latent distributions that yield diverse, data-consistent generations and preserve different forms of underlying structure in the data. As a proof-of-concept, we show that an EAE captures a superposition of the known low-dimensional dynamics of a reaction-diffusion process. Then, we show that an EAE identifies implicit categorical distinctions in MNIST latent representations, and displays a hierarchical understanding of facial structure on the CelebA dataset, from an "all-human" face to individual-dependent features.

Variational Autoencoders (VAEs) often exhibit a polarised regime in which latent variables separate into active, passive, and mixed subsets. Existing criteria for identifying active dimensions depend on a Gaussian prior, limiting their applicability to variational models and specific priors. We propose a simple information-theoretic classification of the polarised regime based on the entropy of the mean representation. We show theoretically how this entropy couples to KL minimisation through entropy--variance bounds, and we relate the resulting criterion to Bonheme's active/passive conditions. We also clarify a key limitation: entropy of the mean alone cannot reliably distinguish active from mixed dimensions without additional signals from the variance representation. Empirically, we evaluate the entropy criterion on $β$-VAEs, identifiable VAEs, Least-Volume Autoencoders, and L2-regularised autoencoders, and find that it consistently recovers a polarised regime when such a regime is present across the model classes studied. Finally, we show that passive dimensions can yield small but consistent improvements on downstream tasks when latent codes are appropriately normalised, suggesting that collapse is often a matter of scale rather than absolute information removal.

The success of deep learning in high-dimensional settings is often attributed to the presence of low-dimensional structure in real-world data. While standard theoretical models typically assume that this structure lies in the target function, projecting unstructured inputs onto a low-dimensional subspace, data such as images, text or genomic sequences exhibit strong spatial correlations within the input space itself. In this paper, we propose a tractable model to study how these correlations affect the sample complexity of learning with gradient descent on shallow neural networks. Specifically, we consider targets that depend on a small number of latent Boolean variables, and input features grouped into clusters and correlated with the latent variables. Under an identifiability assumption, we show that for a layerwise gradient-descent variant, the sample complexity scales with the number of hidden variables and, when the signal-to-noise ratio is sufficiently high, is independent of the input dimension, up to logarithmic terms. We empirically test our theoretical findings on both synthetic and real data.

Acquisition differences across sites, scanners, and protocols in dMRI introduce variability that complicates structural connectome analysis. This motivates deep learning models that can represent high-dimensional connectomes in a low-dimensional space while explicitly separating acquisition-related effects from biological variation. Conventional dimensionality reduction methods model all variance as continuous, so acquisition effects often get absorbed into a continuous latent space. Recent hybrid latent-space models combine discrete and continuous components to address this, but typically require manual capacity tuning to ensure the discrete component captures the intended variability. We introduce an unsupervised framework that removes this manual tuning by architecturally annealing encoder outputs before decoding, allowing the model to adaptively balance discrete and continuous latent variables during training. To evaluate it, we curated a dataset of N=7,416 structural connectomes derived from dMRI, spanning ages 2 to 102 and 13 studies with 25 unique acquisition-parameter combinations. Of these, 5,900 are cognitively unimpaired, 877 have mild cognitive impairment (MCI), and 639 have Alzheimer's disease (AD). We compare against a standard VAE, PCA with k-means clustering, and hybrid models that anneal only through the loss function. Our architectural annealing produces stronger site learning (ARI=0.53, p<0.05) than these baselines. Results show that a hybrid continuous-discrete latent space, with architectural rather than loss-based annealing, provides a useful unsupervised mechanism for capturing acquisition variability in dMRI: by jointly modeling smooth and categorical structure, the Joint-VAE recovers clusters aligned with scanner and protocol differences.

The remarkable achievements of both generative models of 2D images and neural field representations for 3D scenes present a compelling opportunity to integrate the strengths of both approaches. In this work, we propose a methodology that combines a NeRF-based representation of 3D scenes with probabilistic modeling and reasoning using diffusion models. We view 3D reconstruction as a perception problem with inherent uncertainty that can thereby benefit from probabilistic inference methods. The core idea is to represent the 3D scene as a stochastic latent variable for which we can learn a prior and use it to perform posterior inference given a set of observations. We formulate posterior sampling using the score-based inference method of diffusion models in conjunction with a likelihood term computed from a reconstruction model that includes volumetric rendering. We train the model using a two-stage process: first we train the reconstruction model while auto-decoding the latent representations for a dataset of 3D scenes, and then we train the prior over the latents using a diffusion model. By using the model to generate samples from the posterior we demonstrate that various 3D reconstruction tasks can be performed, differing by the type of observation used as inputs. We showcase reconstruction from single-view, multi-view, noisy images, sparse pixels, and sparse depth data. These observations vary in the amount of information they provide for the scene and we show that our method can model the varying levels of inherent uncertainty associated with each task. Our experiments illustrate that this approach yields a comprehensive method capable of accurately predicting 3D structure from diverse types of observations.

Constraint-based causal discovery is widely used for learning causal structures, but heavy reliance on conditional independence (CI) testing makes it computationally expensive in high-dimensional settings. To mitigate this limitation, many divide-and-conquer frameworks have been proposed, but most assume causal sufficiency, i.e., no latent variables. In this paper, we show that divide-and-conquer strategies can be theoretically generalized beyond causal sufficiency to settings with latent variables. Specifically, we propose a recursive decomposition framework, termed DiCoLa, that enables divide-and-conquer causal discovery in the presence of latent variables. It recursively decomposes the global learning task into smaller subproblems and integrates their solutions through a principled reconstruction step to recover the global structure. We theoretically establish the soundness and completeness of the proposed framework. Extensive experiments on synthetic data demonstrate that our approach significantly improves computational efficiency across a range of causal discovery algorithms, while experiments on a real-world dataset further illustrate its practical effectiveness.

Recent work on causal abstraction, in particular graphical approaches focusing on causal structure between clusters of variables, aims to summarize a high-dimensional causal structure in terms of a low-dimensional one. Existing methods for learning such summaries from data assume that both the high- and low-dimensional structures are acyclic, which is helpful for causal effect identification and reasoning but excludes many high-dimensional models and thus limits applicability. We show that in the linear non-Gaussian (LiNG) setting, the high-dimensional acyclicity assumption can be relaxed while still allowing recovery of a low-dimensional causal directed acyclic graph (DAG). We further connect identifiability of this low-dimensional DAG to existing results: LiNG models with cycles are observationally identifiable only up to an equivalence class whose members differ by reversals of directed cycles; our low-dimensional DAG, which is invariant across all members of a given equivalence class, thus forms a natural representative of the class. While existing approaches for learning this observational equivalence class over high-dimensional variables have exponential time complexity, our low-dimensional summary is learned in worst-case cubic time and comes with explicit bounds on the sample complexity. We provide open source code and experiments on synthetic data to corroborate our theoretical results.

We study online estimation in latent-variable models by recasting the problem as tracking a moving empirical equilibrium. Standard online EM and stochastic approximation analyses primarily study convergence toward the population parameter and typically do not isolate the empirical batch optimum from the online tracking error at finite horizon. Our framework decomposes the online estimate into the frozen batch equilibrium at the current running statistic and a tracking lag that captures the algorithm's delay behind this moving target. We prove a batch-to-online transfer theorem: provided $\lVert e_T \rVert_{L^{2}} = o(T^{-1/2})$, the online estimator inherits the batch central limit theorem and the sharp first-order risk constant. Our key observation is that the empirical optimum evolves on a smooth equilibrium manifold indexed by the running statistic. An $m$-th order equilibrium-jet predictor combined with an order-$ν$ frozen corrector yields localized tracking rates $O(T^{-ν(m+1)})$. We formalize EM-compressibility and EM-jet$^R$-compressibility as the structural conditions that make the equilibrium response and the Newton corrector evaluable from a retained streaming statistic. The theory is instantiated in latent linear Gaussian covariance estimation, where the first-order scheme operates on a compressed $d \times d$ statistic with explicit finite-sample risk envelopes and a certified restart rule.

Standard flow matching scales well but typically relies on an unstructured source distribution, limiting its ability to learn interpretable latent structure. Latent-variable models, by contrast, capture structure but often sacrifice generative quality. We bridge this gap by proposing Structured Coupling for Flow Matching (SCFM), a cooperative framework that augments flow matching with structured latent representation learning. By introducing structured latent variables and exogenous noise into the source, SCFM jointly learns a structured prior (via latent variable modeling) and a continuous transport map (via flow matching). It uses a shared time-dependent recognition network for both latent variable model variational inference and intermediate-time flow velocity estimation. This yields a structurally informed yet unconditional, simulation-free flow model, where the latent variable model can also assist flow sampling. Empirically, SCFM facilitates unsupervised latent representation learning for clustering, disentanglement and downstream tasks, while remaining competitive with flow matching in sample quality, showing that meaningful structure can be learned without sacrificing generative fidelity.