Kun Chen

Avijit Mitra, Richeek Pradhan, Rachel D Melamed et al.

Importance: Social determinants of health (SDOH) are known to be associated with increased risk of suicidal behaviors, but few studies utilized SDOH from unstructured electronic health record (EHR) notes. Objective: To investigate associations between suicide and recent SDOH, identified using structured and unstructured data. Design: Nested case-control study. Setting: EHR data from the US Veterans Health Administration (VHA). Participants: 6,122,785 Veterans who received care in the US VHA between October 1, 2010, and September 30, 2015. Exposures: Occurrence of SDOH over a maximum span of two years compared with no occurrence of SDOH. Main Outcomes and Measures: Cases of suicide deaths were matched with 4 controls on birth year, cohort entry date, sex, and duration of follow-up. We developed an NLP system to extract SDOH from unstructured notes. Structured data, NLP on unstructured data, and combining them yielded six, eight and nine SDOH respectively. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were estimated using conditional logistic regression. Results: In our cohort, 8,821 Veterans committed suicide during 23,725,382 person-years of follow-up (incidence rate 37.18/100,000 person-years). Our cohort was mostly male (92.23%) and white (76.99%). Across the five common SDOH as covariates, NLP-extracted SDOH, on average, covered 80.03% of all SDOH occurrences. All SDOH, measured by structured data and NLP, were significantly associated with increased risk of suicide. The SDOH with the largest effects was legal problems (aOR=2.66, 95% CI=.46-2.89), followed by violence (aOR=2.12, 95% CI=1.98-2.27). NLP-extracted and structured SDOH were also associated with suicide. Conclusions and Relevance: NLP-extracted SDOH were always significantly associated with increased risk of suicide among Veterans, suggesting the potential of NLP in public health studies.

Jianmin Chen, Robert H. Aseltine, Fei Wang et al.

Statistical learning with a large number of rare binary features is commonly encountered in analyzing electronic health records (EHR) data, especially in the modeling of disease onset with prior medical diagnoses and procedures. Dealing with the resulting highly sparse and large-scale binary feature matrix is notoriously challenging as conventional methods may suffer from a lack of power in testing and inconsistency in model fitting while machine learning methods may suffer from the inability of producing interpretable results or clinically-meaningful risk factors. To improve EHR-based modeling and utilize the natural hierarchical structure of disease classification, we propose a tree-guided feature selection and logic aggregation approach for large-scale regression with rare binary features, in which dimension reduction is achieved through not only a sparsity pursuit but also an aggregation promoter with the logic operator of ``or''. We convert the combinatorial problem into a convex linearly-constrained regularized estimation, which enables scalable computation with theoretical guarantees. In a suicide risk study with EHR data, our approach is able to select and aggregate prior mental health diagnoses as guided by the diagnosis hierarchy of the International Classification of Diseases. By balancing the rarity and specificity of the EHR diagnosis records, our strategy improves both prediction and model interpretation. We identify important higher-level categories and subcategories of mental health conditions and simultaneously determine the level of specificity needed for each of them in predicting suicide risk.

Kun Chen, Lei Bai, Fenghua Ling et al.

The weather forecasting system is important for science and society, and significant achievements have been made in applying artificial intelligence (AI) to medium-range weather forecasting. However, existing AI-based weather forecasting models rely on analysis or reanalysis products from traditional numerical weather prediction (NWP) systems as initial conditions for making predictions. Initial states are typically generated by traditional data assimilation components, which are computational expensive and time-consuming. Here we present an AI-based data assimilation model, i.e., Adas, for global weather variables. By introducing the confidence matrix, Adas employs gated convolution to handle sparse observations and gated cross-attention for capturing the interactions between the background and observations. Further, we combine Adas with the advanced AI-based forecasting model (i.e., FengWu) to construct the first end-to-end AI-based global weather forecasting system: FengWu-Adas. We demonstrate that Adas can assimilate global observations to produce high-quality analysis, enabling the system operate stably for long term. Moreover, we are the first to apply the methods to real-world scenarios, which is more challenging and has considerable practical application potential. We have also achieved the forecasts based on the analyses generated by AI with a skillful forecast lead time exceeding that of the IFS for the first time.

Siwei Tu, Ben Fei, Weidong Yang et al.

Accurate acquisition of surface meteorological conditions at arbitrary locations holds significant importance for weather forecasting and climate simulation. Due to the fact that meteorological states derived from satellite observations are often provided in the form of low-resolution grid fields, the direct application of spatial interpolation to obtain meteorological states for specific locations often results in significant discrepancies when compared to actual observations. Existing downscaling methods for acquiring meteorological state information at higher resolutions commonly overlook the correlation with satellite observations. To bridge the gap, we propose Satellite-observations Guided Diffusion Model (SGD), a conditional diffusion model pre-trained on ERA5 reanalysis data with satellite observations (GridSat) as conditions, which is employed for sampling downscaled meteorological states through a zero-shot guided sampling strategy and patch-based methods. During the training process, we propose to fuse the information from GridSat satellite observations into ERA5 maps via the attention mechanism, enabling SGD to generate atmospheric states that align more accurately with actual conditions. In the sampling, we employed optimizable convolutional kernels to simulate the upscale process, thereby generating high-resolution ERA5 maps using low-resolution ERA5 maps as well as observations from weather stations as guidance. Moreover, our devised patch-based method promotes SGD to generate meteorological states at arbitrary resolutions. Experiments demonstrate SGD fulfills accurate meteorological states downscaling to 6.25km.

Wannita Takerngsaksiri, Chakkrit Tantithamthavorn, Micheal Fu et al.

Software engineers spend a significant amount of time reading code during the software development process, especially in the age of large language models (LLMs) that can automatically generate code. However, little is known about the readability of the LLM-generated code and whether it is still important from practitioners' perspectives in this new era. In this paper, we conduct a survey to explore the practitioners' perspectives on code readability in the age of LLMs and investigate the readability of our LLM-based software development agents framework, HULA, by comparing its generated code with human-written code in real-world scenarios. Overall, the findings underscore that (1) readability remains a critical aspect of software development; (2) the readability of our LLM-generated code is comparable to human-written code, fostering the establishment of appropriate trust and driving the broad adoption of our LLM-powered software development platform.

Jing-An Sun, Hang Fan, Junchao Gong et al.

Data assimilation (DA) aims to estimate the full state of a dynamical system by combining partial and noisy observations with a prior model forecast, commonly referred to as the background. In atmospheric applications, this problem is fundamentally ill-posed due to the sparsity of observations relative to the high-dimensional state space. Traditional methods address this challenge by simplifying background priors to regularize the solution, which are empirical and require continual tuning for application. Inspired by alignment techniques in text-to-image diffusion models, we propose Align-DA, which formulates DA as a generative process and uses reward signals to guide background priors, replacing manual tuning with data-driven alignment. Specifically, we train a score-based model in the latent space to approximate the background-conditioned prior, and align it using three complementary reward signals for DA: (1) assimilation accuracy, (2) forecast skill initialized from the assimilated state, and (3) physical adherence of the analysis fields. Experiments with multiple reward signals demonstrate consistent improvements in analysis quality across different evaluation metrics and observation-guidance strategies. These results show that preference alignment, implemented as a soft constraint, can automatically adapt complex background priors tailored to DA, offering a promising new direction for advancing the field.

Junchao Gong, Jingyi Xu, Ben Fei et al.

Weather prediction is a critical task for human society, where impressive progress has been made by training artificial intelligence weather prediction (AIWP) methods with reanalysis data. However, reliance on reanalysis data limits the AIWPs with shortcomings, including data assimilation biases and temporal discrepancies. To liberate AIWPs from the reanalysis data, observation forecasting emerges as a transformative paradigm for weather prediction. One of the key challenges in observation forecasting is learning spatiotemporal dynamics across disparate measurement systems with irregular high-resolution observation data, which constrains the design and prediction of AIWPs. To this end, we propose our DAWP as an innovative framework to enable AIWPs to operate in a complete observation space by initialization with an artificial intelligence data assimilation (AIDA) module. Specifically, our AIDA module applies a mask multi-modality autoencoder(MMAE)for assimilating irregular satellite observation tokens encoded by mask ViT-VAEs. For AIWP, we introduce a spatiotemporal decoupling transformer with cross-regional boundary conditioning (CBC), learning the dynamics in observation space, to enable sub-image-based global observation forecasting. Comprehensive experiments demonstrate that AIDA initialization significantly improves the roll out and efficiency of AIWP. Additionally, we show that DAWP holds promising potential to be applied in global precipitation forecasting.

Xiaohui Yin, Shane Sacco, Robert H. Aseltine et al.

The vast repositories of Electronic Health Records (EHR) and medical claims hold untapped potential for studying rare but critical events, such as suicide attempt. Conventional setups often model suicide attempt as a univariate outcome and also exclude any ``single-record'' patients with a single documented encounter due to a lack of historical information. However, patients who were diagnosed with suicide attempts at the only encounter could, to some surprise, represent a substantial proportion of all attempt cases in the data, as high as 70--80%. We innovate a hybrid and integrative learning framework to leverage concurrent outcomes as surrogates and harness the forbidden yet precious information from single-record data. Our approach employs a supervised learning component to learn the latent variables that connect primary (e.g., suicide) and surrogate outcomes (e.g., mental disorders) to historical information. It simultaneously employs an unsupervised learning component to utilize the single-record data, through the shared latent variables. As such, our approach offers a general strategy for information integration that is crucial to modeling rare conditions and events. With hospital inpatient data from Connecticut, we demonstrate that single-record data and concurrent diagnoses indeed carry valuable information, and utilizing them can substantially improve suicide risk modeling.

Kun Chen, Dachao Lin, Zhihua Zhang

In this paper, we follow Eftekhari's work to give a non-local convergence analysis of deep linear networks. Specifically, we consider optimizing deep linear networks which have a layer with one neuron under quadratic loss. We describe the convergent point of trajectories with arbitrary starting point under gradient flow, including the paths which converge to one of the saddle points or the original point. We also show specific convergence rates of trajectories that converge to the global minimizer by stages. To achieve these results, this paper mainly extends the machinery in Eftekhari's work to provably identify the rank-stable set and the global minimizer convergent set. We also give specific examples to show the necessity of our definitions. Crucially, as far as we know, our results appear to be the first to give a non-local global analysis of linear neural networks from arbitrary initialized points, rather than the lazy training regime which has dominated the literature of neural networks, and restricted benign initialization in Eftekhari's work. We also note that extending our results to general linear networks without one hidden neuron assumption remains a challenging open problem.

Weishen Pan, Sen Cui, Hongyi Wen et al.

Selection bias is prevalent in the data for training and evaluating recommendation systems with explicit feedback. For example, users tend to rate items they like. However, when rating an item concerning a specific user, most of the recommendation algorithms tend to rely too much on his/her rating (feedback) history. This introduces implicit bias on the recommendation system, which is referred to as user feedback-loop bias in this paper. We propose a systematic and dynamic way to correct such bias and to obtain more diverse and objective recommendations by utilizing temporal rating information. Specifically, our method includes a deep-learning component to learn each user's dynamic rating history embedding for the estimation of the probability distribution of the items that the user rates sequentially. These estimated dynamic exposure probabilities are then used as propensity scores to train an inverse-propensity-scoring (IPS) rating predictor. We empirically validated the existence of such user feedback-loop bias in real world recommendation systems and compared the performance of our method with the baseline models that are either without de-biasing or with propensity scores estimated by other methods. The results show the superiority of our approach.

Sen Cui, Jian Liang, Weishen Pan et al.

Federated learning (FL) refers to the paradigm of learning models over a collaborative research network involving multiple clients without sacrificing privacy. Recently, there have been rising concerns on the distributional discrepancies across different clients, which could even cause counterproductive consequences when collaborating with others. While it is not necessarily that collaborating with all clients will achieve the best performance, in this paper, we study a rational collaboration called ``collaboration equilibrium'' (CE), where smaller collaboration coalitions are formed. Each client collaborates with certain members who maximally improve the model learning and isolates the others who make little contribution. We propose the concept of benefit graph which describes how each client can benefit from collaborating with other clients and advance a Pareto optimization approach to identify the optimal collaborators. Then we theoretically prove that we can reach a CE from the benefit graph through an iterative graph operation. Our framework provides a new way of setting up collaborations in a research network. Experiments on both synthetic and real world data sets are provided to demonstrate the effectiveness of our method.

Xiaoyu Fan, Guosai Wang, Kun Chen et al.

Privacy-preserving data mining has become an important topic. People have built several multi-party-computation (MPC)-based frameworks to provide theoretically guaranteed privacy, the poor performance of real-world algorithms have always been a challenge. Using Principal Component Analysis (PCA) as an example, we show that by considering the unique performance characters of the MPC platform, we can design highly effective algorithm-level optimizations, such as replacing expensive operators and batching up. We achieve about 200$\times$ performance boost over existing privacy-preserving PCA algorithms with the same level of privacy guarantee. Also, using real-world datasets, we show that by combining multi-party data, we can achieve better training results.

Wenjie Wang, Chongliang Luo, Robert H. Aseltine et al.

Motivated by the pressing need for suicide prevention through improving behavioral healthcare, we use medical claims data to study the risk of subsequent suicide attempts for patients who were hospitalized due to suicide attempts and later discharged. Understanding the risk behaviors of such patients at elevated suicide risk is an important step toward the goal of "Zero Suicide." An immediate and unconventional challenge is that the identification of suicide attempts from medical claims contains substantial uncertainty: almost 20% of "suspected" suicide attempts are identified from diagnosis codes indicating external causes of injury and poisoning with undermined intent. It is thus of great interest to learn which of these undetermined events are more likely actual suicide attempts and how to properly utilize them in survival analysis with severe censoring. To tackle these interrelated problems, we develop an integrative Cox cure model with regularization to perform survival regression with uncertain events and a latent cure fraction. We apply the proposed approach to study the risk of subsequent suicide attempts after suicide-related hospitalization for the adolescent and young adult population, using medical claims data from Connecticut. The identified risk factors are highly interpretable; more intriguingly, our method distinguishes the risk factors that are most helpful in assessing either susceptibility or timing of subsequent attempts. The predicted statuses of the uncertain attempts are further investigated, leading to several new insights on suicide event identification.

Kun Chen, Ruipeng Dong, Wanwan Xu et al.

The sparse factorization of a large matrix is fundamental in modern statistical learning. In particular, the sparse singular value decomposition and its variants have been utilized in multivariate regression, factor analysis, biclustering, vector time series modeling, among others. The appeal of this factorization is owing to its power in discovering a highly-interpretable latent association network, either between samples and variables or between responses and predictors. However, many existing methods are either ad hoc without a general performance guarantee, or are computationally intensive, rendering them unsuitable for large-scale studies. We formulate the statistical problem as a sparse factor regression and tackle it with a divide-and-conquer approach. In the first stage of division, we consider both sequential and parallel approaches for simplifying the task into a set of co-sparse unit-rank estimation (CURE) problems, and establish the statistical underpinnings of these commonly-adopted and yet poorly understood deflation methods. In the second stage of division, we innovate a contended stagewise learning technique, consisting of a sequence of simple incremental updates, to efficiently trace out the whole solution paths of CURE. Our algorithm has a much lower computational complexity than alternating convex search, and the choice of the step size enables a flexible and principled tradeoff between statistical accuracy and computational efficiency. Our work is among the first to enable stagewise learning for non-convex problems, and the idea can be applicable in many multi-convex problems. Extensive simulation studies and an application in genetics demonstrate the effectiveness and scalability of our approach.

Yan Li, Chun Yu, Yize Zhao et al.

Researchers often have to deal with heterogeneous population with mixed regression relationships, increasingly so in the era of data explosion. In such problems, when there are many candidate predictors, it is not only of interest to identify the predictors that are associated with the outcome, but also to distinguish the true sources of heterogeneity, i.e., to identify the predictors that have different effects among the clusters and thus are the true contributors to the formation of the clusters. We clarify the concepts of the source of heterogeneity that account for potential scale differences of the clusters and propose a regularized finite mixture effects regression to achieve heterogeneity pursuit and feature selection simultaneously. As the name suggests, the problem is formulated under an effects-model parameterization, in which the cluster labels are missing and the effect of each predictor on the outcome is decomposed to a common effect term and a set of cluster-specific terms. A constrained sparse estimation of these effects leads to the identification of both the variables with common effects and those with heterogeneous effects. We propose an efficient algorithm and show that our approach can achieve both estimation and selection consistency. Simulation studies further demonstrate the effectiveness of our method under various practical scenarios. Three applications are presented, namely, an imaging genetics study for linking genetic factors and brain neuroimaging traits in Alzheimer's disease, a public health study for exploring the association between suicide risk among adolescents and their school district characteristics, and a sport analytics study for understanding how the salary levels of baseball players are associated with their performance and contractual status.

Xiaokang Liu, Shujie Ma, Kun Chen

We propose a nested reduced-rank regression (NRRR) approach in fitting regression model with multivariate functional responses and predictors, to achieve tailored dimension reduction and facilitate interpretation/visualization of the resulting functional model. Our approach is based on a two-level low-rank structure imposed on the functional regression surfaces. A global low-rank structure identifies a small set of latent principal functional responses and predictors that drives the underlying regression association. A local low-rank structure then controls the complexity and smoothness of the association between the principal functional responses and predictors. Through a basis expansion approach, the functional problem boils down to an interesting integrated matrix approximation task, where the blocks or submatrices of an integrated low-rank matrix share some common row space and/or column space. An iterative algorithm with convergence guarantee is developed. We establish the consistency of NRRR and also show through non-asymptotic analysis that it can achieve at least a comparable error rate to that of the reduced-rank regression. Simulation studies demonstrate the effectiveness of NRRR. We apply NRRR in an electricity demand problem, to relate the trajectories of the daily electricity consumption with those of the daily temperatures.

Xiang Li, Shusen Wang, Kun Chen et al.

We study distributed computing of the truncated singular value decomposition problem. We develop an algorithm that we call \texttt{LocalPower} for improving communication efficiency. Specifically, we uniformly partition the dataset among $m$ nodes and alternate between multiple (precisely $p$) local power iterations and one global aggregation. In the aggregation, we propose to weight each local eigenvector matrix with orthogonal Procrustes transformation (OPT). As a practical surrogate of OPT, sign-fixing, which uses a diagonal matrix with $\pm 1$ entries as weights, has better computation complexity and stability in experiments. We theoretically show that under certain assumptions \texttt{LocalPower} lowers the required number of communications by a factor of $p$ to reach a constant accuracy. We also show that the strategy of periodically decaying $p$ helps obtain high-precision solutions. We conduct experiments to demonstrate the effectiveness of \texttt{LocalPower}.

Lifang He, Kun Chen, Wanwan Xu et al.

We propose a sparse and low-rank tensor regression model to relate a univariate outcome to a feature tensor, in which each unit-rank tensor from the CP decomposition of the coefficient tensor is assumed to be sparse. This structure is both parsimonious and highly interpretable, as it implies that the outcome is related to the features through a few distinct pathways, each of which may only involve subsets of feature dimensions. We take a divide-and-conquer strategy to simplify the task into a set of sparse unit-rank tensor regression problems. To make the computation efficient and scalable, for the unit-rank tensor regression, we propose a stagewise estimation procedure to efficiently trace out its entire solution path. We show that as the step size goes to zero, the stagewise solution paths converge exactly to those of the corresponding regularized regression. The superior performance of our approach is demonstrated on various real-world and synthetic examples.

Gen Li, Xiaokang Liu, Kun Chen

Multi-view data have been routinely collected in various fields of science and engineering. A general problem is to study the predictive association between multivariate responses and multi-view predictor sets, all of which can be of high dimensionality. It is likely that only a few views are relevant to prediction, and the predictors within each relevant view contribute to the prediction collectively rather than sparsely. We cast this new problem under the familiar multivariate regression framework and propose an integrative reduced-rank regression (iRRR), where each view has its own low-rank coefficient matrix. As such, latent features are extracted from each view in a supervised fashion. For model estimation, we develop a convex composite nuclear norm penalization approach, which admits an efficient algorithm via alternating direction method of multipliers. Extensions to non-Gaussian and incomplete data are discussed. Theoretically, we derive non-asymptotic oracle bounds of iRRR under a restricted eigenvalue condition. Our results recover oracle bounds of several special cases of iRRR including Lasso, group Lasso and nuclear norm penalized regression. Therefore, iRRR seamlessly bridges group-sparse and low-rank methods and can achieve substantially faster convergence rate under realistic settings of multi-view learning. Simulation studies and an application in the Longitudinal Studies of Aging further showcase the efficacy of the proposed methods.

Xi Sheryl Zhang, Lifang He, Kun Chen et al.

Parkinson's Disease (PD) is one of the most prevalent neurodegenerative diseases that affects tens of millions of Americans. PD is highly progressive and heterogeneous. Quite a few studies have been conducted in recent years on predictive or disease progression modeling of PD using clinical and biomarkers data. Neuroimaging, as another important information source for neurodegenerative disease, has also arisen considerable interests from the PD community. In this paper, we propose a deep learning method based on Graph Convolutional Networks (GCN) for fusing multiple modalities of brain images in relationship prediction which is useful for distinguishing PD cases from controls. On Parkinson's Progression Markers Initiative (PPMI) cohort, our approach achieved $0.9537\pm 0.0587$ AUC, compared with $0.6443\pm 0.0223$ AUC achieved by traditional approaches such as PCA.

Yoshimasa Uematsu, Yingying Fan, Kun Chen et al.

Many modern big data applications feature large scale in both numbers of responses and predictors. Better statistical efficiency and scientific insights can be enabled by understanding the large-scale response-predictor association network structures via layers of sparse latent factors ranked by importance. Yet sparsity and orthogonality have been two largely incompatible goals. To accommodate both features, in this paper we suggest the method of sparse orthogonal factor regression (SOFAR) via the sparse singular value decomposition with orthogonality constrained optimization to learn the underlying association networks, with broad applications to both unsupervised and supervised learning tasks such as biclustering with sparse singular value decomposition, sparse principal component analysis, sparse factor analysis, and spare vector autoregression analysis. Exploiting the framework of convexity-assisted nonconvex optimization, we derive nonasymptotic error bounds for the suggested procedure characterizing the theoretical advantages. The statistical guarantees are powered by an efficient SOFAR algorithm with convergence property. Both computational and theoretical advantages of our procedure are demonstrated with several simulation and real data examples.

Hongbo Dong, Kun Chen, Jeff Linderoth

Variable selection is a fundamental task in statistical data analysis. Sparsity-inducing regularization methods are a popular class of methods that simultaneously perform variable selection and model estimation. The central problem is a quadratic optimization problem with an l0-norm penalty. Exactly enforcing the l0-norm penalty is computationally intractable for larger scale problems, so dif- ferent sparsity-inducing penalty functions that approximate the l0-norm have been introduced. In this paper, we show that viewing the problem from a convex relaxation perspective offers new insights. In particular, we show that a popular sparsity-inducing concave penalty function known as the Minimax Concave Penalty (MCP), and the reverse Huber penalty derived in a recent work by Pilanci, Wainwright and Ghaoui, can both be derived as special cases of a lifted convex relaxation called the perspective relaxation. The optimal perspective relaxation is a related minimax problem that balances the overall convexity and tightness of approximation to the l0 norm. We show it can be solved by a semidefinite relaxation. Moreover, a probabilistic interpretation of the semidefinite relaxation reveals connections with the boolean quadric polytope in combinatorial optimization. Finally by reformulating the l0-norm pe- nalized problem as a two-level problem, with the inner level being a Max-Cut problem, our proposed semidefinite relaxation can be realized by replacing the inner level problem with its semidefinite relaxation studied by Goemans and Williamson. This interpretation suggests using the Goemans-Williamson rounding procedure to find approximate solutions to the l0-norm penalized problem. Numerical experiments demonstrate the tightness of our proposed semidefinite relaxation, and the effectiveness of finding approximate solutions by Goemans-Williamson rounding.