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Ji Zhu

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17 papers
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17

JMLR Journal 2025 Journal Article

Latent Process Models for Functional Network Data

  • Peter W. MacDonald
  • Elizaveta Levina
  • Ji Zhu

Network data are often sampled with auxiliary information or collected through the observation of a complex system over time, leading to multiple network snapshots indexed by a continuous variable. Many methods in statistical network analysis are traditionally designed for a single network, and can be applied to an aggregated network in this setting, but that approach can miss important functional structure. Here we develop an approach to estimating the expected network explicitly as a function of a continuous index, be it time or another indexing variable. We parameterize the network expectation through low dimensional latent processes, whose components we represent with a fixed, finite-dimensional functional basis. We derive a gradient descent estimation algorithm, establish theoretical guarantees for recovery of the low dimensional structure, compare our method to competitors, and apply it to a data set of international political interactions over time, showing our proposed method to adapt well to data, outperform competitors, and provide interpretable and meaningful results. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2025. ( edit, beta )

JMLR Journal 2024 Journal Article

Variational Estimators of the Degree-corrected Latent Block Model for Bipartite Networks

  • Yunpeng Zhao
  • Ning Hao
  • Ji Zhu

Bipartite graphs are ubiquitous across various scientific and engineering fields. Simultaneously grouping the two types of nodes in a bipartite graph via biclustering represents a fundamental challenge in network analysis for such graphs. The latent block model (LBM) is a commonly used model-based tool for biclustering. However, the effectiveness of the LBM is often limited by the influence of row and column sums in the data matrix. To address this limitation, we introduce the degree-corrected latent block model (DC-LBM), which accounts for the varying degrees in row and column clusters, significantly enhancing performance on real-world data sets and simulated data. We develop an efficient variational expectation-maximization algorithm by creating closed-form solutions for parameter estimates in the M steps. Furthermore, we prove the label consistency and the rate of convergence of the variational estimator under the DC-LBM, allowing the expected graph density to approach zero as long as the average expected degrees of rows and columns approach infinity when the size of the graph increases. [abs] [ pdf ][ bib ] &copy JMLR 2024. ( edit, beta )

JMLR Journal 2023 Journal Article

Community models for networks observed through edge nominations

  • Tianxi Li
  • Elizaveta Levina
  • Ji Zhu

Communities are a common and widely studied structure in networks, typically assuming that the network is fully and correctly observed. In practice, network data are often collected by querying nodes about their connections. In some settings, all edges of a sampled node will be recorded, and in others, a node may be asked to name its connections. These sampling mechanisms introduce noise and bias, which can obscure the community structure and invalidate assumptions underlying standard community detection methods. We propose a general model for a class of network sampling mechanisms based on recording edges via querying nodes, designed to improve community detection for network data collected in this fashion. We model edge sampling probabilities as a function of both individual preferences and community parameters, and show community detection can be performed by spectral clustering under this general class of models. We also propose, as a special case of the general framework, a parametric model for directed networks we call the nomination stochastic block model, which allows for meaningful parameter interpretations and can be fitted by the method of moments. In this case, spectral clustering and the method of moments are computationally efficient and come with theoretical guarantees of consistency. We evaluate the proposed model in simulation studies on unweighted and weighted networks and under misspecified models. The method is applied to a faculty hiring dataset, discovering a meaningful hierarchy of communities among US business schools. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2023. ( edit, beta )

JMLR Journal 2023 Journal Article

Distributed Community Detection in Large Networks

  • Sheng Zhang
  • Rui Song
  • Wenbin Lu
  • Ji Zhu

Community detection for large networks poses challenges due to the high computational cost as well as heterogeneous community structures. In this paper, we consider widely existing real-world networks with “grouped communities” (or “the group structure”), where nodes within grouped communities are densely connected and nodes across grouped communities are relatively loosely connected. We propose a two-step community detection approach for such networks. Firstly, we leverage modularity optimization methods to partition the network into groups, where between-group connectivity is low. Secondly, we employ the stochastic block model (SBM) or degree-corrected SBM (DCSBM) to further partition the groups into communities, allowing for varying levels of between-community connectivity. By incorporating this two-step structure, we introduce a novel divide-and-conquer algorithm that asymptotically recovers both the group structure and the community structure. Numerical studies confirm that our approach significantly reduces computational costs while achieving competitive performance. This framework provides a comprehensive solution for detecting community structures in networks with grouped communities, offering a valuable tool for various applications. [abs] [ pdf ][ bib ] &copy JMLR 2023. ( edit, beta )

JMLR Journal 2022 Journal Article

SODEN: A Scalable Continuous-Time Survival Model through Ordinary Differential Equation Networks

  • Weijing Tang
  • Jiaqi Ma
  • Qiaozhu Mei
  • Ji Zhu

In this paper, we propose a flexible model for survival analysis using neural networks along with scalable optimization algorithms. One key technical challenge for directly applying maximum likelihood estimation (MLE) to censored data is that evaluating the objective function and its gradients with respect to model parameters requires the calculation of integrals. To address this challenge, we recognize from a novel perspective that the MLE for censored data can be viewed as a differential-equation constrained optimization problem. Following this connection, we model the distribution of event time through an ordinary differential equation and utilize efficient ODE solvers and adjoint sensitivity analysis to numerically evaluate the likelihood and the gradients. Using this approach, we are able to 1) provide a broad family of continuous-time survival distributions without strong structural assumptions, 2) obtain powerful feature representations using neural networks, and 3) allow efficient estimation of the model in large-scale applications using stochastic gradient descent. Through both simulation studies and real-world data examples, we demonstrate the effectiveness of the proposed method in comparison to existing state-of-the-art deep learning survival analysis models. The implementation of the proposed SODEN approach has been made publicly available at https://github.com/jiaqima/SODEN. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2022. ( edit, beta )

ICML Conference 2020 Conference Paper

A Flexible Latent Space Model for Multilayer Networks

  • Xuefei Zhang
  • Songkai Xue
  • Ji Zhu

Entities often interact with each other through multiple types of relations, which are often represented as multilayer networks. Multilayer networks among the same set of nodes usually share common structures, while each layer can possess its distinct node connecting behaviors. This paper proposes a flexible latent space model for multilayer networks for the purpose of capturing such characteristics. Specifically, the proposed model embeds each node with a latent vector shared among layers and a layer-specific effect for each layer; both elements together with a layer-specific connectivity matrix determine edge formations. To fit the model, we develop a projected gradient descent algorithm for efficient parameter estimation. We also establish theoretical properties of the maximum likelihood estimators and show that the upper bound of the common latent structure’s estimation error is inversely proportional to the number of layers under mild conditions. The superior performance of the proposed model is demonstrated through simulation studies and applications to two real-world data examples.

JMLR Journal 2020 Journal Article

High-dimensional Gaussian graphical models on network-linked data

  • Tianxi Li
  • Cheng Qian
  • Elizaveta Levina
  • Ji Zhu

Graphical models are commonly used to represent conditional dependence relationships between variables. There are multiple methods available for exploring them from high-dimensional data, but almost all of them rely on the assumption that the observations are independent and identically distributed. At the same time, observations connected by a network are becoming increasingly common, and tend to violate these assumptions. Here we develop a Gaussian graphical model for observations connected by a network with potentially different mean vectors, varying smoothly over the network. We propose an efficient estimation algorithm and demonstrate its effectiveness on both simulated and real data, obtaining meaningful and interpretable results on a statistics coauthorship network. We also prove that our method estimates both the inverse covariance matrix and the corresponding graph structure correctly under the assumption of network “cohesion”, which refers to the empirically observed phenomenon of network neighbors sharing similar traits. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2020. ( edit, beta )

NeurIPS Conference 2019 Conference Paper

A Flexible Generative Framework for Graph-based Semi-supervised Learning

  • Jiaqi Ma
  • Weijing Tang
  • Ji Zhu
  • Qiaozhu Mei

We consider a family of problems that are concerned about making predictions for the majority of unlabeled, graph-structured data samples based on a small proportion of labeled samples. Relational information among the data samples, often encoded in the graph/network structure, is shown to be helpful for these semi-supervised learning tasks. However, conventional graph-based regularization methods and recent graph neural networks do not fully leverage the interrelations between the features, the graph, and the labels. In this work, we propose a flexible generative framework for graph-based semi-supervised learning, which approaches the joint distribution of the node features, labels, and the graph structure. Borrowing insights from random graph models in network science literature, this joint distribution can be instantiated using various distribution families. For the inference of missing labels, we exploit recent advances of scalable variational inference techniques to approximate the Bayesian posterior. We conduct thorough experiments on benchmark datasets for graph-based semi-supervised learning. Results show that the proposed methods outperform state-of-the-art models under most settings.

NeurIPS Conference 2005 Conference Paper

Computing the Solution Path for the Regularized Support Vector Regression

  • Lacey Gunter
  • Ji Zhu

In this paper we derive an algorithm that computes the entire solu- tion path of the support vector regression, with essentially the same computational cost as fitting one SVR model. We also propose an unbiased estimate for the degrees of freedom of the SVR model, which allows convenient selection of the regularization parameter.

NeurIPS Conference 2004 Conference Paper

A Method for Inferring Label Sampling Mechanisms in Semi-Supervised Learning

  • Saharon Rosset
  • Ji Zhu
  • Hui Zou
  • Trevor Hastie

We consider the situation in semi-supervised learning, where the "label sampling" mechanism stochastically depends on the true response (as well as potentially on the features). We suggest a method of moments for estimating this stochastic dependence using the unlabeled data. This is potentially useful for two distinct purposes: a. As an input to a super- vised learning procedure which can be used to "de-bias" its results using labeled data only and b. As a potentially interesting learning task in it- self. We present several examples to illustrate the practical usefulness of our method. 1 Introduction In semi-supervised learning, we assume we have a sample (xi, yi, si)n i=1, of i. i. d. draws from a joint distribution on (X, Y, S), where: 1 xi Rp are p-vectors of features. yi is a label, or response (yi R for regression, yi {0, 1} for 2-class classifica- tion). si {0, 1} is a "labeling indicator", that is yi is observed if and only if si = 1, while xi is observed for all i. In this paper we consider the interesting case of semi-supervised learning, where the prob- ability of observing the response depends on the data through the true response, as well as 1Our notation here differs somewhat from many semi-supervised learning papers, where the un- labeled part of the sample is separated from the labeled part and sometimes called "test set". potentially through the features. Our goal is to model this unknown dependence: l(x, y) = P r(S = 1|x, y) (1) Note that the dependence on y (which is unobserved when S = 0) prevents us from using standard supervised modeling approaches to learn l. We show here that we can use the whole data-set (labeled+unlabeled data) to obtain estimates of this probability distribution within a parametric family of distributions, without needing to "impute" the unobserved responses. 2 We believe this setup is of significant practical interest. Here are a couple of examples of realistic situations: 1. The problem of learning from positive examples and unlabeled data is of significant interest in document topic learning [4, 6, 8]. Consider a generalization of that problem, where we observe a sample of positive and negative examples and unlabeled data, but we believe that the positive and negative labels are supplied with different probabilities (in the document learning example, positive examples are typically more likely to be labeled than negative ones, which are much more abundant). These probabilities may also not be uniform within each class, and depend on the features as well. Our methods allow us to infer these labeling probabilities by utilizing the unlabeled data. 2. Consider a satisfaction survey, where clients of a company are requested to report their level of satisfaction, but they can choose whether or not they do so. It is reasonable to assume that their willingness to report their satisfaction depends on their actual satisfaction level. Using our methods, we can infer the dependence of the reporting probability on the actual satisfaction by utilizing the unlabeled data, i. e. , the customers who declined to respond. Being able to infer the labeling mechanism is important for two distinct reasons. First, it may be useful for "de-biasing" the results of supervised learning, which uses only the labeled examples. The generic approach for achieving this is to use "inverse sampling" weights (i. e. weigh labeled examples by 1/l(x, y)). The us of this for maximum likeli- hood estimation is well established in the literature as a method for correcting sampling bias (of which semi-supervised learning is an example) [10]. We can also use the learned mechanism to post-adjust the probabilities from a probability estimation methods such as logistic regression to attain "unbiasedness" and consistency [11]. Second, understanding the labeling mechanism may be an interesting and useful learning task in itself. Consider, for example, the "satisfaction survey" scenario described above. Understanding the way in which satisfaction affects the customers' willingness to respond to the survey can be used to get a better picture of overall satisfaction and to design better future surveys, regardless of any supervised learning task which models the actual satisfaction. Our approach is described in section 2, and is based on a method of moments. Observe that for every function of the features g(x), we can get an unbiased estimate of its mean n as 1 g(x n i=1 i). We show that if we know the underlying label sampling mechanism l(x, y) we can get a different unbiased estimate of Eg(x), which uses only the labeled examples, weighted by 1/l(x, y). We suggest inferring the unknown function l(x, y) by requiring that we get identical estimates of Eg(x) using both approaches. We illustrate our method's implementation on the California Housing data-set in section 3. In section 4 we review related work in the machine learning and statistics literature, and we conclude with a discussion in section 5. 2The importance of this is that we are required to hypothesize and fit a conditional probability model for l(x, y) only, as opposed to the full probability model for (S, X, Y ) required for, say, EM.

JMLR Journal 2004 Journal Article

Boosting as a Regularized Path to a Maximum Margin Classifier

  • Saharon Rosset
  • Ji Zhu
  • Trevor Hastie

In this paper we study boosting methods from a new perspective. We build on recent work by Efron et al. to show that boosting approximately (and in some cases exactly) minimizes its loss criterion with an l 1 constraint on the coefficient vector. This helps understand the success of boosting with early stopping as regularized fitting of the loss criterion. For the two most commonly used criteria (exponential and binomial log-likelihood), we further show that as the constraint is relaxed---or equivalently as the boosting iterations proceed---the solution converges (in the separable case) to an " l 1 -optimal" separating hyper-plane. We prove that this l 1 -optimal separating hyper-plane has the property of maximizing the minimal l 1 -margin of the training data, as defined in the boosting literature. An interesting fundamental similarity between boosting and kernel support vector machines emerges, as both can be described as methods for regularized optimization in high-dimensional predictor space, using a computational trick to make the calculation practical, and converging to margin-maximizing solutions. While this statement describes SVMs exactly, it applies to boosting only approximately. [abs] [ pdf ] [ ps.gz ] [ ps ]

NeurIPS Conference 2004 Conference Paper

The Entire Regularization Path for the Support Vector Machine

  • Saharon Rosset
  • Robert Tibshirani
  • Ji Zhu
  • Trevor Hastie

In this paper we argue that the choice of the SVM cost parameter can be critical. We then derive an algorithm that can fit the entire path of SVM solutions for every value of the cost parameter, with essentially the same computational cost as fitting one SVM model.

JMLR Journal 2004 Journal Article

The Entire Regularization Path for the Support Vector Machine

  • Trevor Hastie
  • Saharon Rosset
  • Robert Tibshirani
  • Ji Zhu

The support vector machine (SVM) is a widely used tool for classification. Many efficient implementations exist for fitting a two-class SVM model. The user has to supply values for the tuning parameters: the regularization cost parameter, and the kernel parameters. It seems a common practice is to use a default value for the cost parameter, often leading to the least restrictive model. In this paper we argue that the choice of the cost parameter can be critical. We then derive an algorithm that can fit the entire path of SVM solutions for every value of the cost parameter, with essentially the same computational cost as fitting one SVM model. We illustrate our algorithm on some examples, and use our representation to give further insight into the range of SVM solutions. [abs] [ pdf ]

NeurIPS Conference 2003 Conference Paper

1-norm Support Vector Machines

  • Ji Zhu
  • Saharon Rosset
  • Robert Tibshirani
  • Trevor Hastie

The standard 2-norm SVM is known for its good performance in two- In this paper, we consider the 1-norm SVM. We class classi£cation. argue that the 1-norm SVM may have some advantage over the standard 2-norm SVM, especially when there are redundant noise features. We also propose an ef£cient algorithm that computes the whole solution path of the 1-norm SVM, hence facilitates adaptive selection of the tuning parameter for the 1-norm SVM.

NeurIPS Conference 2003 Conference Paper

Margin Maximizing Loss Functions

  • Saharon Rosset
  • Ji Zhu
  • Trevor Hastie

Margin maximizing properties play an important role in the analysis of classi£- cation models, such as boosting and support vector machines. Margin maximiza- tion is theoretically interesting because it facilitates generalization error analysis, and practically interesting because it presents a clear geometric interpretation of the models being built. We formulate and prove a suf£cient condition for the solutions of regularized loss functions to converge to margin maximizing separa- tors, as the regularization vanishes. This condition covers the hinge loss of SVM, the exponential loss of AdaBoost and logistic regression loss. We also generalize it to multi-class classi£cation problems, and present margin maximizing multi- class versions of logistic regression and support vector machines.

NeurIPS Conference 2001 Conference Paper

Kernel Logistic Regression and the Import Vector Machine

  • Ji Zhu
  • Trevor Hastie

The support vector machine (SVM) is known for its good performance in binary classification, but its extension to multi-class classification is still an on-going research issue. In this paper, we propose a new approach for classification, called the import vector machine (IVM), which is built on kernel logistic regression (KLR). We show that the IVM not only per- forms as well as the SVM in binary classification, but also can naturally be generalized to the multi-class case. Furthermore, the IVM provides an estimate of the underlying probability. Similar to the “support points” of the SVM, the IVM model uses only a fraction of the training data to index kernel basis functions, typically a much smaller fraction than the SVM. This gives the IVM a computational advantage over the SVM, especially when the size of the training data set is large. is qualitative and assumes values in a finite set  , where the output  from . We, to it. Usually it is assumed that the training data are an independently and identically distributed sample from an unknown probability distribution

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