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Xiaoyue Xi

Publications and source records attributed to Xiaoyue Xi.

6 recordsLinked to original sources

PTL-Diffusion: Manifold-Aware Diffusion with Periodic Terminal Laws

Standard diffusion models typically use a single time-homogeneous Gaussian terminal distribution as the reference law for generation. While this choice is analytically convenient and empirically powerful, it provides little explicit structure for data concentrated near low-dimensional manifolds, where different regions of the data distribution may correspond to distinct local geometric or semantic factors. As a result, the reverse model must recover manifold-level structure almost entirely from an unstructured terminal reference distribution. We propose PTL-Diffusion, a proof-of-concept diffusion framework whose forward noising process converges to a nonconstant periodic family of Gaussian terminal laws rather than to a single invariant law. Unlike a phase-conditioned DDPM, where phase information only enters the denoising network while the forward process remains unchanged, PTL-Diffusion embeds phase structure directly into the forward noising dynamics. The proposed construction remains close to standard denoising diffusion models: for a periodically forced Ornstein--Uhlenbeck-type forward process, we derive closed-form forward marginals, the limiting periodic Gaussian terminal family, and explicit Gaussian reverse posteriors, enabling standard noise-prediction training. We also introduce an invariant-average regularization term coupling the phase-conditioned reverse dynamics through the averaged periodic reference law. Experiments on torus and cylinder point-cloud benchmarks and the Olivetti face dataset show that PTL-Diffusion improves manifold-level distributional matching over matched DDPM baselines, reducing phase-conditioned errors, feature-space covariance errors, and nearest-neighbour manifold distances. These results suggest structured terminal reference laws as a promising direction, while motivating more expressive phase constructions and larger-scale evaluations.

cs.CV

NExON-Bayes: A Bayesian approach to network estimation informed by ordinal covariates

In heterogeneous disease settings, accounting for intrinsic sample variability is crucial for obtaining reliable and interpretable omic network estimates. However, most graphical model analyses of biomedical data assume homogeneous conditional dependence structures, potentially leading to misleading conclusions. To address this, we propose a joint Gaussian graphical model that leverages sample-level ordinal covariates (e.g., disease stage) to account for heterogeneity and improve the estimation of partial correlation structures. Our modelling framework, called NExON-Bayes, extends the graphical spike-and-slab framework to account for ordinal covariates, jointly estimating their relevance to the graph structure and leveraging them to improve the accuracy of network estimation. To scale to high-dimensional omic settings, we develop an efficient variational inference algorithm tailored to our model. Through simulations, we demonstrate that our method outperforms the vanilla graphical spike-and-slab (with no covariate information), as well as other state-of-the-art network approaches which exploit covariate information. Applying our method to reverse phase protein array data from patients diagnosed with stage I, II or III breast carcinoma, we estimate the behaviour of proteomic networks as breast carcinoma progresses. Our model provides insights not only through inspection of the estimated proteomic networks, but also of the estimated ordinal covariate dependencies of key groups of proteins within those networks, offering a comprehensive understanding of how biological pathways shift across disease stages. Availability and Implementation: A user-friendly R package for NExON-Bayes with tutorials is available on Github at github.com/jf687/NExON.

stat.ME

A modelling framework for detecting and leveraging node-level information in Bayesian network inference

Bayesian graphical models are powerful tools to infer complex relationships in high dimension, yet are often fraught with computational and statistical challenges. If exploited in a principled way, the increasing information collected alongside the data of primary interest constitutes an opportunity to mitigate these difficulties by guiding the detection of dependence structures. For instance, gene network inference may be informed by the use of publicly available summary statistics on the regulation of genes by genetic variants. Here we present a novel Gaussian graphical modelling framework to identify and leverage information on the centrality of nodes in conditional independence graphs. Specifically, we consider a fully joint hierarchical model to simultaneously infer (i) sparse precision matrices and (ii) the relevance of node-level information for uncovering the sought-after network structure. We encode such information as candidate auxiliary variables using a spike-and-slab submodel on the propensity of nodes to be hubs, which allows hypothesis-free selection and interpretation of a sparse subset of relevant variables. As efficient exploration of large posterior spaces is needed for real-world applications, we develop a variational expectation conditional maximisation algorithm that scales inference to hundreds of samples, nodes and auxiliary variables. We illustrate and exploit the advantages of our approach in simulations and in a gene network study which identifies hub genes involved in biological pathways relevant to immune-mediated diseases.

stat.ME

Inferring the sources of HIV infection in Africa from deep sequence data with semi-parametric Bayesian Poisson flow models

Pathogen deep-sequencing is an increasingly routinely used technology in infectious disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit these emerging data for inferring infectious disease transmission flows and the sources of infection at the population level. The framework is computationally scalable in high dimensional flow spaces thanks to Hilbert Space Gaussian process approximations, allows for sampling bias adjustments, and estimation of gender- and age-specific transmission flows at finer resolution than previously possible. We apply the approach to densely sampled, population-based HIV deep-sequence data from Rakai, Uganda, and find substantive evidence that adolescent and young women are predominantly infected through age-disparate relationships.

stat.AP

Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update

Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing including local and national lockdowns. In this technical update, we extend a semi-mechanistic Bayesian hierarchical model that infers the impact of these interventions and estimates the number of infections over time. Our methods assume that changes in the reproductive number - a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from temporal data on observed to estimate the number of infections and rate of transmission that occurred several weeks prior, allowing for a probabilistic time lag between infection and death. In this update we extend our original model [Flaxman, Mishra, Gandy et al 2020, Report #13, Imperial College London] to include (a) population saturation effects, (b) prior uncertainty on the infection fatality ratio, (c) a more balanced prior on intervention effects and (d) partial pooling of the lockdown intervention covariate. We also (e) included another 3 countries (Greece, the Netherlands and Portugal). The model code is available at https://github.com/ImperialCollegeLondon/covid19model/ We are now reporting the results of our updated model online at https://mrc-ide.github.io/covid19estimates/ We estimated parameters jointly for all M=14 countries in a single hierarchical model. Inference is performed in the probabilistic programming language Stan using an adaptive Hamiltonian Monte Carlo (HMC) sampler.

stat.AP

Bayesian Quadrature for Multiple Related Integrals

Bayesian probabilistic numerical methods are a set of tools providing posterior distributions on the output of numerical methods. The use of these methods is usually motivated by the fact that they can represent our uncertainty due to incomplete/finite information about the continuous mathematical problem being approximated. In this paper, we demonstrate that this paradigm can provide additional advantages, such as the possibility of transferring information between several numerical methods. This allows users to represent uncertainty in a more faithful manner and, as a by-product, provide increased numerical efficiency. We propose the first such numerical method by extending the well-known Bayesian quadrature algorithm to the case where we are interested in computing the integral of several related functions. We then prove convergence rates for the method in the well-specified and misspecified cases, and demonstrate its efficiency in the context of multi-fidelity models for complex engineering systems and a problem of global illumination in computer graphics.

stat.CO