arXiv subjects

Doudou Zhou

Publications and source records attributed to Doudou Zhou.

47 records · Page 3Linked to original sources

arXiv2025

Time-Aware Attention for Enhanced Electronic Health Records Modeling

Electronic Health Records (EHR) contain valuable clinical information for predicting patient outcomes and guiding healthcare decisions. However, effectively modeling Electronic Health Records (EHRs) requires addressing data heterogeneity and complex temporal patterns. Standard approaches often struggle with irregular time intervals between clinical events. We propose TALE-EHR, a Transformer-based framework featuring a novel time-aware attention mechanism that explicitly models continuous temporal gaps to capture fine-grained sequence dynamics. To complement this temporal modeling with robust semantics, TALE-EHR leverages embeddings derived from standardized code descriptions using a pre-trained Large Language Model (LLM), providing a strong foundation for understanding clinical concepts. Experiments on the MIMIC-IV and PIC dataset demonstrate that our approach outperforms state-of-the-art baselines on tasks such as disease progression forecasting. TALE-EHR underscores the benefit of integrating explicit, continuous temporal modeling with strong semantic representations provides a powerful solution for advancing EHR analysis.

cs.LG↗

arXiv2025

Toward Fair Federated Learning under Demographic Disparities and Data Imbalance

Ensuring fairness is critical when applying artificial intelligence to high-stakes domains such as healthcare, where predictive models trained on imbalanced and demographically skewed data risk exacerbating existing disparities. Federated learning (FL) enables privacy-preserving collaboration across institutions, but remains vulnerable to both algorithmic bias and subgroup imbalance - particularly when multiple sensitive attributes intersect. We propose FedIDA (Fed erated Learning for Imbalance and D isparity A wareness), a framework-agnostic method that combines fairness-aware regularization with group-conditional oversampling. FedIDA supports multiple sensitive attributes and heterogeneous data distributions without altering the convergence behavior of the underlying FL algorithm. We provide theoretical analysis establishing fairness improvement bounds using Lipschitz continuity and concentration inequalities, and show that FedIDA reduces the variance of fairness metrics across test sets. Empirical results on both benchmark and real-world clinical datasets confirm that FedIDA consistently improves fairness while maintaining competitive predictive performance, demonstrating its effectiveness for equitable and privacy-preserving modeling in healthcare. The source code is available on GitHub.

cs.CY↗

arXiv2024

MATES: Multi-view Aggregated Two-Sample Test

The two-sample test is a fundamental problem in statistics with a wide range of applications. In the realm of high-dimensional data, nonparametric methods have gained prominence due to their flexibility and minimal distributional assumptions. However, many existing methods tend to be more effective when the two distributions differ primarily in their first and/or second moments. In many real-world scenarios, distributional differences may arise in higher-order moments, rendering traditional methods less powerful. To address this limitation, we propose a novel framework to aggregate information from multiple moments to build a test statistic. Each moment is regarded as one view of the data and contributes to the detection of some specific type of discrepancy, thus allowing the test statistic to capture more complex distributional differences. The novel multi-view aggregated two-sample test (MATES) leverages a graph-based approach, where the test statistic is constructed from the weighted similarity graphs of the pooled sample. Under mild conditions on the multi-view weighted similarity graphs, we establish theoretical properties of MATES, including a distribution-free limiting distribution under the null hypothesis, which enables straightforward type-I error control. Extensive simulation studies demonstrate that MATES effectively distinguishes subtle differences between distributions. We further validate the method on the S&P100 data, showcasing its power in detecting complex distributional variations.

stat.ME↗

arXiv2024

Consensus Knowledge Graph Learning via Multi-view Sparse Low Rank Block Model

Network analysis has been a powerful tool to unveil relationships and interactions among a large number of objects. Yet its effectiveness in accurately identifying important node-node interactions is challenged by the rapidly growing network size, with data being collected at an unprecedented granularity and scale. Common wisdom to overcome such high dimensionality is collapsing nodes into smaller groups and conducting connectivity analysis on the group level. Dividing efforts into two phases inevitably opens a gap in consistency and drives down efficiency. Consensus learning emerges as a new normal for common knowledge discovery with multiple data sources available. In this paper, we propose a unified multi-view sparse low-rank block model (msLBM) framework, which enables simultaneous grouping and connectivity analysis by combining multiple data sources. The msLBM framework efficiently represents overlapping information across large scale concepts and accommodates different types of heterogeneity across sources. Both features are desirable when analyzing high dimensional electronic health record (EHR) datasets from multiple health systems. An estimating procedure based on the alternating minimization algorithm is proposed. Our theoretical results demonstrate that a consensus knowledge graph can be more accurately learned by leveraging multi-source datasets, and statistically optimal rates can be achieved under mild conditions. Applications to the real world EHR data suggest that our proposed msLBM algorithm can more reliably reveal network structure among clinical concepts by effectively combining summary level EHR data from multiple health systems.

stat.ML↗

arXiv2024

The Wreaths of KHAN: Uniform Graph Feature Selection with False Discovery Rate Control

Graphical models find numerous applications in biology, chemistry, sociology, neuroscience, etc. While substantial progress has been made in graph estimation, it remains largely unexplored how to select significant graph signals with uncertainty assessment, especially those graph features related to topological structures including cycles (i.e., wreaths), cliques, hubs, etc. These features play a vital role in protein substructure analysis, drug molecular design, and brain network connectivity analysis. To fill the gap, we propose a novel inferential framework for general high dimensional graphical models to select graph features with false discovery rate controlled. Our method is based on the maximum of $p$-values from single edges that comprise the topological feature of interest, thus is able to detect weak signals. Moreover, we introduce the $K$-dimensional persistent Homology Adaptive selectioN (KHAN) algorithm to select all the homological features within $K$ dimensions with the uniform control of the false discovery rate over continuous filtration levels. The KHAN method applies a novel discrete Gram-Schmidt algorithm to select statistically significant generators from the homology group. We apply the structural screening method to identify the important residues of the SARS-CoV-2 spike protein during the binding process to the ACE2 receptors. We score the residues for all domains in the spike protein by the $p$-value weighted filtration level in the network persistent homology for the closed, partially open, and open states and identify the residues crucial for protein conformational changes and thus being potential targets for inhibition.

math.ST↗

arXiv2024

Federated Offline Reinforcement Learning

Evidence-based or data-driven dynamic treatment regimes are essential for personalized medicine, which can benefit from offline reinforcement learning (RL). Although massive healthcare data are available across medical institutions, they are prohibited from sharing due to privacy constraints. Besides, heterogeneity exists in different sites. As a result, federated offline RL algorithms are necessary and promising to deal with the problems. In this paper, we propose a multi-site Markov decision process model that allows for both homogeneous and heterogeneous effects across sites. The proposed model makes the analysis of the site-level features possible. We design the first federated policy optimization algorithm for offline RL with sample complexity. The proposed algorithm is communication-efficient, which requires only a single round of communication interaction by exchanging summary statistics. We give a theoretical guarantee for the proposed algorithm, where the suboptimality for the learned policies is comparable to the rate as if data is not distributed. Extensive simulations demonstrate the effectiveness of the proposed algorithm. The method is applied to a sepsis dataset in multiple sites to illustrate its use in clinical settings.

stat.ML↗

arXiv2023

A new ranking scheme for modern data and its application to two-sample hypothesis testing

Rank-based approaches are among the most popular nonparametric methods for univariate data in tackling statistical problems such as hypothesis testing due to their robustness and effectiveness. However, they are unsatisfactory for more complex data. In the era of big data, high-dimensional and non-Euclidean data, such as networks and images, are ubiquitous and pose challenges for statistical analysis. Existing multivariate ranks such as component-wise, spatial, and depth-based ranks do not apply to non-Euclidean data and have limited performance for high-dimensional data. Instead of dealing with the ranks of observations, we propose two types of ranks applicable to complex data based on a similarity graph constructed on observations: a graph-induced rank defined by the inductive nature of the graph and an overall rank defined by the weight of edges in the graph. To illustrate their utilization, both the new ranks are used to construct test statistics for the two-sample hypothesis testing, which converge to the $χ_2^2$ distribution under the permutation null distribution and some mild conditions of the ranks, enabling an easy type-I error control. Simulation studies show that the new method exhibits good power under a wide range of alternatives compared to existing methods. The new test is illustrated on the New York City taxi data for comparing travel patterns in consecutive months and a brain network dataset comparing male and female subjects.

stat.ME↗

arXiv2023

Hierarchical Pretraining for Biomedical Term Embeddings

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

cs.CL↗

arXiv2022

Doubly Robust Augmented Model Accuracy Transfer Inference with High Dimensional Features

Due to label scarcity and covariate shift happening frequently in real-world studies, transfer learning has become an essential technique to train models generalizable to some target populations using existing labeled source data. Most existing transfer learning research has been focused on model estimation, while there is a paucity of literature on transfer inference for model accuracy despite its importance. We propose a novel $\mathbf{D}$oubly $\mathbf{R}$obust $\mathbf{A}$ugmented $\mathbf{M}$odel $\mathbf{A}$ccuracy $\mathbf{T}$ransfer $\mathbf{I}$nferen$\mathbf{C}$e (DRAMATIC) method for point and interval estimation of commonly used classification performance measures in an unlabeled target population using labeled source data. Specifically, DRAMATIC derives and evaluates the risk model for a binary response $Y$ against some low dimensional predictors $\mathbf{A}$ on the target population, leveraging $Y$ from source data only and high dimensional adjustment features $\mathbf{X}$ from both the source and target data. The proposed estimators are doubly robust in the sense that they are $n^{1/2}$ consistent when at least one model is correctly specified and certain model sparsity assumptions hold. Simulation results demonstrate that the point estimation have negligible bias and the confidence intervals derived by DRAMATIC attain satisfactory empirical coverage levels. We further illustrate the utility of our method to transfer the genetic risk prediction model and its accuracy evaluation for type II diabetes across two patient cohorts in Mass General Brigham (MGB) collected using different sampling mechanisms and at different time points.

stat.ME↗

arXiv2021

Multi-source Learning via Completion of Block-wise Overlapping Noisy Matrices

Matrix completion has attracted attention in many fields, including statistics, applied mathematics, and electrical engineering. Most of the works focus on the independent sampling models under which the observed entries are sampled independently. Motivated by applications in the integration of knowledge graphs derived from multi-source biomedical data such as those from Electronic Health Records (EHR) and biomedical text, we propose the {\bf B}lock-wise {\bf O}verlapping {\bf N}oisy {\bf M}atrix {\bf I}ntegration (BONMI) to treat blockwise missingness of symmetric matrices representing relatedness between entity pairs. Our idea is to exploit the orthogonal Procrustes problem to align the eigenspace of the two sub-matrices, then complete the missing blocks by the inner product of the two low-rank components. Besides, we prove the statistical rate for the eigenspace of the underlying matrix, which is comparable to the rate under the independently missing assumption. Simulation studies show that the method performs well under a variety of configurations. In the real data analysis, the method is applied to two tasks: (i) the integrating of several point-wise mutual information matrices built by English EHR and Chinese medical text data, and (ii) the machine translation between English and Chinese medical concepts. Our method shows an advantage over existing methods.

stat.ML↗

arXiv2020

Double/Debiased Machine Learning for Logistic Partially Linear Model

We propose double/debiased machine learning approaches to infer (at the parametric rate) the parametric component of a logistic partially linear model with the binary response following a conditional logistic model of a low dimensional linear parametric function of some key (exposure) covariates and a nonparametric function adjusting for the confounding effect of other covariates. We consider a Neyman orthogonal (doubly robust) score equation consisting of two nuisance functions: nonparametric component in the logistic model and conditional mean of the exposure on the other covariates and with the response fixed. To estimate the nuisance models, we separately consider the use of high dimensional (HD) sparse parametric models and more general (typically nonparametric) machine learning (ML) methods. In the HD case, we derive certain moment equations to calibrate the first-order bias of the nuisance models and grant our method a model double robustness property in the sense that our estimator achieves the desirable rate when at least one of the nuisance models is correctly specified and both of them are ultra-sparse. In the ML case, the non-linearity of the logit link makes it substantially harder than the partially linear setting to use an arbitrary conditional mean learning algorithm to estimate the nuisance component of the logistic model. We handle this obstacle through a novel full model refitting procedure that is easy-to-implement and facilitates the use of nonparametric ML algorithms in our framework. Our ML estimator is rate doubly robust in the same sense as Chernozhukov et al. (2018a). We evaluate our methods through simulation studies and apply them in assessing the effect of emergency contraceptive (EC) pill on early gestation foetal with a policy reform in Chile in 2008 (Bentancor and Clarke, 2017).

stat.ME↗