arXiv subjects

Yang Ni

Publications and source records attributed to Yang Ni.

At least 73 records · Page 4Linked to original sources

arXiv2023

Directed Cyclic Graph for Causal Discovery from Multivariate Functional Data

Discovering causal relationship using multivariate functional data has received a significant amount of attention very recently. In this article, we introduce a functional linear structural equation model for causal structure learning when the underlying graph involving the multivariate functions may have cycles. To enhance interpretability, our model involves a low-dimensional causal embedded space such that all the relevant causal information in the multivariate functional data is preserved in this lower-dimensional subspace. We prove that the proposed model is causally identifiable under standard assumptions that are often made in the causal discovery literature. To carry out inference of our model, we develop a fully Bayesian framework with suitable prior specifications and uncertainty quantification through posterior summaries. We illustrate the superior performance of our method over existing methods in terms of causal graph estimation through extensive simulation studies. We also demonstrate the proposed method using a brain EEG dataset.

stat.ME↗

arXiv2023

Robust Bayesian Graphical Regression Models for Assessing Tumor Heterogeneity in Proteomic Networks

Graphical models are powerful tools to investigate complex dependency structures in high-throughput datasets. However, most existing graphical models make one of the 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 across two cancers: lung and ovarian, to systematically investigate the effects of immunogenic heterogeneity within tumors. Our analyses reveal several important protein-protein interactions that are differentially impacted by the immune cell abundance; some corroborate existing biological knowledge whereas others are novel findings.

stat.ME↗

arXiv2023

Covariate-Assisted Bayesian Graph Learning for Heterogeneous Data

In a traditional Gaussian graphical model, data homogeneity is routinely assumed with no extra variables affecting the conditional independence. In modern genomic datasets, there is an abundance of auxiliary information, which often gets under-utilized in determining the joint dependency structure. In this article, we consider a Bayesian approach to model undirected graphs underlying heterogeneous multivariate observations with additional assistance from covariates. Building on product partition models, we propose a novel covariate-dependent Gaussian graphical model that allows graphs to vary with covariates so that observations whose covariates are similar share a similar undirected graph. To efficiently embed Gaussian graphical models into our proposed framework, we explore both Gaussian likelihood and pseudo-likelihood functions. For Gaussian likelihood, a G-Wishart distribution is used as a natural conjugate prior, and for the pseudo-likelihood, a product of Gaussian-conditionals is used. Moreover, the proposed model has large prior support and is flexible to approximate any $ν$-Hölder conditional variance-covariance matrices with $ν\in(0,1]$. We further show that based on the theory of fractional likelihood, the rate of posterior contraction is minimax optimal assuming the true density to be a Gaussian mixture with a known number of components. The efficacy of the approach is demonstrated via simulation studies and an analysis of a protein network for a breast cancer dataset assisted by mRNA gene expression as covariates.

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arXiv2023

Graphical Dirichlet Process for Clustering Non-Exchangeable Grouped Data

We consider the problem of clustering grouped data with possibly non-exchangeable groups whose dependencies can be characterized by a known directed acyclic graph. To allow the sharing of clusters among the non-exchangeable groups, we propose a Bayesian nonparametric approach, termed graphical Dirichlet process, that jointly models the dependent group-specific random measures by assuming each random measure to be distributed as a Dirichlet process whose concentration parameter and base probability measure depend on those of its parent groups. The resulting joint stochastic process respects the Markov property of the directed acyclic graph that links the groups. We characterize the graphical Dirichlet process using a novel hypergraph representation as well as the stick-breaking representation, the restaurant-type representation, and the representation as a limit of a finite mixture model. We develop an efficient posterior inference algorithm and illustrate our model with simulations and a real grouped single-cell dataset.

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arXiv2023

Efficient Off-Policy Reinforcement Learning via Brain-Inspired Computing

Reinforcement Learning (RL) has opened up new opportunities to enhance existing smart systems that generally include a complex decision-making process. However, modern RL algorithms, e.g., Deep Q-Networks (DQN), are based on deep neural networks, resulting in high computational costs. In this paper, we propose QHD, an off-policy value-based Hyperdimensional Reinforcement Learning, that mimics brain properties toward robust and real-time learning. QHD relies on a lightweight brain-inspired model to learn an optimal policy in an unknown environment. On both desktop and power-limited embedded platforms, QHD achieves significantly better overall efficiency than DQN while providing higher or comparable rewards. QHD is also suitable for highly-efficient reinforcement learning with great potential for online and real-time learning. Our solution supports a small experience replay batch size that provides 12.3 times speedup compared to DQN while ensuring minimal quality loss. Our evaluation shows QHD capability for real-time learning, providing 34.6 times speedup and significantly better quality of learning than DQN.

cs.LG↗

arXiv2023

Bayesian Covariate-Dependent Quantile Directed Acyclic Graphical Models for Individualized Inference

We propose an approach termed ``qDAGx'' for Bayesian covariate-dependent quantile directed acyclic graphs (DAGs) where these DAGs are individualized, in the sense that they depend on individual-specific covariates. The individualized DAG structure of the proposed approach can be uniquely identified at any given quantile, based on purely observational data without strong assumptions such as a known topological ordering. To scale the proposed method to a large number of variables and covariates, we propose for the model parameters a novel parameter expanded horseshoe prior that affords a number of attractive theoretical and computational benefits to our approach. By modeling the conditional quantiles, qDAGx overcomes the common limitations of mean regression for DAGs, which can be sensitive to the choice of likelihood, e.g., an assumption of multivariate normality, as well as to the choice of priors. We demonstrate the performance of qDAGx through extensive numerical simulations and via an application in precision medicine, which infers patient-specific protein--protein interaction networks in lung cancer.

stat.ME↗

arXiv2023

Bayesian Flexible Modelling of Spatially Resolved Transcriptomic Data

Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the measurement of gene expressions at the single cell level along with the spatial locations of these cells in the tissue. Dimension-reduction and spatial clustering are two of the most common exploratory analysis strategies for spatial transcriptomic data. However, existing dimension reduction methods may lead to a loss of inherent dependency structure among genes at any spatial location in the tissue and hence do not provide insights of gene co-expression pattern. In spatial transcriptomics, the matrix-variate gene expression data, along with spatial co-ordinates of the single cells, provides information on both gene expression dependencies and cell spatial dependencies through its row and column covariances. In this work, we propose a flexible Bayesian approach to simultaneously estimate the row and column covariances for the matrix-variate spatial transcriptomic data. The posterior estimates of the row and column covariances provide data summaries for downstream exploratory analysis. We illustrate our method with simulations and two analyses of real data generated from a recent spatial transcriptomic platform. Our work elucidates gene co-expression networks as well as clear spatial clustering patterns of the cells.

stat.AP↗

arXiv2023

Bayesian Nonlinear Tensor Regression with Functional Fused Elastic Net Prior

Tensor regression methods have been widely used to predict a scalar response from covariates in the form of a multiway array. In many applications, the regions of tensor covariates used for prediction are often spatially connected with unknown shapes and discontinuous jumps on the boundaries. Moreover, the relationship between the response and the tensor covariates can be nonlinear. In this article, we develop a nonlinear Bayesian tensor additive regression model to accommodate such spatial structure. A functional fused elastic net prior is proposed over the additive component functions to comprehensively model the nonlinearity and spatial smoothness, detect the discontinuous jumps, and simultaneously identify the active regions. The great flexibility and interpretability of the proposed method against the alternatives are demonstrated by a simulation study and an analysis on facial feature data.

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arXiv2022

Ordinal Causal Discovery

Causal discovery for purely observational, categorical data is a long-standing challenging problem. Unlike continuous data, the vast majority of existing methods for categorical data focus on inferring the Markov equivalence class only, which leaves the direction of some causal relationships undetermined. This paper proposes an identifiable ordinal causal discovery method that exploits the ordinal information contained in many real-world applications to uniquely identify the causal structure. The proposed method is applicable beyond ordinal data via data discretization. Through real-world and synthetic experiments, we demonstrate that the proposed ordinal causal discovery method combined with simple score-and-search algorithms has favorable and robust performance compared to state-of-the-art alternative methods in both ordinal categorical and non-categorical data. An accompanied R package OrdCD is freely available on CRAN and at https://web.stat.tamu.edu/~yni/files/OrdCD_1.0.0.tar.gz.

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arXiv2022

Bivariate Causal Discovery for Categorical Data via Classification with Optimal Label Permutation

Causal discovery for quantitative data has been extensively studied but less is known for categorical data. We propose a novel causal model for categorical data based on a new classification model, termed classification with optimal label permutation (COLP). By design, COLP is a parsimonious classifier, which gives rise to a provably identifiable causal model. A simple learning algorithm via comparing likelihood functions of causal and anti-causal models suffices to learn the causal direction. Through experiments with synthetic and real data, we demonstrate the favorable performance of the proposed COLP-based causal model compared to state-of-the-art methods. We also make available an accompanying R package COLP, which contains the proposed causal discovery algorithm and a benchmark dataset of categorical cause-effect pairs.

stat.ML↗

arXiv2022

Functional Bayesian Networks for Discovering Causality from Multivariate Functional Data

Multivariate functional data arise in a wide range of applications. One fundamental task is to understand the causal relationships among these functional objects of interest, which has not yet been fully explored. In this article, we develop a novel Bayesian network model for multivariate functional data where the conditional independence and causal structure are both encoded by a directed acyclic graph. Specifically, we allow the functional objects to deviate from Gaussian process, which is adopted by most existing functional data analysis models. The more reasonable non-Gaussian assumption is the key for unique causal structure identification even when the functions are measured with noises. A fully Bayesian framework is designed to infer the functional Bayesian network model with natural uncertainty quantification through posterior summaries. Simulation studies and real data examples are used to demonstrate the practical utility of the proposed model.

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arXiv2022

Sparse semiparametric discriminant analysis for high-dimensional zero-inflated data

Sequencing-based technologies provide an abundance of high-dimensional biological datasets with skewed and zero-inflated measurements. Classification of such data with linear discriminant analysis leads to poor performance due to the violation of the Gaussian distribution assumption. To address this limitation, we propose a new semiparametric discriminant analysis framework based on the truncated latent Gaussian copula model that accommodates both skewness and zero inflation. By applying sparsity regularization, we demonstrate that the proposed method leads to the consistent estimation of classification direction in high-dimensional settings. On simulated data, the proposed method shows superior performance compared to the existing method. We apply the method to discriminate healthy controls from patients with Crohn's disease based on microbiome data and to identify genera with the most influence on the classification rule.

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arXiv2022

Efficient Personalized Learning for Wearable Health Applications using HyperDimensional Computing

Health monitoring applications increasingly rely on machine learning techniques to learn end-user physiological and behavioral patterns in everyday settings. Considering the significant role of wearable devices in monitoring human body parameters, on-device learning can be utilized to build personalized models for behavioral and physiological patterns, and provide data privacy for users at the same time. However, resource constraints on most of these wearable devices prevent the ability to perform online learning on them. To address this issue, it is required to rethink the machine learning models from the algorithmic perspective to be suitable to run on wearable devices. Hyperdimensional computing (HDC) offers a well-suited on-device learning solution for resource-constrained devices and provides support for privacy-preserving personalization. Our HDC-based method offers flexibility, high efficiency, resilience, and performance while enabling on-device personalization and privacy protection. We evaluate the efficacy of our approach using three case studies and show that our system improves the energy efficiency of training by up to $45.8\times$ compared with the state-of-the-art Deep Neural Network (DNN) algorithms while offering a comparable accuracy.

cs.LG↗

arXiv2022

Causal Discovery with Heterogeneous Observational Data

We consider the problem of causal discovery (structure learning) from heterogeneous observational data. Most existing methods assume a homogeneous sampling scheme, which leads to misleading conclusions when violated in many applications. To this end, we propose a novel approach that exploits data heterogeneity to infer possibly cyclic causal structures from causally insufficient systems. The core idea is to model the direct causal effects as functions of exogenous covariates that properly explain data heterogeneity. We investigate structure identifiability properties of the proposed model. Structure learning is carried out in a fully Bayesian fashion, which provides natural uncertainty quantification. We demonstrate its utility through extensive simulations and a real-world application.

stat.ME↗

arXiv2021

GRB 210121A: A Typical Fireball Burst Detected by Two Small Missions

The Chinese CubeSat Mission, Gamma Ray Integrated Detectors (GRID), recently detected its first gamma-ray burst, GRB 210121A, which was jointly observed by the Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM). This burst is confirmed by several other missions, including \fermi and \textit{Insight}-HXMT. We combined multi-mission observational data and performed a comprehensive analysis of the burst's temporal and spectral properties. Our results show that the burst is relatively special in its high peak energy, thermal-like low energy indices, and large fluence. By putting it to the $E_{\rm p}$-$E_{\rmγ, iso}$ relation diagram with assumed distance, we found this burst can be constrained at the redshift range of [0.3,3.0]. The thermal spectral component is also confirmed by the direct fit of the physical models to the observed spectra. Interestingly, the physical photosphere model also constrained a redshift of $z\sim$ 0.3 for this burst, which help us to identify a host galaxy candidate at such a distance within the location error box. Assuming the host galaxy is real, we found the burst can be best explained by the photosphere emission of a typical fireball with an initial radius of $r_0\sim$ 3.2 $\times 10^7$ cm.

astro-ph.HE↗

arXiv2021

Phylogenetically informed Bayesian truncated copula graphical models for microbial association networks

Microorganisms play a critical role in host health. The advancement of high-throughput sequencing technology provides opportunities for a deeper understanding of microbial interactions. However, due to the limitations of 16S ribosomal RNA sequencing, microbiome data are zero-inflated, and a quantitative comparison of microbial abundances cannot be made across subjects. By leveraging a recent microbiome profiling technique that quantifies 16S ribosomal RNA microbial counts, we propose a novel Bayesian graphical model that incorporates microorganisms' evolutionary history through a phylogenetic tree prior and explicitly accounts for zero-inflation using the truncated Gaussian copula. Our simulation study reveals that the evolutionary information substantially improves the network estimation accuracy. We apply the proposed model to the quantitative gut microbiome data of 106 healthy subjects, and identify three distinct microbial communities that are not determined by existing microbial network estimation models. We further find that these communities are discriminated based on microorganisms' ability to utilize oxygen as an energy source.

stat.ME↗

arXiv2020

Bayesian biclustering for microbial metagenomic sequencing data via multinomial matrix factorization

High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious challenges for statistical modeling. We propose an identifiable Bayesian multinomial matrix factorization model to infer overlapping clusters on both microbes and hosts. The proposed method represents the observed over-dispersed zero-inflated count matrix as Dirichlet-multinomial mixtures on which latent cluster structures are built hierarchically. Under the Bayesian framework, the number of clusters is automatically determined and available information from a taxonomic rank tree of microbes is naturally incorporated, which greatly improves the interpretability of our findings. We demonstrate the utility of the proposed approach by comparing to alternative methods in simulations. An application to a human gut microbiome dataset involving patients with inflammatory bowel disease reveals interesting clusters, which contain bacteria families Bacteroidaceae, Bifidobacteriaceae, Enterobacteriaceae, Fusobacteriaceae, Lachnospiraceae, Ruminococcaceae, Pasteurellaceae, and Porphyromonadaceae that are known to be related to the inflammatory bowel disease and its subtypes according to biological literature. Our findings can help generate potential hypotheses for future investigation of the heterogeneity of the human gut microbiome.

stat.ME↗

arXiv2020

BAGEL: A Bayesian Graphical Model for Inferring Drug Effect Longitudinally on Depression in People with HIV

Access and adherence to antiretroviral therapy (ART) has transformed the face of HIV infection from a fatal to a chronic disease. However, ART is also known for its side effects. Studies have reported that ART is associated with depressive symptomatology. Large-scale HIV clinical databases with individuals' longitudinal depression records, ART medications, and clinical characteristics offer researchers unprecedented opportunities to study the effects of ART drugs on depression over time. We develop BAGEL, a Bayesian graphical model to investigate longitudinal effects of ART drugs on a range of depressive symptoms while adjusting for participants' demographic, behavior, and clinical characteristics, and taking into account the heterogeneous population through a Bayesian nonparametric prior. We evaluate BAGEL through simulation studies. Application to a dataset from the Women's Interagency HIV Study yields interpretable and clinically useful results. BAGEL not only can improve our understanding of ART drugs effects on disparate depression symptoms, but also has clinical utility in guiding informed and effective treatment selection to facilitate precision medicine in HIV.

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