arXiv subjects

Hongtu Zhu

Publications and source records attributed to Hongtu Zhu.

At least 73 records · Page 4Linked to original sources

arXiv2023

Leveraging Brain Modularity Prior for Interpretable Representation Learning of fMRI

Resting-state functional magnetic resonance imaging (rs-fMRI) can reflect spontaneous neural activities in brain and is widely used for brain disorder analysis.Previous studies propose to extract fMRI representations through diverse machine/deep learning methods for subsequent analysis. But the learned features typically lack biological interpretability, which limits their clinical utility. From the view of graph theory, the brain exhibits a remarkable modular structure in spontaneous brain functional networks, with each module comprised of functionally interconnected brain regions-of-interest (ROIs). However, most existing learning-based methods for fMRI analysis fail to adequately utilize such brain modularity prior. In this paper, we propose a Brain Modularity-constrained dynamic Representation learning (BMR) framework for interpretable fMRI analysis, consisting of three major components: (1) dynamic graph construction, (2) dynamic graph learning via a novel modularity-constrained graph neural network(MGNN), (3) prediction and biomarker detection for interpretable fMRI analysis. Especially, three core neurocognitive modules (i.e., salience network, central executive network, and default mode network) are explicitly incorporated into the MGNN, encouraging the nodes/ROIs within the same module to share similar representations. To further enhance discriminative ability of learned features, we also encourage the MGNN to preserve the network topology of input graphs via a graph topology reconstruction constraint. Experimental results on 534 subjects with rs-fMRI scans from two datasets validate the effectiveness of the proposed method. The identified discriminative brain ROIs and functional connectivities can be regarded as potential fMRI biomarkers to aid in clinical diagnosis.

q-bio.QM↗

arXiv2023

Evaluating Dynamic Conditional Quantile Treatment Effects with Applications in Ridesharing

Many modern tech companies, such as Google, Uber, and Didi, utilize online experiments (also known as A/B testing) to evaluate new policies against existing ones. While most studies concentrate on average treatment effects, situations with skewed and heavy-tailed outcome distributions may benefit from alternative criteria, such as quantiles. However, assessing dynamic quantile treatment effects (QTE) remains a challenge, particularly when dealing with data from ride-sourcing platforms that involve sequential decision-making across time and space. In this paper, we establish a formal framework to calculate QTE conditional on characteristics independent of the treatment. Under specific model assumptions, we demonstrate that the dynamic conditional QTE (CQTE) equals the sum of individual CQTEs across time, even though the conditional quantile of cumulative rewards may not necessarily equate to the sum of conditional quantiles of individual rewards. This crucial insight significantly streamlines the estimation and inference processes for our target causal estimand. We then introduce two varying coefficient decision process (VCDP) models and devise an innovative method to test the dynamic CQTE. Moreover, we expand our approach to accommodate data from spatiotemporal dependent experiments and examine both conditional quantile direct and indirect effects. To showcase the practical utility of our method, we apply it to three real-world datasets from a ride-sourcing platform. Theoretical findings and comprehensive simulation studies further substantiate our proposal.

stat.ME↗

arXiv2023

Nearest-Neighbor Sampling Based Conditional Independence Testing

The conditional randomization test (CRT) was recently proposed to test whether two random variables X and Y are conditionally independent given random variables Z. The CRT assumes that the conditional distribution of X given Z is known under the null hypothesis and then it is compared to the distribution of the observed samples of the original data. The aim of this paper is to develop a novel alternative of CRT by using nearest-neighbor sampling without assuming the exact form of the distribution of X given Z. Specifically, we utilize the computationally efficient 1-nearest-neighbor to approximate the conditional distribution that encodes the null hypothesis. Then, theoretically, we show that the distribution of the generated samples is very close to the true conditional distribution in terms of total variation distance. Furthermore, we take the classifier-based conditional mutual information estimator as our test statistic. The test statistic as an empirical fundamental information theoretic quantity is able to well capture the conditional-dependence feature. We show that our proposed test is computationally very fast, while controlling type I and II errors quite well. Finally, we demonstrate the efficiency of our proposed test in both synthetic and real data analyses.

cs.LG↗

arXiv2023

A Multi-Agent Reinforcement Learning Framework for Off-Policy Evaluation in Two-sided Markets

The two-sided markets such as ride-sharing companies often involve a group of subjects who are making sequential decisions across time and/or location. With the rapid development of smart phones and internet of things, they have substantially transformed the transportation landscape of human beings. In this paper we consider large-scale fleet management in ride-sharing companies that involve multiple units in different areas receiving sequences of products (or treatments) over time. Major technical challenges, such as policy evaluation, arise in those studies because (i) spatial and temporal proximities induce interference between locations and times; and (ii) the large number of locations results in the curse of dimensionality. To address both challenges simultaneously, we introduce a multi-agent reinforcement learning (MARL) framework for carrying policy evaluation in these studies. We propose novel estimators for mean outcomes under different products that are consistent despite the high-dimensionality of state-action space. The proposed estimator works favorably in simulation experiments. We further illustrate our method using a real dataset obtained from a two-sided marketplace company to evaluate the effects of applying different subsidizing policies. A Python implementation of our proposed method is available at https://github.com/RunzheStat/CausalMARL.

stat.ML↗

arXiv2023

A Partially Functional Linear Modeling Framework for Integrating Genetic, Imaging, and Clinical Data

This paper is motivated by the joint analysis of genetic, imaging, and clinical (GIC) data collected in the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. We propose a regression framework based on partially functional linear regression models to map high-dimensional GIC-related pathways for Alzheimer's Disease (AD). We develop a joint model selection and estimation procedure by embedding imaging data in the reproducing kernel Hilbert space and imposing the L0 penalty for the coefficients of genetic variables. We apply the proposed method to the ADNI dataset to identify important features from tens of thousands of genetic polymorphisms (reduced from millions using a preprocessing step) and study the effects of a certain set of informative genetic variants and the baseline hippocampus surface on thirteen future cognitive scores measuring different aspects of cognitive function. We explore the shared and different heritability patterns of these cognitive scores. Analysis results suggest that both the hippocampal and genetic data have heterogeneous effects on different scores, with the trend that the value of both hippocampi is negatively associated with the severity of cognition deficits. Polygenic effects are observed for all thirteen cognitive scores. The well-known APOE4 genotype only explains a small part of cognitive function. Shared genetic etiology exists, however, greater genetic heterogeneity exists within disease classifications after accounting for the baseline diagnosis status. These analyses are useful in further investigation of functional mechanisms for AD evolution.

stat.ME↗

arXiv2023

Source-Free Unsupervised Domain Adaptation: A Survey

Unsupervised domain adaptation (UDA) via deep learning has attracted appealing attention for tackling domain-shift problems caused by distribution discrepancy across different domains. Existing UDA approaches highly depend on the accessibility of source domain data, which is usually limited in practical scenarios due to privacy protection, data storage and transmission cost, and computation burden. To tackle this issue, many source-free unsupervised domain adaptation (SFUDA) methods have been proposed recently, which perform knowledge transfer from a pre-trained source model to unlabeled target domain with source data inaccessible. A comprehensive review of these works on SFUDA is of great significance. In this paper, we provide a timely and systematic literature review of existing SFUDA approaches from a technical perspective. Specifically, we categorize current SFUDA studies into two groups, i.e., white-box SFUDA and black-box SFUDA, and further divide them into finer subcategories based on different learning strategies they use. We also investigate the challenges of methods in each subcategory, discuss the advantages/disadvantages of white-box and black-box SFUDA methods, conclude the commonly used benchmark datasets, and summarize the popular techniques for improved generalizability of models learned without using source data. We finally discuss several promising future directions in this field.

cs.CV↗

arXiv2022

Off-Policy Confidence Interval Estimation with Confounded Markov Decision Process

This paper is concerned with constructing a confidence interval for a target policy's value offline based on a pre-collected observational data in infinite horizon settings. Most of the existing works assume no unmeasured variables exist that confound the observed actions. This assumption, however, is likely to be violated in real applications such as healthcare and technological industries. In this paper, we show that with some auxiliary variables that mediate the effect of actions on the system dynamics, the target policy's value is identifiable in a confounded Markov decision process. Based on this result, we develop an efficient off-policy value estimator that is robust to potential model misspecification and provide rigorous uncertainty quantification. Our method is justified by theoretical results, simulated and real datasets obtained from ridesharing companies. A Python implementation of the proposed procedure is available at https://github.com/Mamba413/cope.

stat.ML↗

arXiv2022

Dynamic Causal Effects Evaluation in A/B Testing with a Reinforcement Learning Framework

A/B testing, or online experiment is a standard business strategy to compare a new product with an old one in pharmaceutical, technological, and traditional industries. Major challenges arise in online experiments of two-sided marketplace platforms (e.g., Uber) where there is only one unit that receives a sequence of treatments over time. In those experiments, the treatment at a given time impacts current outcome as well as future outcomes. The aim of this paper is to introduce a reinforcement learning framework for carrying A/B testing in these experiments, while characterizing the long-term treatment effects. Our proposed testing procedure allows for sequential monitoring and online updating. It is generally applicable to a variety of treatment designs in different industries. In addition, we systematically investigate the theoretical properties (e.g., size and power) of our testing procedure. Finally, we apply our framework to both simulated data and a real-world data example obtained from a technological company to illustrate its advantage over the current practice. A Python implementation of our test is available at https://github.com/callmespring/CausalRL.

cs.LG↗

arXiv2022

Reinforcement Learning for Ridesharing: An Extended Survey

In this paper, we present a comprehensive, in-depth survey of the literature on reinforcement learning approaches to decision optimization problems in a typical ridesharing system. Papers on the topics of rideshare matching, vehicle repositioning, ride-pooling, routing, and dynamic pricing are covered. Most of the literature has appeared in the last few years, and several core challenges are to continue to be tackled: model complexity, agent coordination, and joint optimization of multiple levers. Hence, we also introduce popular data sets and open simulation environments to facilitate further research and development. Subsequently, we discuss a number of challenges and opportunities for reinforcement learning research on this important domain.

cs.LG↗

arXiv2022

Statistical learning methods for neuroimaging data analysis with applications

The aim of this paper is to provide a comprehensive review of statistical challenges in neuroimaging data analysis from neuroimaging techniques to large-scale neuroimaging studies to statistical learning methods. We briefly review eight popular neuroimaging techniques and their potential applications in neuroscience research and clinical translation. We delineate the four common themes of neuroimaging data and review major image processing analysis methods for processing neuroimaging data at the individual level. We briefly review four large-scale neuroimaging-related studies and a consortium on imaging genomics and discuss four common themes of neuroimaging data analysis at the population level. We review nine major population-based statistical analysis methods and their associated statistical challenges and present recent progress in statistical methodology to address these challenges.

stat.AP↗

arXiv2022

GCF: Generalized Causal Forest for Heterogeneous Treatment Effect Estimation in Online Marketplace

Uplift modeling is a rapidly growing approach that utilizes causal inference and machine learning methods to directly estimate the heterogeneous treatment effects, which has been widely applied to various online marketplaces to assist large-scale decision-making in recent years. The existing popular models, like causal forest (CF), are limited to either discrete treatments or posing parametric assumptions on the outcome-treatment relationship that may suffer model misspecification. However, continuous treatments (e.g., price, duration) often arise in marketplaces. To alleviate these restrictions, we use a kernel-based doubly robust estimator to recover the non-parametric dose-response functions that can flexibly model continuous treatment effects. Moreover, we propose a generic distance-based splitting criterion to capture the heterogeneity for the continuous treatments. We call the proposed algorithm generalized causal forest (GCF) as it generalizes the use case of CF to a much broader setting. We show the effectiveness of GCF by deriving the asymptotic property of the estimator and comparing it to popular uplift modeling methods on both synthetic and real-world datasets. We implement GCF on Spark and successfully deploy it into a large-scale online pricing system at a leading ride-sharing company. Online A/B testing results further validate the superiority of GCF.

stat.ML↗

arXiv2022

D-GCCA: Decomposition-based Generalized Canonical Correlation Analysis for Multi-view High-dimensional Data

Modern biomedical studies often collect multi-view data, that is, multiple types of data measured on the same set of objects. A popular model in high-dimensional multi-view data analysis is to decompose each view's data matrix into a low-rank common-source matrix generated by latent factors common across all data views, a low-rank distinctive-source matrix corresponding to each view, and an additive noise matrix. We propose a novel decomposition method for this model, called decomposition-based generalized canonical correlation analysis (D-GCCA). The D-GCCA rigorously defines the decomposition on the L2 space of random variables in contrast to the Euclidean dot product space used by most existing methods, thereby being able to provide the estimation consistency for the low-rank matrix recovery. Moreover, to well calibrate common latent factors, we impose a desirable orthogonality constraint on distinctive latent factors. Existing methods, however, inadequately consider such orthogonality and may thus suffer from substantial loss of undetected common-source variation. Our D-GCCA takes one step further than generalized canonical correlation analysis by separating common and distinctive components among canonical variables, while enjoying an appealing interpretation from the perspective of principal component analysis. Furthermore, we propose to use the variable-level proportion of signal variance explained by common or distinctive latent factors for selecting the variables most influenced. Consistent estimators of our D-GCCA method are established with good finite-sample numerical performance, and have closed-form expressions leading to efficient computation especially for large-scale data. The superiority of D-GCCA over state-of-the-art methods is also corroborated in simulations and real-world data examples.

stat.ML↗

arXiv2022

Statistically Efficient Advantage Learning for Offline Reinforcement Learning in Infinite Horizons

We consider reinforcement learning (RL) methods in offline domains without additional online data collection, such as mobile health applications. Most of existing policy optimization algorithms in the computer science literature are developed in online settings where data are easy to collect or simulate. Their generalizations to mobile health applications with a pre-collected offline dataset remain unknown. The aim of this paper is to develop a novel advantage learning framework in order to efficiently use pre-collected data for policy optimization. The proposed method takes an optimal Q-estimator computed by any existing state-of-the-art RL algorithms as input, and outputs a new policy whose value is guaranteed to converge at a faster rate than the policy derived based on the initial Q-estimator. Extensive numerical experiments are conducted to back up our theoretical findings. A Python implementation of our proposed method is available at https://github.com/leyuanheart/SEAL.

stat.ML↗

arXiv2022

Mapping the Genetic-Imaging-Clinical Pathway with Applications to Alzheimer's Disease

Alzheimer's disease is a progressive form of dementia that results in problems with memory, thinking, and behavior. It often starts with abnormal aggregation and deposition of beta amyloid and tau, followed by neuronal damage such as atrophy of the hippocampi, leading to Alzheimer's Disease (AD). The aim of this paper is to map the genetic-imaging-clinical pathway for AD in order to delineate the genetically regulated brain changes that drive disease progression based on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. We develop a novel two-step approach to delineate the association between high-dimensional 2D hippocampal surface exposures and the Alzheimer's Disease Assessment Scale (ADAS) cognitive score, while taking into account the ultra-high dimensional clinical and genetic covariates at baseline. Analysis results suggest that the radial distance of each pixel of both hippocampi is negatively associated with the severity of behavioral deficits conditional on observed clinical and genetic covariates. These associations are stronger in Cornu Ammonis region 1 (CA1) and subiculum subregions compared to Cornu Ammonis region 2 (CA2) and Cornu Ammonis region 3 (CA3) subregions.

stat.AP↗

arXiv2022

mFI-PSO: A Flexible and Effective Method in Adversarial Image Generation for Deep Neural Networks

Deep neural networks (DNNs) have achieved great success in image classification, but can be very vulnerable to adversarial attacks with small perturbations to images. To improve adversarial image generation for DNNs, we develop a novel method, called mFI-PSO, which utilizes a Manifold-based First-order Influence measure for vulnerable image and pixel selection and the Particle Swarm Optimization for various objective functions. Our mFI-PSO can thus effectively design adversarial images with flexible, customized options on the number of perturbed pixels, the misclassification probability, and the targeted incorrect class. Experiments demonstrate the flexibility and effectiveness of our mFI-PSO in adversarial attacks and its appealing advantages over some popular methods.

cs.LG↗

arXiv2022

Estimating trans-ancestry genetic correlation with unbalanced data resources

The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in genome-wide association studies (GWAS). Our new estimator corrects for prediction errors caused by high-dimensional weak GWAS signals, while addressing the heterogeneity of GWAS data across ethnicities, such as linkage disequilibrium (LD) differences, which can lead to biased findings in homogeneity-agnostic analyses. Moreover, our estimator only requires one population to have a large GWAS sample size, and the second population can only have a much smaller number of participants (for example, hundreds). It is designed to specifically address the unbalanced data resources such that the GWAS sample size for European populations is usually larger than that of non-European ancestry groups. Extensive simulations and real data analyses of 30 complex traits in the UK Biobank study show that our method is capable of providing reliable estimates of a wide range of complex traits. Our results provide deep insights into the transferability of population-specific genetic findings.

stat.ME↗

arXiv2022

On block-wise and reference panel-based estimators for genetic data prediction in high dimensions

Genetic prediction of complex traits and diseases has attracted enormous attention in precision medicine, mainly because it has the potential to translate discoveries from genome-wide association studies (GWAS) into medical advances. As the high dimensional covariance matrix (or the linkage disequilibrium (LD) pattern) of genetic variants has a block-diagonal structure, many existing methods attempt to account for the dependence among variants in predetermined local LD blocks/regions. Moreover, due to privacy restrictions and data protection concerns, genetic variant dependence in each LD block is typically estimated from external reference panels rather than the original training dataset. This paper presents a unified analysis of block-wise and reference panel-based estimators in a high-dimensional prediction framework without sparsity restrictions. We find that, surprisingly, even when the covariance matrix has a block-diagonal structure with well-defined boundaries, block-wise estimation methods adjusting for local dependence can be substantially less accurate than methods controlling for the whole covariance matrix. Further, estimation methods built on the original training dataset and external reference panels are likely to have varying performance in high dimensions, which may reflect the cost of having only access to summary level data from the training dataset. This analysis is based on our novel results in random matrix theory for block-diagonal covariance matrix. We numerically evaluate our results using extensive simulations and the large-scale UK Biobank real data analysis of 36 complex traits.

stat.ME↗

arXiv2021

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

q-bio.PE↗