This paper is devoted to the estimation of a partial graphical model with a structural Bayesian penalization. Precisely, we are interested in the linear regression setting where the estimation is made through the direct links between potentially high-dimensional predictors and multiple responses, since it is known that Gaussian graphical models enable to exhibit direct links only, whereas coefficients in linear regressions contain both direct and indirect relations (due \textit{e.g.} to strong correlations among the variables). A smooth penalty reflecting a generalized Gaussian Bayesian prior on the covariates is added, either enforcing patterns (like row structures) in the direct links or regulating the joint influence of predictors. We give a theoretical guarantee for our method, taking the form of an upper bound on the estimation error arising with high probability, provided that the model is suitably regularized. Empirical studies on synthetic data and a real dataset are conducted.
We propose a novel unsupervised approach for linking records across arbitrarily many files, while simultaneously detecting duplicate records within files. Our key innovation is to represent the pattern of links between records as a {\em bipartite} graph, in which records are directly linked to latent true individuals, and only indirectly linked to other records. This flexible new representation of the linkage structure naturally allows us to estimate the attributes of the unique observable people in the population, calculate $k$-way posterior probabilities of matches across records, and propag…
We introduce a mixture-model of beta distributions to identify significant correlations among $P$ predictors when $P$ is large. The method relies on theorems in convex geometry, which we use to show how to control the error rate of edge detection in graphical models. Our `betaMix' method does not require any assumptions about the network structure, nor does it assume that the network is sparse. The results in this article hold for a wide class of data generating distributions that include light-tailed and heavy-tailed spherically symmetric distributions.
Record linkage involves merging records in large, noisy databases to remove duplicate entities. It has become an important area because of its widespread occurrence in bibliometrics, public health, official statistics production, political science, and beyond. Traditional linkage methods directly linking records to one another are computationally infeasible as the number of records grows. As a result, it is increasingly common for researchers to treat record linkage as a clustering task, in which each latent entity is associated with one or more noisy database records. We critically assess per…
We explore various Bayesian approaches to estimate partial Gaussian graphical models. Our hierarchical structures enable to deal with single-output as well as multiple-output linear regressions, in small or high dimension, enforcing either no sparsity, sparsity, group sparsity or even sparse-group sparsity for a bi-level selection through partial correlations (direct links) between predictors and responses, thanks to spike-and-slab priors corresponding to each setting. Adaptative and global shrinkages are also incorporated in the Bayesian modeling of the direct links. An existing result for mo…
In many structured prediction problems, complex relationships between variables are compactly defined using graphical structures. The most prevalent graphical prediction methods---probabilistic graphical models and large margin methods---have their own distinct strengths but also possess significant drawbacks. Conditional random fields (CRFs) are Fisher consistent, but they do not permit integration of customized loss metrics into their learning process. Large-margin models, such as structured support vector machines (SSVMs), have the flexibility to incorporate customized loss metrics, but lac…
Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested in characterizing the heterogeneity of individual networks across subjects with respect to subject-level covariates. Examples include assessments of how the network varies with patient-specific prognostic scores or comparisons of tumor and normal graphs while accounting for tumor purity as a continuous predictor. In this paper, we propose a novel edge regre…
We propose an unsupervised approach for linking records across arbitrarily many files, while simultaneously detecting duplicate records within files. Our key innovation involves the representation of the pattern of links between records as a bipartite graph, in which records are directly linked to latent true individuals, and only indirectly linked to other records. This flexible representation of the linkage structure naturally allows us to estimate the attributes of the unique observable people in the population, calculate transitive linkage probabilities across records (and represent this v…
Traffic flow forecasting, especially the short-term case, is an important topic in intelligent transportation systems (ITS). This paper does a lot of research on network-scale modeling and forecasting of short-term traffic flows. Firstly, we propose the concepts of single-link and multi-link models of traffic flow forecasting. Secondly, we construct four prediction models by combining the two models with single-task learning and multi-task learning. The combination of the multi-link model and multi-task learning not only improves the experimental efficiency but also the prediction accuracy. Mo…
The recently introduced class of simultaneous graphical dynamic linear models (SGDLMs) defines an ability to scale on-line Bayesian analysis and forecasting to higher-dimensional time series. This paper advances the methodology of SGDLMs, developing and embedding a novel, adaptive method of simultaneous predictor selection in forward filtering for on-line learning and forecasting. The advances include developments in Bayesian computation for scalability, and a case study in exploring the resulting potential for improved short-term forecasting of large-scale volatility matrices. A case study co…
Entity resolution (record linkage or deduplication) is the process of identifying and linking duplicate records in databases. In this paper, we propose a Bayesian graphical approach for entity resolution that links records to latent entities, where the prior representation on the linkage structure is exchangeable. First, we adopt a flexible and tractable set of priors for the linkage structure, which corresponds to a special class of random partition models. Second, we propose a more realistic distortion model for categorical/discrete record attributes, which corrects a logical inconsistency w…
Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is flawed given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes as it does not represent the adjacency matrix. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experiment…
University of Massachusetts（马萨诸塞大学）；Microsoft Research（微软研究院）
Instead of requiring a domain expert to specify the probabilistic dependencies of the data, in this work we present an approach that uses the relational DB schema to automatically construct a Bayesian graphical model for a database. This resulting model contains customized distributions for columns, latent variables that cluster the data, and factors that reflect and represent the foreign key links. Experiments demonstrate the accuracy of the model and the scalability of inference on synthetic and real-world data.
Quantum Graphical Models (QGMs) generalize classical graphical models by adopting the formalism for reasoning about uncertainty from quantum mechanics. Unlike classical graphical models, QGMs represent uncertainty with density matrices in complex Hilbert spaces. Hilbert space embeddings (HSEs) also generalize Bayesian inference in Hilbert spaces. We investigate the link between QGMs and HSEs and show that the sum rule and Bayes rule for QGMs are equivalent to the kernel sum rule in HSEs and a special case of Nadaraya-Watson kernel regression, respectively. We show that these operations can be …
INRA（法国国家农业研究院）；INRA UR 875 MIAT（法国国家农业研究院UR 875 MIAT研究所）；INRA UMR 1202（法国国家农业研究院UMR 1202研究所）；AgroParisTech（巴黎高等农业学院）；UM R518 MIA（UM R518 MIA研究所）；Institute of Fundamental Sciences, Massey University（梅西大学基础科学研究所）
Probabilistic graphical models offer a powerful framework to account for the dependence structure between variables, which is represented as a graph. However, the dependence between variables may render inference tasks intractable. In this paper we review techniques exploiting the graph structure for exact inference, borrowed from optimisation and computer science. They are built on the principle of variable elimination whose complexity is dictated in an intricate way by the order in which variables are eliminated. The so-called treewidth of the graph characterises this algorithmic complexity:…
Hawkes (1971) introduced a powerful multivariate point process model of mutually exciting processes to explain causal structure in data. In this paper it is shown that the Granger causality structure of such processes is fully encoded in the corresponding link functions of the model. A new nonparametric estimator of the link functions based on a time-discretized version of the point process is introduced by using an infinite order autoregression. Consistency of the new estimator is derived. The estimator is applied to simulated data and to neural spike train data from the spinal dorsal horn of…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group heterogeneities among samples and the existence of potential confounding variables that, when ignored, increase the chance of false discoveries and reduce the power for identifying true differences. We propose a probabilistic framework to overcome these issues by combining three ideas: (i) a phylogenetic tree-based decomposition of the cross-group comparison proble…
We investigate the effect of cadmium (a toxic environmental pollutant) on the correlation structure of a number of urinary metabolites using Gaussian graphical models (GGMs). The inferred metabolic associations can provide important information on the physiological state of a metabolic system and insights on complex metabolic relationships. Using the fitted GGMs, we construct differential networks, which highlight significant changes in metabolite interactions under different experimental conditions. The analysis of such metabolic association networks can reveal differences in the underlying b…
Time Varying Functional Connectivity (TVFC) investigates how the interactions among brain regions vary over the course of an fMRI experiment. The transitions between different individual connectivity states can be modulated by changes in underlying physiological mechanisms that drive functional network dynamics, e.g., changes in attention or cognitive effort as measured by pupil dilation. In this paper, we develop a multi-subject Bayesian framework for estimating dynamic functional networks as a function of time-varying exogenous physiological covariates that are simultaneously recorded in eac…
A.I. SQUARE CONNECT；LAMSADE；Paris Dauphine University（巴黎多芬大学）；Université Paris Dauphine（巴黎多芬大学）
In this paper, we revisit the Kalman filter theory. After giving the intuition on a simplified financial markets example, we revisit the maths underlying it. We then show that Kalman filter can be presented in a very different fashion using graphical models. This enables us to establish the connection between Kalman filter and Hidden Markov Models. We then look at their application in financial markets and provide various intuitions in terms of their applicability for complex systems such as financial markets. Although this paper has been written more like a self contained work connecting Kalm…
Testing (conditional) independence of multivariate random variables is a task central to statistical inference and modelling in general - though unfortunately one for which to date there does not exist a practicable workflow. State-of-art workflows suffer from the need for heuristic or subjective manual choices, high computational complexity, or strong parametric assumptions. We address these problems by establishing a theoretical link between multivariate/conditional independence testing, and model comparison in the multivariate predictive modelling aka supervised learning task. This link all…
The ability to identify reliably a positive or negative partial correlation between the expression levels of two genes is influenced by the number $p$ of genes, the number $n$ of analyzed samples, and the statistical properties of the measurements. Classical statistical theory teaches that the product of the root sample size multiplied by the size of the partial correlation is the crucial quantity. But this has to be combined with some adjustment for multiplicity depending on $p$, which makes the classical analysis somewhat arbitrary. We investigate this problem through the lens of the Kullbac…
We show that under a linearity condition on the distribution of the predictors, the coefficient in single-index regression can be estimated with the same efficiency as in the case when the link function is known. Thus, the linearity condition seems to substitute for knowing the exact conditional distribution of the response given the linear combinations of the predictors.
We propose a generalized functional linear regression model for a regression situation where the response variable is a scalar and the predictor is a random function. A linear predictor is obtained by forming the scalar product of the predictor function with a smooth parameter function, and the expected value of the response is related to this linear predictor via a link function. If, in addition, a variance function is specified, this leads to a functional estimating equation which corresponds to maximizing a functional quasi-likelihood. This general approach includes the special cases of the…
Though Gaussian graphical models have been widely used in many scientific fields, relatively limited progress has been made to link graph structures to external covariates. We propose a Gaussian graphical regression model, which regresses both the mean and the precision matrix of a Gaussian graphical model on covariates. In the context of co-expression quantitative trait locus (QTL) studies, our method can determine how genetic variants and clinical conditions modulate the subject-level network structures, and recover both the population-level and subject-level gene networks. Our framework enc…
Gaussian graphical models (GGMs) are well-established tools for probabilistic exploration of dependence structures using precision matrices. We develop a Bayesian method to incorporate covariate information in this GGMs setup in a nonlinear seemingly unrelated regression framework. We propose a joint predictor and graph selection model and develop an efficient collapsed Gibbs sampler algorithm to search the joint model space. Furthermore, we investigate its theoretical variable selection properties. We demonstrate our method on a variety of simulated data, concluding with a real data set from …
The functional generalized additive model (FGAM) provides a more flexible nonlinear functional regression model than the well-studied functional linear regression model. This paper restricts attention to the FGAM with identity link and additive errors, which we will call the additive functional model, a generalization of the functional linear model. This paper studies the minimax rate of convergence of predictions from the additive functional model in the framework of reproducing kernel Hilbert space. It is shown that the optimal rate is determined by the decay rate of the eigenvalues of a spe…
