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Yuqi Gu

Publications and source records attributed to Yuqi Gu.

At least 19 recordsLinked to original sources
arXiv2026

From Good Starts to Optimal Inference: Generalized Latent Factor Models with Missingness and Implicit Regularization

Generalized latent factor models provide a flexible framework for analyzing high-dimensional non-Gaussian data, but principled estimation and uncertainty quantification under missingness remain substantially less developed. We develop a theory that connects a computationally tractable nonconvex procedure directly to statistical inference for nonlinear latent factor models with exponential-family links and partially observed entries. Our procedure combines a link-aware double-SVD initialization, a unilateral refinement that achieves rowwise consistency, and vanilla gradient descent. We show that the refined initializer enters a region of incoherence and contraction and that gradient descent remains in this region through implicit regularization, contracting rapidly down to the statistical estimation error without explicit incoherence or balancing regularization. Our central result is a uniform rowwise linear approximation for the actual output of gradient descent that isolates the leading score fluctuations from higher-order estimation and optimization errors. These expansions yield asymptotically valid individual and Gaussian multiplier-bootstrap simultaneous inference for latent factors, together with simultaneous confidence bands for missing-entry means, without requiring an additional debiasing step. The resulting estimation rate matches a restricted-class minimax lower bound up to logarithmic factors, while the theory accommodates severe missingness, weak low-rank signals, and diminishing local curvature. Simulations support the theoretical findings, and an application to large language model evaluation illustrates uncertainty-aware estimation and ranking of latent model capabilities.

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arXiv2026

A4A: Cross-Embodiment Transfer of Action-Oriented 4D Affordances from Human Demonstrations

Human demonstrations contain rich manipulation knowledge, but it remains unclear what information can be transferred effectively to robot control. Existing affordance representations are typically formulated as 2D masks, 3D regions, contact points, or actionability scores, and therefore primarily identify where interaction may occur. However, effective manipulation also requires modeling how interaction-relevant geometry evolves during task execution. To bridge this gap, we introduce action-oriented 4D affordances, which represent the language-conditioned future trajectories of interaction-relevant 3D points. These trajectories capture task-conditioned geometric evolution rather than embodiment-specific actions, enabling transferable interaction priors across humans and robots. Based on this representation, we construct a large-scale action-oriented 4D affordance dataset from existing human--object interaction video data and complementary RGB-D demonstrations, and introduce A4A, an affordance-to-action framework that uses 4D affordance trajectory prediction to pretrain robot policies before manipulation fine-tuning. Experiments in both simulation and the real world validate the effectiveness of A4A, showing that pretraining with action-oriented 4D affordance data consistently improves the manipulation performance of diverse VLA policies. These results establish action-oriented 4D affordances as an effective cross-embodiment representation for transferring manipulation knowledge from human demonstrations to robot control.

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arXiv2026

Mixed Membership Model of Low-rank Matrices with Multimodal Extension

Matrix-valued observations arise in multiplex networks, neuroimaging, and other domains where population-level patterns are often low-rank and subjects may express several latent patterns simultaneously. Existing tensor PCA methods provide continuous subject scores but their loading matrices can be difficult to interpret as population prototypes, while low-rank clustering yields interpretable prototypes with hard labels. We introduce a low-rank mixed membership model for matrix-valued data in which the expected value of each subject's matrix is a convex combination of latent low-rank basis matrices. The model yields both interpretable population-level extreme profiles and continuous subject-level memberships. Our multimodal extension shares memberships across modalities with modality-specific basis matrices and can restore identifiability when one modality is insufficient. We establish identifiability under a pure-subject condition, propose a constrained least-squares estimator and scalable algorithm with spectral initialization and low-rank refinement, and derive nonasymptotic error bounds. The estimator achieves a minimax-optimal reconstruction rate up to a logarithmic factor, with separate basis and membership convergence rates under a geometric condition. Simulations corroborate the theoretical rates and show strong performance. In an analysis of Human Connectome Project functional connectivity data, the proposed method identifies interpretable brain connectivity profiles whose estimated memberships are strongly associated with cognitive phenotypes.

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arXiv2026

Beyond Local Independence: High-Dimensional Latent Class Graphical Models with Shared Block Structure

Latent class models are central tools for multivariate categorical data from heterogeneous populations, but their standard local-independence assumption is often unrealistic in modern high-dimensional applications. We propose a high-dimensional latent class graphical model for ordinal responses with block-structured local dependence. The model retains the interpretability and parsimony of classical latent class analysis by imposing a shared block partition of variables, while allowing class-specific graphical dependence within each block. We develop a scalable three-step estimator that first recovers latent classes by spectral clustering of a flattened response matrix, then estimates class-specific latent covariance matrices and aggregates them to recover the shared block partition, and finally estimates sparse within-block precision matrices. We establish finite-sample error bounds for clustering, covariance estimation, block recovery, and precision-matrix estimation, yielding end-to-end consistency of all model components under high-dimensional scaling. Simulations demonstrate accurate recovery of latent classes, the shared block partition, and class-specific dependence graphs with scalable computation. Applications to American National Election Studies survey data and HapMap3 genotype data show that the method uncovers interpretable local dependence structures while accounting for latent heterogeneity.

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arXiv2026

Identifiable Bayesian Deep Generative Copulas with Unknown Layer Widths for Data with Arbitrary Marginal Distributions

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.

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arXiv2026

BridgeACT: Bridging Human Demonstrations to Robot Actions via Unified Tool-Target Affordances

Learning robot manipulation from human videos is appealing due to the scale and diversity of human demonstrations, but transferring such demonstrations to executable robot behavior remains challenging. Prior work either relies on robot data for downstream adaptation or learns affordance representations that remain at the perception level and do not directly support real-world execution. We present BridgeACT, an affordance-driven framework that learns robotic manipulation directly from human videos without requiring any robot demonstration data. Our key idea is to model affordance as an embodiment-agnostic intermediate representation that bridges human demonstrations and robot actions. BridgeACT decomposes manipulation into two complementary problems: where to grasp and how to move. To this end, BridgeACT first grounds task-relevant affordance regions in the current scene, and then predicts task-conditioned 3D motion affordances from human demonstrations. The resulting affordances are mapped to robot actions through a grasping module and a lightweight closed-loop motion controller, enabling direct deployment on real robots. In addition, we represent complex manipulation tasks as compositions of affordance operations, which allows a unified treatment of diverse tasks and object-to-object interactions. Experiments on real-world manipulation tasks show that BridgeACT outperforms prior baselines and generalizes to unseen objects, scenes, and viewpoints.

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arXiv2026

Discrete Causal Representation Learning

Causal representation learning seeks to uncover causal relationships among high-level latent variables from low-level, entangled, and noisy observations. Existing approaches often either rely on deep neural networks, which lack interpretability and formal guarantees, or impose restrictive assumptions like linearity, continuous-only observations, and strong structural priors. These limitations particularly challenge applications with a large number of discrete latent variables and mixed-type observations. To address these challenges, we propose discrete causal representation learning (DCRL), a generative framework that models a directed acyclic graph among discrete latent variables, along with a sparse bipartite graph linking latent and observed layers. This design accommodates continuous, count, and binary responses through flexible measurement models while maintaining interpretability. Under mild conditions, we prove that both the bipartite measurement graph and the latent causal graph are identifiable from the observed data distribution alone. We further propose a three-stage estimate-resample-discovery pipeline: penalized estimation of the generative model parameters, resampling of latent configurations from the fitted model, and score-based causal discovery on the resampled latents. We establish the consistency of this procedure, ensuring reliable recovery of the latent causal structure. Empirical studies on educational assessment and synthetic image data demonstrate that DCRL recovers sparse and interpretable latent causal structures.

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arXiv2026

Scalable Text-Embedding-informed Cognitive Diagnosis of Large Language Models

Large language models (LLMs) have achieved remarkable performance on diverse benchmarks, yet existing evaluation practices largely rely on coarse summary metrics that obscure underlying reasoning abilities. In this work, we propose novel methodologies to adapt cognitive diagnosis models (CDMs) in psychometrics to LLM evaluation, enabling fine-grained diagnosis via multidimensional discrete capability profiles and interpretable characterizations of LLM strengths and weaknesses. First, to enable CDM-based evaluation at benchmark scale (more than 1000 items), we propose a scalable method that jointly estimates LLM mastery profiles and the item-attribute Q-matrix, addressing key challenges posed by high-dimensional latent attributes (K > 20), large item pools, and the prohibitive computational cost of existing marginal maximum likelihood-based estimation. Second, we incorporate item-level textual information to construct AI-embedding-informed priors for the Q-matrix, stabilizing high-dimensional estimation while reducing reliance on costly human specification. We develop an efficient stochastic-approximation algorithm to jointly estimate LLM mastery profiles and the Q-matrix that balances data fit with text-embedding-informed priors. Simulation studies demonstrate accurate parameter recovery. An application to the MATH Level 5 benchmark illustrates the practical utility of our method for LLM evaluation and uncovers useful insights into LLMs' fine-grained capabilities.

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arXiv2026

Covariate-assisted Grade of Membership Models via Shared Latent Geometry

The grade of membership model is a flexible latent variable model for analyzing multivariate categorical data through individual-level mixed membership scores. In many modern applications, auxiliary covariates are collected alongside responses and encode information about the same latent structure. Traditional approaches to incorporating such covariates typically rely on fully specified joint likelihoods, which are computationally intensive and sensitive to misspecification. We introduce a covariate-assisted grade of membership model that integrates response and covariate information by exploiting their shared low-rank simplex geometry, rather than modeling their joint distribution. We propose a likelihood-free spectral estimation procedure that combines heterogeneous data sources through a balance parameter controlling their relative contribution. To accommodate high-dimensional and heteroskedastic noise, we employ heteroskedastic principal component analysis before performing simplex-based geometric recovery. Our theoretical analysis establishes weaker identifiability conditions than those required in the covariate-free model, and further derives finite-sample, entrywise error bounds for both mixed membership scores and item parameters. These results demonstrate that auxiliary covariates can provably improve latent structure recovery, yielding faster convergence rates in high-dimensional regimes. Simulation studies and an application to educational assessment data illustrate the computational efficiency, statistical accuracy, and interpretability gains of the proposed method. The code for reproducing these results is open-source and available at \texttt{https://github.com/Toby-X/Covariate-Assisted-GoM}

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arXiv2025

Valid and Efficient Two-Stage Latent Subgroup Analysis with Observational Data

Subgroup analysis evaluates treatment effects across multiple sub-populations. When subgroups are defined by latent memberships inferred from imperfect measurements, the analysis typically involves two inter-connected models, a latent class model and a subgroup outcome model. The classical one-stage framework, which models the joint distribution of the two models, may be infeasible with observational data containing many confounders. The two-stage framework, which first estimates the latent class model and then performs subgroup analysis using estimated latent memberships, can accommodate potential confounders but may suffer from bias issues due to misclassification of latent subgroup memberships. This paper focuses on latent subgroups inferred from binary item responses and addresses when and how a valid two-stage latent subgroup analysis can be made with observational data. We investigate the maximum misclassification rate that a valid two-stage framework can tolerate. Introducing a spectral method perspective, we propose a two-stage approach to achieve the desired misclassification rate with the blessing of many item responses. Our method accommodates high-dimensional confounders, is computationally efficient and robust to noninformative items. In observational studies, our methods lead to consistent estimation and valid inference on latent subgroup effects. We demonstrate its merit through simulation studies and an application to educational assessment data.

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arXiv2025

Latency-Response Theory Model: Evaluating Large Language Models via Response Accuracy and Chain-of-Thought Length

The proliferation of Large Language Models (LLMs) necessitates valid evaluation methods to provide guidance for both downstream applications and actionable future improvements. The Item Response Theory (IRT) model with Computerized Adaptive Testing has recently emerged as a promising framework for evaluating LLMs via their response accuracy. Beyond simple response accuracy, LLMs' chain of thought (CoT) lengths serve as a vital indicator of their reasoning ability. To leverage the CoT length information to assist LLM evaluation, we propose the \textbf{La}tency-\textbf{R}esponse \textbf{T}heory (LaRT) model, which jointly models both the response accuracy and CoT length by introducing a key correlation parameter between the latent ability and the latent speed. We derive an efficient stochastic approximation Expectation-Maximization algorithm for parameter estimation. We establish rigorous identifiability results for the latent ability and latent speed parameters to ensure the statistical validity of their estimation. Through both theoretical asymptotic analyses and simulation studies, we demonstrate LaRT's advantages over IRT in terms of superior estimation accuracy and shorter confidence intervals for latent trait estimation. To evaluate LaRT in real data, we collect responses from diverse LLMs on popular benchmark datasets. We find that LaRT yields different LLM rankings than IRT and outperforms IRT across multiple key evaluation metrics including predictive power, item efficiency, ranking validity, and LLM evaluation efficiency. Code and data are available at https://github.com/Toby-X/Latency-Response-Theory-Model

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arXiv2025

Spectral Clustering with Likelihood Refinement for High-dimensional Latent Class Recovery

Latent class models are widely used for identifying unobserved subgroups from multivariate categorical data in social sciences, with binary data as a particularly popular example. However, accurately recovering individual latent class memberships remains challenging, especially when handling high-dimensional datasets with many items. This work proposes a novel two-stage algorithm for latent class models suited for high-dimensional binary responses. Our method first initializes latent class assignments by an easy-to-implement spectral clustering algorithm, and then refines these assignments with a one-step likelihood-based update. This approach combines the computational efficiency of spectral clustering with the improved statistical accuracy of likelihood-based estimation. We establish theoretical guarantees showing that this method is minimax-optimal for latent class recovery in the statistical decision theory sense. The method also leads to exact clustering of subjects with high probability under mild conditions. As a byproduct, we propose a computationally efficient consistent estimator for the number of latent classes. Extensive experiments on both simulated data and real data validate our theoretical results and demonstrate our method's superior performance over alternative methods.

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arXiv2025

On Theoretical Identifiability of Discrete Latent Causal Graphical Models

This paper considers a challenging problem of identifying a causal graphical model under the presence of latent variables. While various identifiability conditions have been proposed in the literature, they often require multiple pure children per latent variable or restrictions on the latent causal graph. Furthermore, it is common for all observed variables to exhibit the same modality. Consequently, the existing identifiability conditions are often too stringent for complex real-world data. We consider a general nonparametric measurement model with arbitrary observed variable types and binary latent variables, and propose a double triangular graphical condition that guarantees identifiability of the entire causal graphical model. The proposed condition significantly relaxes the popular pure children condition. We also establish necessary conditions for identifiability and provide valuable insights into fundamental limits of identifiability. Simulation studies verify that latent structures satisfying our conditions can be accurately estimated from data.

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arXiv2025

Bayesian Latent Class Regression with Interpretable Binary Profiles

High-dimensional categorical data arise in diverse scientific domains and are often accompanied by covariates. Latent class regression models are routinely used in such settings, reducing dimensionality by assuming conditional independence of the categorical variables given a single latent class that depends on covariates through a logistic regression model. However, such methods become unreliable as the dimensionality increases. To address this, we propose Bayesian latent class regression with interpretable binary profiles (BLIP), a flexible family of models that introduces a binary latent-attribute layer between the covariate-dependent latent class and the observed categorical responses. BLIP satisfies key theoretical properties, including identifiability and posterior consistency, and we establish a Bayes oracle clustering property that ensures robustness against the curse of dimensionality. We develop efficient posterior computation methods, validate them through simulation studies, and use BLIP to infer regions of common profile in ecological data.

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arXiv2025

Minimax-Optimal Spectral Clustering with Covariance Projection for High-Dimensional Anisotropic Mixtures

In mixture models, anisotropic noise within each cluster is widely present in real-world data. This work investigates both computationally efficient procedures and fundamental statistical limits for clustering in high-dimensional anisotropic mixtures. We propose a new clustering method, Covariance Projected Spectral Clustering (COPO), which adapts to a wide range of dependent noise structures. We first project the data onto a low-dimensional space via eigen-decomposition of a diagonal-deleted Gram matrix. Our central methodological idea is to sharpen clustering in this embedding space by a covariance-aware reassignment step, using quadratic distances induced by estimated projected covariances. Through a novel row-wise analysis of the subspace estimation step in weak-signal regimes, which is of independent interest, we establish tight performance guarantees and algorithmic upper bounds for COPO, covering both Gaussian noise with flexible covariance and general noise with local dependence. To characterize the fundamental difficulty of clustering high-dimensional anisotropic Gaussian mixtures, we further establish two distinct and complementary minimax lower bounds, each highlighting different covariance-driven barriers. Our results show that COPO attains minimax-optimal misclustering rates in Gaussian settings. Extensive simulation studies across diverse noise structures, along with a real data application, demonstrate the superior empirical performance of our method.

math.ST↗
arXiv2025

Unfolding Tensors to Identify the Graph in Discrete Latent Bipartite Graphical Models

We use a tensor unfolding technique to prove a new identifiability result for discrete bipartite graphical models, which have a bipartite graph between an observed and a latent layer. This model family includes popular models such as Noisy-Or Bayesian networks for medical diagnosis and Restricted Boltzmann Machines in machine learning. These models are also building blocks for deep generative models. Our result on identifying the graph structure enjoys the following nice properties. First, our identifiability proof is constructive, in which we innovatively unfold the population tensor under the model into matrices and inspect the rank properties of the resulting matrices to uncover the graph. This proof itself gives a population-level structure learning algorithm that outputs both the number of latent variables and the bipartite graph. Second, we allow various forms of nonlinear dependence among the variables, unlike many continuous latent variable graphical models that rely on linearity to show identifiability. Third, our identifiability condition is interpretable, only requiring each latent variable to connect to at least two "pure" observed variables in the bipartite graph. The new result not only brings novel advances in algebraic statistics, but also has useful implications for these models' trustworthy applications in scientific disciplines and interpretable machine learning.

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arXiv2025

Deep Discrete Encoders: Identifiable Deep Generative Models for Rich Data with Discrete Latent Layers

In the era of generative AI, deep generative models (DGMs) with latent representations have gained tremendous popularity. Despite their impressive empirical performance, the statistical properties of these models remain underexplored. DGMs are often overparametrized, non-identifiable, and uninterpretable black boxes, raising serious concerns when deploying them in high-stakes applications. Motivated by this, we propose interpretable deep generative models for rich data types with discrete latent layers, called Deep Discrete Encoders (DDEs). A DDE is a directed graphical model with multiple binary latent layers. Theoretically, we propose transparent identifiability conditions for DDEs, which imply progressively smaller sizes of the latent layers as they go deeper. Identifiability ensures consistent parameter estimation and inspires an interpretable design of the deep architecture. Computationally, we propose a scalable estimation pipeline of a layerwise nonlinear spectral initialization followed by a penalized stochastic approximation EM algorithm. This procedure can efficiently estimate models with exponentially many latent components. Extensive simulation studies for high-dimensional data and deep architectures validate our theoretical results and demonstrate the excellent performance of our algorithms. We apply DDEs to three diverse real datasets with different data types to perform hierarchical topic modeling, image representation learning, and response time modeling in educational testing.

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arXiv2024

Generalized Grade-of-Membership Estimation for High-dimensional Locally Dependent Data

This work focuses on the mixed membership models for multivariate categorical data widely used for analyzing survey responses and population genetics data. These grade of membership (GoM) models offer rich modeling power but present significant estimation challenges for high-dimensional polytomous data. Popular existing approaches, such as Bayesian MCMC inference, are not scalable and lack theoretical guarantees in high-dimensional settings. To address this, we first observe that data from this model can be reformulated as a three-way (quasi-)tensor, with many subjects responding to many items with varying numbers of categories. We introduce a novel and simple approach that flattens the three-way quasi-tensor into a "fat" matrix, and then perform a singular value decomposition of it to estimate parameters by exploiting the singular subspace geometry. Our fast spectral method can accommodate a broad range of data distributions with arbitrarily locally dependent noise, which we formalize as the generalized-GoM models. We establish finite-sample entrywise error bounds for the generalized-GoM model parameters. This is supported by a new sharp two-to-infinity singular subspace perturbation theory for locally dependent and flexibly distributed noise, a contribution of independent interest. Simulations and applications to data in political surveys, population genetics, and single-cell sequencing demonstrate our method's superior performance.

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