arXiv subjects

Jason Xu

Publications and source records attributed to Jason Xu.

At least 37 records · Page 2Linked to original sources

arXiv2022

Distance-to-Set Priors and Constrained Bayesian Inference

Constrained learning is prevalent in many statistical tasks. Recent work proposes distance-to-set penalties to derive estimators under general constraints that can be specified as sets, but focuses on obtaining point estimates that do not come with corresponding measures of uncertainty. To remedy this, we approach distance-to-set regularization from a Bayesian lens. We consider a class of smooth distance-to-set priors, showing that they yield well-defined posteriors toward quantifying uncertainty for constrained learning problems. We discuss relationships and advantages over prior work on Bayesian constraint relaxation. Moreover, we prove that our approach is optimal in an information geometric-sense for finite penalty parameters $ρ$, and enjoys favorable statistical properties when $ρ\to\infty$. The method is designed to perform effectively within gradient-based MCMC samplers, as illustrated on a suite of simulated and real data applications.

stat.ME↗

arXiv2022

Exact Inference for Stochastic Epidemic Models via Uniformly Ergodic Block Sampling

Stochastic epidemic models provide an interpretable probabilistic description of the spread of a disease through a population. Yet, fitting these models to partially observed data is a notoriously difficult task due to intractability of the likelihood for many classical models. To remedy this issue, this article introduces a novel data-augmented MCMC algorithm for exact Bayesian inference under the stochastic SIR model, given only discretely observed counts of infection. In a Metropolis-Hastings step, the latent data are jointly proposed from a surrogate process carefully designed to closely resemble the SIR model, from which we can efficiently generate epidemics consistent with the observed data. This yields a method that explores the high-dimensional latent space efficiently, and scales to outbreaks with hundreds of thousands of individuals. We show that the Markov chain underlying the algorithm is uniformly ergodic, and validate its performance via thorough simulation experiments and a case study on the 2013-2015 outbreak of Ebola Haemorrhagic Fever in Western Africa.

stat.CO↗

arXiv2022

Community Detection in Weighted Multilayer Networks with Ambient Noise

We introduce a novel model for multilayer weighted networks that accounts for global noise in addition to local signals. The model is similar to a multilayer stochastic blockmodel (SBM), but the key difference is that between-block interactions independent across layers are common for the whole system, which we call ambient noise. A single block is also characterized by these fixed ambient parameters to represent members that do not belong anywhere else. This approach allows simultaneous clustering and typologizing of blocks into signal or noise in order to better understand their roles in the overall system, which is not accounted for by existing Blockmodels. We employ a novel application of hierarchical variational inference to jointly detect and differentiate types of blocks. We call this model for multilayer weighted networks the Stochastic Block (with) Ambient Noise Model (SBANM) and develop an associated community detection algorithm. We apply this method to subjects in the Philadelphia Neurodevelopmental Cohort to discover communities of subjects with co-occurrent psychopathologies in relation to psychosis.

cs.SI↗

arXiv2022

Wi-Fi and Bluetooth Contact Tracing Without User Intervention

Previous contact tracing systems required the users to perform many manual actions, such as installing smartphone applications, joining wireless networks, or carrying custom user devices. This increases the barrier to entry and lowers the user adoption rate. As a result, the contact tracing effectiveness is reduced. Unlike the systems above, we propose a new privacy preserving Wi-Fi and Bluetooth (BLE) contact tracing system that does not require smartphone applications, joining wireless networks, or custom user devices. Our specially built routers seamlessly track smartphones, laptops, smartwatches, BLE headphones, and tablets without any user action, but do not trace user identity. Mapping between devices and users is only carried out for confirmed cases and suspected contacts. Moreover, we can track the absolute positions of user devices within 1.0 m due to using bidirectional long short-term memory neural networks that are trained with data pre-collected by an autonomous robot. This allows public health authorities to track indirect droplet and surface transmissions that other contact tracing systems often overlook.

eess.SP↗

arXiv2022

Bregman Power k-Means for Clustering Exponential Family Data

Recent progress in center-based clustering algorithms combats poor local minima by implicit annealing, using a family of generalized means. These methods are variations of Lloyd's celebrated $k$-means algorithm, and are most appropriate for spherical clusters such as those arising from Gaussian data. In this paper, we bridge these algorithmic advances to classical work on hard clustering under Bregman divergences, which enjoy a bijection to exponential family distributions and are thus well-suited for clustering objects arising from a breadth of data generating mechanisms. The elegant properties of Bregman divergences allow us to maintain closed form updates in a simple and transparent algorithm, and moreover lead to new theoretical arguments for establishing finite sample bounds that relax the bounded support assumption made in the existing state of the art. Additionally, we consider thorough empirical analyses on simulated experiments and a case study on rainfall data, finding that the proposed method outperforms existing peer methods in a variety of non-Gaussian data settings.

stat.ML↗

arXiv2022

A unified analysis of convex and non-convex lp-ball projection problems

The task of projecting onto $\ell_p$ norm balls is ubiquitous in statistics and machine learning, yet the availability of actionable algorithms for doing so is largely limited to the special cases of $p = \left\{ 0, 1,2, \infty \right\}$. In this paper, we introduce novel, scalable methods for projecting onto the $\ell_p$ ball for general $p>0$. For $p \geq1 $, we solve the univariate Lagrangian dual via a dual Newton method. We then carefully design a bisection approach for $p<1$, presenting theoretical and empirical evidence of zero or a small duality gap in the non-convex case. The success of our contributions is thoroughly assessed empirically, and applied to large-scale regularized multi-task learning and compressed sensing.

math.OC↗

arXiv2022

Quasi-Newton acceleration of EM and MM algorithms via Broyden$'$s method

The principle of majorization-minimization (MM) provides a general framework for eliciting effective algorithms to solve optimization problems. However, they often suffer from slow convergence, especially in large-scale and high-dimensional data settings. This has drawn attention to acceleration schemes designed exclusively for MM algorithms, but many existing designs are either problem-specific or rely on approximations and heuristics loosely inspired by the optimization literature. We propose a novel, rigorous quasi-Newton method for accelerating any valid MM algorithm, cast as seeking a fixed point of the MM \textit{algorithm map}. The method does not require specific information or computation from the objective function or its gradient and enjoys a limited-memory variant amenable to efficient computation in high-dimensional settings. By connecting our approach to Broyden's classical root-finding methods, we establish convergence guarantees and identify conditions for linear and super-linear convergence. These results are validated numerically and compared to peer methods in a thorough empirical study, showing that it achieves state-of-the-art performance across a diverse range of problems.

math.OC↗

arXiv2021

Likelihood-based inference for partially observed stochastic epidemics with individual heterogeneity

We develop a stochastic epidemic model progressing over dynamic networks, where infection rates are heterogeneous and may vary with individual-level covariates. The joint dynamics are modeled as a continuous-time Markov chain such that disease transmission is constrained by the contact network structure, and network evolution is in turn influenced by individual disease statuses. To accommodate partial epidemic observations commonly seen in real-world data, we propose a likelihood-based inference method based on the stochastic EM algorithm, introducing key innovations that include efficient conditional samplers for imputing missing infection and recovery times which respect the dynamic contact network. Experiments on both synthetic and real datasets demonstrate that our inference method can accurately and efficiently recover model parameters and provide valuable insight at the presence of unobserved disease episodes in epidemic data.

stat.ME↗

arXiv2021

Computational tools for assessing gene therapy under branching process models of mutation

Multitype branching processes are ideal for studying the population dynamics of stem cell populations undergoing mutation accumulation over the years following transplant. In such stochastic models, several quantities are of clinical interest as insertional mutagenesis carries the potential threat of leukemogenesis following gene therapy with autologous stem cell transplantation. In this paper, we develop a three-type branching process model describing accumulations of mutations in a population of stem cells distinguished by their ability for long-term self-renewal. Our outcome of interest is the appearance of a double-mutant cell, which carries a high potential for leukemic transformation. In our model, a single-hit mutation carries a slight proliferative advantage over a wild-type stem cells. We compute marginalized transition probabilities that allow us to capture important quantitative aspects of our model, including the probability of observing a double-hit mutant and relevant moments of a single-hit mutation population over time. We thoroughly explore the model behavior numerically, varying birth rates across the initial sizes and populations of wild type stem cells and single-hit mutants, and compare the probability of observing a double-hit mutant under these conditions. We find that increasing the number of single-mutants over wild-type particles initially present has a large effect on the occurrence of a double-mutant, and that it is relatively safe for single-mutants to be quite proliferative, provided the lentiviral gene addition avoids creating single mutants in the original insertion process. Our approach is broadly applicable to an important set of questions in cancer modeling and other population processes involving multiple stages, compartments, or types.

q-bio.PE↗

arXiv2021

Uniform Concentration Bounds toward a Unified Framework for Robust Clustering

Recent advances in center-based clustering continue to improve upon the drawbacks of Lloyd's celebrated $k$-means algorithm over $60$ years after its introduction. Various methods seek to address poor local minima, sensitivity to outliers, and data that are not well-suited to Euclidean measures of fit, but many are supported largely empirically. Moreover, combining such approaches in a piecemeal manner can result in ad hoc methods, and the limited theoretical results supporting each individual contribution may no longer hold. Toward addressing these issues in a principled way, this paper proposes a cohesive robust framework for center-based clustering under a general class of dissimilarity measures. In particular, we present a rigorous theoretical treatment within a Median-of-Means (MoM) estimation framework, showing that it subsumes several popular $k$-means variants. In addition to unifying existing methods, we derive uniform concentration bounds that complete their analyses, and bridge these results to the MoM framework via Dudley's chaining arguments. Importantly, we neither require any assumptions on the distribution of the outlying observations nor on the relative number of observations $n$ to features $p$. We establish strong consistency and an error rate of $O(n^{-1/2})$ under mild conditions, surpassing the best-known results in the literature. The methods are empirically validated thoroughly on real and synthetic datasets.

stat.ML↗

arXiv2021

A Proximal Distance Algorithm for Likelihood-Based Sparse Covariance Estimation

This paper addresses the task of estimating a covariance matrix under a patternless sparsity assumption. In contrast to existing approaches based on thresholding or shrinkage penalties, we propose a likelihood-based method that regularizes the distance from the covariance estimate to a symmetric sparsity set. This formulation avoids unwanted shrinkage induced by more common norm penalties and enables optimization of the resulting non-convex objective by solving a sequence of smooth, unconstrained subproblems. These subproblems are generated and solved via the proximal distance version of the majorization-minimization principle. The resulting algorithm executes rapidly, gracefully handles settings where the number of parameters exceeds the number of cases, yields a positive definite solution, and enjoys desirable convergence properties. Empirically, we demonstrate that our approach outperforms competing methods by several metrics across a suite of simulated experiments. Its merits are illustrated on an international migration dataset and a classic case study on flow cytometry. Our findings suggest that the marginal and conditional dependency networks for the cell signalling data are more similar than previously concluded.

stat.ME↗

arXiv2021

Biconvex Clustering

Convex clustering has recently garnered increasing interest due to its attractive theoretical and computational properties, but its merits become limited in the face of high-dimensional data. In such settings, pairwise affinity terms that rely on $k$-nearest neighbors become poorly specified and Euclidean measures of fit provide weaker discriminating power. To surmount these issues, we propose to modify the convex clustering objective so that feature weights are optimized jointly with the centroids. The resulting problem becomes biconvex, and as such remains well-behaved statistically and algorithmically. In particular, we derive a fast algorithm with closed form updates and convergence guarantees, and establish finite-sample bounds on its prediction error. Under interpretable regularity conditions, the error bound analysis implies consistency of the proposed estimator. Biconvex clustering performs feature selection throughout the clustering task: as the learned weights change the effective feature representation, pairwise affinities can be updated adaptively across iterations rather than precomputed within a dubious feature space. We validate the contributions on real and simulated data, showing that our method effectively addresses the challenges of dimensionality while reducing dependence on carefully tuned heuristics typical of existing approaches.

stat.ME↗

arXiv2020

Kernel k-Means, By All Means: Algorithms and Strong Consistency

Kernel $k$-means clustering is a powerful tool for unsupervised learning of non-linearly separable data. Since the earliest attempts, researchers have noted that such algorithms often become trapped by local minima arising from non-convexity of the underlying objective function. In this paper, we generalize recent results leveraging a general family of means to combat sub-optimal local solutions to the kernel and multi-kernel settings. Called Kernel Power $k$-Means, our algorithm makes use of majorization-minimization (MM) to better solve this non-convex problem. We show the method implicitly performs annealing in kernel feature space while retaining efficient, closed-form updates, and we rigorously characterize its convergence properties both from computational and statistical points of view. In particular, we characterize the large sample behavior of the proposed method by establishing strong consistency guarantees. Its merits are thoroughly validated on a suite of simulated datasets and real data benchmarks that feature non-linear and multi-view separation.

stat.ML↗

arXiv2020

Simple and Scalable Sparse k-means Clustering via Feature Ranking

Clustering, a fundamental activity in unsupervised learning, is notoriously difficult when the feature space is high-dimensional. Fortunately, in many realistic scenarios, only a handful of features are relevant in distinguishing clusters. This has motivated the development of sparse clustering techniques that typically rely on k-means within outer algorithms of high computational complexity. Current techniques also require careful tuning of shrinkage parameters, further limiting their scalability. In this paper, we propose a novel framework for sparse k-means clustering that is intuitive, simple to implement, and competitive with state-of-the-art algorithms. We show that our algorithm enjoys consistency and convergence guarantees. Our core method readily generalizes to several task-specific algorithms such as clustering on subsets of attributes and in partially observed data settings. We showcase these contributions thoroughly via simulated experiments and real data benchmarks, including a case study on protein expression in trisomic mice.

stat.ML↗

arXiv2020

Likelihood-based Inference for Partially Observed Epidemics on Dynamic Networks

We propose a generative model and an inference scheme for epidemic processes on dynamic, adaptive contact networks. Network evolution is formulated as a link-Markovian process, which is then coupled to an individual-level stochastic SIR model, in order to describe the interplay between epidemic dynamics on a network and network link changes. A Markov chain Monte Carlo framework is developed for likelihood-based inference from partial epidemic observations, with a novel data augmentation algorithm specifically designed to deal with missing individual recovery times under the dynamic network setting. Through a series of simulation experiments, we demonstrate the validity and flexibility of the model as well as the efficacy and efficiency of the data augmentation inference scheme. The model is also applied to a recent real-world dataset on influenza-like-illness transmission with high-resolution social contact tracking records.

stat.ME↗

arXiv2020

Entropy Regularized Power k-Means Clustering

Despite its well-known shortcomings, $k$-means remains one of the most widely used approaches to data clustering. Current research continues to tackle its flaws while attempting to preserve its simplicity. Recently, the \textit{power $k$-means} algorithm was proposed to avoid trapping in local minima by annealing through a family of smoother surfaces. However, the approach lacks theoretical justification and fails in high dimensions when many features are irrelevant. This paper addresses these issues by introducing \textit{entropy regularization} to learn feature relevance while annealing. We prove consistency of the proposed approach and derive a scalable majorization-minimization algorithm that enjoys closed-form updates and convergence guarantees. In particular, our method retains the same computational complexity of $k$-means and power $k$-means, but yields significant improvements over both. Its merits are thoroughly assessed on a suite of real and synthetic data experiments.

stat.ML↗

arXiv2018

Statistical inference in partially observed branching processes with application to cell lineage tracking of in vivo hematopoiesis

Single-cell lineage tracking strategies enabled by recent experimental technologies have produced significant insights into cell fate decisions, but lack the quantitative framework necessary for rigorous statistical analysis of mechanistic models describing cell division and differentiation. In this paper, we develop such a framework with corresponding moment-based parameter estimation techniques for continuous-time, multi-type branching processes. Such processes provide a probabilistic model of how cells divide and differentiate, and we apply our method to study hematopoiesis, the mechanism of blood cell production. We derive closed-form expressions for higher moments in a general class of such models. These analytical results allow us to efficiently estimate parameters of much richer statistical models of hematopoiesis than those used in previous statistical studies. After validating the methodology in simulation studies, we apply our estimator to hematopoietic lineage tracking data from rhesus macaques. Our analysis provides a more complete understanding of cell fate decisions during hematopoiesis in non-human primates, which may be more relevant to human biology and clinical strategies than previous findings from murine studies. For example, in addition to previously estimated hematopoietic stem cell self-renewal rate, we are able to estimate fate decision probabilities and to compare structurally distinct models of hematopoiesis using cross validation. These estimates of fate decision probabilities and our model selection results should help biologists compare competing hypotheses about how progenitor cells differentiate. The methodology is transferrable to a large class of stochastic compartmental models and multi-type branching models, commonly used in studies of cancer progression, epidemiology, and many other fields.

stat.ME↗

arXiv2018

Structural Risk Minimization for $C^{1,1}(\mathbb{R}^d)$ Regression

One means of fitting functions to high-dimensional data is by providing smoothness constraints. Recently, the following smooth function approximation problem was proposed: given a finite set $E \subset \mathbb{R}^d$ and a function $f: E \rightarrow \mathbb{R}$, interpolate the given information with a function $\widehat{f} \in \dot{C}^{1, 1}(\mathbb{R}^d)$ (the class of first-order differentiable functions with Lipschitz gradients) such that $\widehat{f}(a) = f(a)$ for all $a \in E$, and the value of $\mathrm{Lip}(\nabla \widehat{f})$ is minimal. An algorithm is provided that constructs such an approximating function $\widehat{f}$ and estimates the optimal Lipschitz constant $\mathrm{Lip}(\nabla \widehat{f})$ in the noiseless setting. We address statistical aspects of reconstructing the approximating function $\widehat{f}$ from a closely-related class $C^{1, 1}(\mathbb{R}^d)$ given samples from noisy data. We observe independent and identically distributed samples $y(a) = f(a) + ξ(a)$ for $a \in E$, where $ξ(a)$ is a noise term and the set $E \subset \mathbb{R}^d$ is fixed and known. We obtain uniform bounds relating the empirical risk and true risk over the class $\mathcal{F}_{\widetilde{M}} = \{f \in C^{1, 1}(\mathbb{R}^d) \mid \mathrm{Lip}(\nabla f) \leq \widetilde{M}\}$, where the quantity $\widetilde{M}$ grows with the number of samples at a rate governed by the metric entropy of the class $C^{1, 1}(\mathbb{R}^d)$. Finally, we provide an implementation using Vaidya's algorithm, supporting our results via numerical experiments on simulated data.

stat.ML↗