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1. Graph Learning from Multi-Attribute Smooth Signals

   https://doi.org/10.1109/MLSP49062.2020.9231563  

   Tugnait, Jitendra K. (September 2020, 2020 IEEE 30th International Workshop on Machine Learning for Signal Processing (MLSP))

   null (Ed.)

   We consider the problem of estimating the structure of an undirected weighted graph underlying a set of smooth multi -attribute signals. Most existing methods for graph estimation are based on single-attribute models where one associates a scalar data variable with each node of the graph, and the problem is to infer the graph topology that captures the relationships between these variables. An example is image graphs for grayscale texture images for modeling dependence of a pixel on neighboring pixels. In multi-attribute graphical models, each node represents a vector, as for example, in color image graphs where one has three variables (RGB color components) per pixel node. In this paper, we extend the single attribute approach of Kalofolias (2016) to multi -attribute data. An alternating direction method of multipliers (ADMM) algorithm is presented to optimize the objective function to infer the graph topology. Numerical results based on synthetic as well as real data are presented. 

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2. Learning High-Dimensional Differential Graphs From Multi-Attribute Data

   https://doi.org/10.1109/TSP.2023.3343553  

   Tugnait, Jitendra K. (December 2023, IEEE Transactions on Signal Processing)

   We consider the problem of estimating differences in two Gaussian graphical models (GGMs) which are known to have similar structure. The GGM structure is encoded in its precision (inverse covariance) matrix. In many applications one is interested in estimating the difference in two precision matrices to characterize underlying changes in conditional dependencies of two sets of data. Existing methods for differential graph estimation are based on single-attribute (SA) models where one associates a scalar random variable with each node. In multi-attribute (MA) graphical models, each node represents a random vector. In this paper, we analyze a group lasso penalized D-trace loss function approach for differential graph learning from multi-attribute data. An alternating direction method of multipliers (ADMM) algorithm is presented to optimize the objective function. Theoretical analysis establishing consistency in support recovery and estimation in high-dimensional settings is provided. Numerical results based on synthetic as well as real data are presented. 

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3. Variational Graph Recurrent Neural Networks

   Hajiramezanali, Ehsan; Hasanzadeh, Arman; Narayanan, Krishna Duffield; Zhou, Mingyuan; Qian, Xiaoning (December 2019, Advances in neural information processing systems)

   Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph recurrent neural network (GRNN) to capture both topology and node attribute changes in dynamic graphs. We argue that the use of high-level latent random variables in this variational GRNN (VGRNN) can better capture potential variability observed in dynamic graphs as well as the uncertainty of node latent representation. With semi-implicit variational inference developed for this new VGRNN architecture (SI-VGRNN), we show that flexible non-Gaussian latent representations can further help dynamic graph analytic tasks. Our experiments with multiple real-world dynamic graph datasets demonstrate that SI-VGRNN and VGRNN consistently outperform the existing baseline and state-of-the-art methods by a significant margin in dynamic link prediction. 

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4. Variational Graph Recurrent Neural Networks

   Hasanzadeh, Arman; Hajiramezanali, Ehsan; Narayanan, Krishna; Duffield, Nick; Zhou, Mingyuan; Qian, Xiaoning (January 2019, Advances in neural information processing systems)

   Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph recurrent neural network (GRNN) to capture both topology and node attribute changes in dynamic graphs. We argue that the use of high-level latent random variables in this variational GRNN (VGRNN) can better capture potential variability observed in dynamic graphs as well as the uncertainty of node latent representation. With semi-implicit variational inference developed for this new VGRNN architecture (SI-VGRNN), we show that flexible non-Gaussian latent representations can further help dynamic graph analytic tasks. Our experiments with multiple real-world dynamic graph datasets demonstrate that SI-VGRNN and VGRNN consistently outperform the existing baseline and state-of-the-art methods by a significant margin in dynamic link prediction. 

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5. Robust Bayesian graphical regression models for assessing tumor heterogeneity in proteomic networks

   https://doi.org/10.1093/biomtc/ujae160  

   Yao, Tsung-Hung; Ni, Yang; Bhadra, Anindya; Kang, Jian; Baladandayuthapani, Veerabhadran (January 2025, Biometrics)

   ABSTRACT Graphical models are powerful tools to investigate complex dependency structures in high-throughput datasets. However, most existing graphical models make one of two canonical assumptions: (i) a homogeneous graph with a common network for all subjects or (ii) an assumption of normality, especially in the context of Gaussian graphical models. Both assumptions are restrictive and can fail to hold in certain applications such as proteomic networks in cancer. To this end, we propose an approach termed robust Bayesian graphical regression (rBGR) to estimate heterogeneous graphs for non-normally distributed data. rBGR is a flexible framework that accommodates non-normality through random marginal transformations and constructs covariate-dependent graphs to accommodate heterogeneity through graphical regression techniques. We formulate a new characterization of edge dependencies in such models called conditional sign independence with covariates, along with an efficient posterior sampling algorithm. In simulation studies, we demonstrate that rBGR outperforms existing graphical regression models for data generated under various levels of non-normality in both edge and covariate selection. We use rBGR to assess proteomic networks in lung and ovarian cancers to systematically investigate the effects of immunogenic heterogeneity within tumors. Our analyses reveal several important protein–protein interactions that are differentially associated with the immune cell abundance; some corroborate existing biological knowledge, whereas others are novel findings. 

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