arXiv subjects

Zongming Ma

Publications and source records attributed to Zongming Ma.

At least 19 recordsLinked to original sources

arXiv2025

MoDaH achieves rate optimal batch correction

Batch effects pose a significant challenge in the analysis of single-cell omics data, introducing technical artifacts that confound biological signals. While various computational methods have achieved empirical success in correcting these effects, they lack the formal theoretical guarantees required to assess their reliability and generalization. To bridge this gap, we introduce Mixture-Model-based Data Harmonization (MoDaH), a principled batch correction algorithm grounded in a rigorous statistical framework. Under a new Gaussian-mixture-model with explicit parametrization of batch effects, we establish the minimax optimal error rates for batch correction and prove that MoDaH achieves this rate by leveraging the recent theoretical advances in clustering data from anisotropic Gaussian mixtures. This constitutes, to the best of our knowledge, the first theoretical guarantee for batch correction. Extensive experiments on diverse single-cell RNA-seq and spatial proteomics datasets demonstrate that MoDaH not only attains theoretical optimality but also achieves empirical performance comparable to or even surpassing those of state-of-the-art heuristics (e.g., Harmony, Seurat-V5, and LIGER), effectively balancing the removal of technical noise with the conservation of biological signal.

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arXiv2025

IndiSeek learns information-guided disentangled representations

Learning disentangled representations is a fundamental task in multi-modal learning. In modern applications such as single-cell multi-omics, both shared and modality-specific features are critical for characterizing cell states and supporting downstream analyses. Ideally, modality-specific features should be independent of shared ones while also capturing all complementary information within each modality. This tradeoff is naturally expressed through information-theoretic criteria, but mutual-information-based objectives are difficult to estimate reliably, and their variational surrogates often underperform in practice. In this paper, we introduce IndiSeek, a novel disentangled representation learning approach that addresses this challenge by combining an independence-enforcing objective with a computationally efficient reconstruction loss that bounds conditional mutual information. This formulation explicitly balances independence and completeness, enabling principled extraction of modality-specific features. We demonstrate the effectiveness of IndiSeek on synthetic simulations, a CITE-seq dataset and multiple real-world multi-modal benchmarks.

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arXiv2025

Multi-modal contrastive learning adapts to intrinsic dimensions of shared latent variables

Multi-modal contrastive learning as a self-supervised representation learning technique has achieved great success in foundation model training, such as CLIP~\citep{radford2021learning}. In this paper, we study the theoretical properties of the learned representations from multi-modal contrastive learning beyond linear representations and specific data distributions. Our analysis reveals that, enabled by temperature optimization, multi-modal contrastive learning not only maximizes mutual information between modalities but also adapts to intrinsic dimensions of data, which can be much lower than user-specified dimensions for representation vectors. Experiments on both synthetic and real-world datasets demonstrate the ability of contrastive learning to learn low-dimensional and informative representations, bridging theoretical insights and practical performance.

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arXiv2024

Multimodal data integration and cross-modal querying via orchestrated approximate message passing

The need for multimodal data integration arises naturally when multiple complementary sets of features are measured on the same sample. Under a dependent multifactor model, we develop a fully data-driven orchestrated approximate message passing algorithm for integrating information across these feature sets to achieve statistically optimal signal recovery. In practice, these reference data sets are often queried later by new subjects that are only partially observed. Leveraging on asymptotic normality of estimates generated by our data integration method, we further develop an asymptotically valid prediction set for the latent representation of any such query subject. We demonstrate the prowess of both the data integration and the prediction set construction algorithms on both synthetic examples and real world single-cell datasets.

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arXiv2023

Sparse GCA and Thresholded Gradient Descent

Generalized correlation analysis (GCA) is concerned with uncovering linear relationships across multiple datasets. It generalizes canonical correlation analysis that is designed for two datasets. We study sparse GCA when there are potentially multiple generalized correlation tuples in data and the loading matrix has a small number of nonzero rows. It includes sparse CCA and sparse PCA of correlation matrices as special cases. We first formulate sparse GCA as generalized eigenvalue problems at both population and sample levels via a careful choice of normalization constraints. Based on a Lagrangian form of the sample optimization problem, we propose a thresholded gradient descent algorithm for estimating GCA loading vectors and matrices in high dimensions. We derive tight estimation error bounds for estimators generated by the algorithm with proper initialization. We also demonstrate the prowess of the algorithm on a number of synthetic datasets.

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arXiv2023

Community Detection with Contextual Multilayer Networks

In this paper, we study community detection when we observe $m$ sparse networks and a high dimensional covariate matrix, all encoding the same community structure among $n$ subjects. In the asymptotic regime where the number of features $p$ and the number of subjects $n$ grows proportionally, we derive an exact formula of asymptotic minimum mean square error (MMSE) for estimating the common community structure in the balanced two block case. The formula implies the necessity of integrating information from multiple data sources. Consequently, it induces a sharp threshold of phase transition between the regime where detection (i.e., weak recovery) is possible and the regime where no procedure performs better than a random guess. The asymptotic MMSE depends on the covariate signal-to-noise ratio in a more subtle way than the phase transition threshold does. In the special case of $m=1$, our asymptotic MMSE formula complements the pioneering work of Deshpande et. al. (2018) which found the sharp threshold when $m=1$.

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arXiv2022

Testing Equivalence of Clustering

In this paper, we test whether two datasets share a common clustering structure. As a leading example, we focus on comparing clustering structures in two independent random samples from two mixtures of multivariate normal distributions. Mean parameters of these normal distributions are treated as potentially unknown nuisance parameters and are allowed to differ. Assuming knowledge of mean parameters, we first determine the phase diagram of the testing problem over the entire range of signal-to-noise ratios by providing both lower bounds and tests that achieve them. When nuisance parameters are unknown, we propose tests that achieve the detection boundary adaptively as long as ambient dimensions of the datasets grow at a sub-linear rate with the sample size.

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arXiv2022

One-Way Matching of Datasets with Low Rank Signals

We study one-way matching of a pair of datasets with low rank signals. Under a stylized model, we first derive information-theoretic limits of matching under a mismatch proportion loss. We then show that linear assignment with projected data achieves fast rates of convergence and sometimes even minimax rate optimality for this task. The theoretical error bounds are corroborated by simulated examples. Furthermore, we illustrate practical use of the matching procedure on two single-cell data examples.

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arXiv2022

Sample canonical correlation coefficients of high-dimensional random vectors with finite rank correlations

Consider two random vectors $\widetilde{\mathbf x} \in \mathbb R^p$ and $\widetilde{\mathbf y} \in \mathbb R^q$ of the forms $\widetilde{\mathbf x}=A\mathbf z+\mathbf C_1^{1/2}\mathbf x$ and $\widetilde{\mathbf y}=B\mathbf z+\mathbf C_2^{1/2}\mathbf y$, where $\mathbf x\in \mathbb R^p$, $\mathbf y\in \mathbb R^q$ and $\mathbf z\in \mathbb R^r$ are independent vectors with i.i.d. entries of mean 0 and variance 1, $\mathbf C_1$ and $\mathbf C_2$ are $p \times p$ and $q\times q$ deterministic covariance matrices, and $A$ and $B$ are $p\times r$ and $q\times r$ deterministic matrices. With $n$ independent observations of $(\widetilde{\mathbf x},\widetilde{\mathbf y})$, we study the sample canonical correlations between $\widetilde{\mathbf x} $ and $\widetilde{\mathbf y}$. We consider the high-dimensional setting with finite rank correlations. Let $t_1\ge t_2 \ge \cdots\ge t_r$ be the squares of the nontrivial population canonical correlation coefficients, and let $\widetildeλ_1 \ge\widetildeλ_2\ge\cdots\ge\widetildeλ_{p\wedge q}$ be the squares of the sample canonical correlation coefficients. If the entries of $\mathbf x$, $\mathbf y$ and $\mathbf z$ are i.i.d. Gaussian, then the following dichotomy has been shown in [7] for a fixed threshold $t_c \in(0, 1)$: for $1\le i \le r$, if $t_i < t_c$, then $\widetildeλ_i$ converges to the right-edge $λ_+$ of the limiting eigenvalue spectrum of the sample canonical correlation matrix; if $t_i>t_c$, then $\widetildeλ_i$ converges to a deterministic limit $θ_i \in (λ_+,1)$ determined by $t_i$. In this paper, we prove that these results hold universally under the sharp fourth moment conditions on the entries of $\mathbf x$ and $\mathbf y$. Moreover, we prove the results in full generality, in the sense that they also hold for near-degenerate $t_i$'s and for $t_i$'s that are close to the threshold $t_c$.

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arXiv2022

Global and Individualized Community Detection in Inhomogeneous Multilayer Networks

In network applications, it has become increasingly common to obtain datasets in the form of multiple networks observed on the same set of subjects, where each network is obtained in a related but different experiment condition or application scenario. Such datasets can be modeled by multilayer networks where each layer is a separate network itself while different layers are associated and share some common information. The present paper studies community detection in a stylized yet informative inhomogeneous multilayer network model. In our model, layers are generated by different stochastic block models, the community structures of which are (random) perturbations of a common global structure while the connecting probabilities in different layers are not related. Focusing on the symmetric two block case, we establish minimax rates for both global estimation of the common structure and individualized estimation of layer-wise community structures. Both minimax rates have sharp exponents. In addition, we provide an efficient algorithm that is simultaneously asymptotic minimax optimal for both estimation tasks under mild conditions. The optimal rates depend on the parity of the number of most informative layers, a phenomenon that is caused by inhomogeneity across layers. The method is extended to handle multiple and potentially asymmetric community cases. We demonstrate its effectiveness on both simulated examples and a real multi-modal single-cell dataset.

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arXiv2022

Nonconvex Matrix Completion with Linearly Parameterized Factors

Techniques of matrix completion aim to impute a large portion of missing entries in a data matrix through a small portion of observed ones. In practice including collaborative filtering, prior information and special structures are usually employed in order to improve the accuracy of matrix completion. In this paper, we propose a unified nonconvex optimization framework for matrix completion with linearly parameterized factors. In particular, by introducing a condition referred to as Correlated Parametric Factorization, we can conduct a unified geometric analysis for the nonconvex objective by establishing uniform upper bounds for low-rank estimation resulting from any local minimum. Perhaps surprisingly, the condition of Correlated Parametric Factorization holds for important examples including subspace-constrained matrix completion and skew-symmetric matrix completion. The effectiveness of our unified nonconvex optimization method is also empirically illustrated by extensive numerical simulations.

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arXiv2020

Community detection in sparse latent space models

We show that a simple community detection algorithm originated from stochastic blockmodel literature achieves consistency, and even optimality, for a broad and flexible class of sparse latent space models. The class of models includes latent eigenmodels (arXiv:0711.1146). The community detection algorithm is based on spectral clustering followed by local refinement via normalized edge counting.

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arXiv2020

Efficient random graph matching via degree profiles

Random graph matching refers to recovering the underlying vertex correspondence between two random graphs with correlated edges; a prominent example is when the two random graphs are given by Erdős-Rényi graphs $G(n,\frac{d}{n})$. This can be viewed as an average-case and noisy version of the graph isomorphism problem. Under this model, the maximum likelihood estimator is equivalent to solving the intractable quadratic assignment problem. This work develops an $\tilde{O}(n d^2+n^2)$-time algorithm which perfectly recovers the true vertex correspondence with high probability, provided that the average degree is at least $d = Ω(\log^2 n)$ and the two graphs differ by at most $δ= O( \log^{-2}(n) )$ fraction of edges. For dense graphs and sparse graphs, this can be improved to $δ= O( \log^{-2/3}(n) )$ and $δ= O( \log^{-2}(d) )$ respectively, both in polynomial time. The methodology is based on appropriately chosen distance statistics of the degree profiles (empirical distribution of the degrees of neighbors). Before this work, the best known result achieves $δ=O(1)$ and $n^{o(1)} \leq d \leq n^c$ for some constant $c$ with an $n^{O(\log n)}$-time algorithm \cite{barak2018nearly} and $δ=\tilde O((d/n)^4)$ and $d = \tildeΩ(n^{4/5})$ with a polynomial-time algorithm \cite{dai2018performance}.

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arXiv2019

Minimax Rates in Network Analysis: Graphon Estimation, Community Detection and Hypothesis Testing

This paper surveys some recent developments in fundamental limits and optimal algorithms for network analysis. We focus on minimax optimal rates in three fundamental problems of network analysis: graphon estimation, community detection, and hypothesis testing. For each problem, we review state-of-the-art results in the literature followed by general principles behind the optimal procedures that lead to minimax estimation and testing. This allows us to connect problems in network analysis to other statistical inference problems from a general perspective.

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arXiv2018

Optimal Estimation and Completion of Matrices with Biclustering Structures

Biclustering structures in data matrices were first formalized in a seminal paper by John Hartigan (1972) where one seeks to cluster cases and variables simultaneously. Such structures are also prevalent in block modeling of networks. In this paper, we develop a unified theory for the estimation and completion of matrices with biclustering structures, where the data is a partially observed and noise contaminated data matrix with a certain biclustering structure. In particular, we show that a constrained least squares estimator achieves minimax rate-optimal performance in several of the most important scenarios. To this end, we derive unified high probability upper bounds for all sub-Gaussian data and also provide matching minimax lower bounds in both Gaussian and binary cases. Due to the close connection of graphon to stochastic block models, an immediate consequence of our general results is a minimax rate-optimal estimator for sparse graphons.

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arXiv2018

Asymptotic normality and analysis of variance of log-likelihood ratios in spiked random matrix models

The present manuscript studies signal detection by likelihood ratio tests in a number of spiked random matrix models, including but not limited to Gaussian mixtures and spiked Wishart covariance matrices. We work directly with multi-spiked cases in these models and with flexible priors on the signal component that allow dependence across spikes. We derive asymptotic normality for the log-likelihood ratios when the signal-to- noise ratios are below certain thresholds. In addition, we show that the variances of the log-likelihood ratios can be asymptotically decomposed as the sums of those of a collection of statistics which we call bipartite signed cycles.

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arXiv2017

Exploration of Large Networks with Covariates via Fast and Universal Latent Space Model Fitting

Latent space models are effective tools for statistical modeling and exploration of network data. These models can effectively model real world network characteristics such as degree heterogeneity, transitivity, homophily, etc. Due to their close connection to generalized linear models, it is also natural to incorporate covariate information in them. The current paper presents two universal fitting algorithms for networks with edge covariates: one based on nuclear norm penalization and the other based on projected gradient descent. Both algorithms are motivated by maximizing likelihood for a special class of inner-product models while working simultaneously for a wide range of different latent space models, such as distance models, which allow latent vectors to affect edge formation in flexible ways. These fitting methods, especially the one based on projected gradient descent, are fast and scalable to large networks. We obtain their rates of convergence for both inner-product models and beyond. The effectiveness of the modeling approach and fitting algorithms is demonstrated on five real world network datasets for different statistical tasks, including community detection with and without edge covariates, and network assisted learning.

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arXiv2017

Optimal hypothesis testing for stochastic block models with growing degrees

The present paper considers testing an Erdos--Renyi random graph model against a stochastic block model in the asymptotic regime where the average degree of the graph grows with the graph size n. Our primary interest lies in those cases in which the signal-to-noise ratio is at a constant level. Focusing on symmetric two block alternatives, we first derive joint central limit theorems for linear spectral statistics of power functions for properly rescaled graph adjacency matrices under both the null and local alternative hypotheses. The powers in the linear spectral statistics are allowed to grow to infinity together with the graph size. In addition, we show that linear spectral statistics of Chebyshev polynomials are closely connected to signed cycles of growing lengths that determine the asymptotic likelihood ratio test for the hypothesis testing problem of interest. This enables us to construct a sequence of test statistics that achieves the exact optimal asymptotic power within $O(n^3 \log n)$ time complexity in the contiguous regime when $n^2 p_{n,av}^3 \to\infty$ where $p_{n,av}$ is the average connection probability. We further propose a class of adaptive tests that are computationally tractable and completely data-driven. They achieve nontrivial powers in the contiguous regime and consistency in the singular regime whenever $n p_{n,av} \to\infty$. These tests remain powerful when the alternative becomes a more general stochastic block model with more than two blocks.

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