Feng Xie

Lingjing Kong, Biwei Huang, Feng Xie et al.

Identifying latent variables and causal structures from observational data is essential to many real-world applications involving biological data, medical data, and unstructured data such as images and languages. However, this task can be highly challenging, especially when observed variables are generated by causally related latent variables and the relationships are nonlinear. In this work, we investigate the identification problem for nonlinear latent hierarchical causal models in which observed variables are generated by a set of causally related latent variables, and some latent variables may not have observed children. We show that the identifiability of causal structures and latent variables (up to invertible transformations) can be achieved under mild assumptions: on causal structures, we allow for multiple paths between any pair of variables in the graph, which relaxes latent tree assumptions in prior work; on structural functions, we permit general nonlinearity and multi-dimensional continuous variables, alleviating existing work's parametric assumptions. Specifically, we first develop an identification criterion in the form of novel identifiability guarantees for an elementary latent variable model. Leveraging this criterion, we show that both causal structures and latent variables of the hierarchical model can be identified asymptotically by explicitly constructing an estimation procedure. To the best of our knowledge, our work is the first to establish identifiability guarantees for both causal structures and latent variables in nonlinear latent hierarchical models.

Biwei Huang, Charles Jia Han Low, Feng Xie et al.

Most causal discovery procedures assume that there are no latent confounders in the system, which is often violated in real-world problems. In this paper, we consider a challenging scenario for causal structure identification, where some variables are latent and they form a hierarchical graph structure to generate the measured variables; the children of latent variables may still be latent and only leaf nodes are measured, and moreover, there can be multiple paths between every pair of variables (i.e., it is beyond tree structure). We propose an estimation procedure that can efficiently locate latent variables, determine their cardinalities, and identify the latent hierarchical structure, by leveraging rank deficiency constraints over the measured variables. We show that the proposed algorithm can find the correct Markov equivalence class of the whole graph asymptotically under proper restrictions on the graph structure.

Mingxuan Liu, Siqi Li, Han Yuan et al.

Objective: The proper handling of missing values is critical to delivering reliable estimates and decisions, especially in high-stakes fields such as clinical research. The increasing diversity and complexity of data have led many researchers to develop deep learning (DL)-based imputation techniques. We conducted a systematic review to evaluate the use of these techniques, with a particular focus on data types, aiming to assist healthcare researchers from various disciplines in dealing with missing values. Methods: We searched five databases (MEDLINE, Web of Science, Embase, CINAHL, and Scopus) for articles published prior to August 2021 that applied DL-based models to imputation. We assessed selected publications from four perspectives: health data types, model backbone (i.e., main architecture), imputation strategies, and comparison with non-DL-based methods. Based on data types, we created an evidence map to illustrate the adoption of DL models. Results: We included 64 articles, of which tabular static (26.6%, 17/64) and temporal data (37.5%, 24/64) were the most frequently investigated. We found that model backbone(s) differed among data types as well as the imputation strategy. The "integrated" strategy, that is, the imputation task being solved concurrently with downstream tasks, was popular for tabular temporal (50%, 12/24) and multi-modal data (71.4%, 5/7), but limited for other data types. Moreover, DL-based imputation methods yielded better imputation accuracy in most studies, compared with non-DL-based methods. Conclusion: DL-based imputation models can be customized based on data type, addressing the corresponding missing patterns, and its associated "integrated" strategy can enhance the efficacy of imputation, especially in scenarios where data is complex. Future research may focus on the portability and fairness of DL-based models for healthcare data imputation.

Feng Xie, Biwei Huang, Zhengming Chen et al.

We investigate the task of learning causal structure in the presence of latent variables, including locating latent variables and determining their quantity, and identifying causal relationships among both latent and observed variables. To this end, we propose a Generalized Independent Noise (GIN) condition for linear non-Gaussian acyclic causal models that incorporate latent variables, which establishes the independence between a linear combination of certain measured variables and some other measured variables. Specifically, for two observed random vectors $\bf{Y}$ and $\bf{Z}$, GIN holds if and only if $ω^{\intercal}\mathbf{Y}$ and $\mathbf{Z}$ are independent, where $ω$ is a non-zero parameter vector determined by the cross-covariance between $\mathbf{Y}$ and $\mathbf{Z}$. We then give necessary and sufficient graphical criteria of the GIN condition in linear non-Gaussian acyclic models. Roughly speaking, GIN implies the existence of a set $\mathcal{S}$ such that $\mathcal{S}$ is causally earlier (w.r.t. the causal ordering) than $\mathbf{Y}$, and that every active (collider-free) path between $\mathbf{Y}$ and $\mathbf{Z}$ must contain a node from $\mathcal{S}$. Interestingly, we find that the independent noise condition (i.e., if there is no confounder, causes are independent of the residual derived from regressing the effect on the causes) can be seen as a special case of GIN. With such a connection between GIN and latent causal structures, we further leverage the proposed GIN condition, together with a well-designed search procedure, to efficiently estimate Linear, Non-Gaussian Latent Hierarchical Models (LiNGLaHs), where latent confounders may also be causally related and may even follow a hierarchical structure. We show that the causal structure of a LiNGLaH is identifiable in light of GIN conditions. Experimental results show the effectiveness of the proposed method.

Siqi Li, Pinyan Liu, Gustavo G. Nascimento et al.

Federated learning (FL) has gained popularity in clinical research in recent years to facilitate privacy-preserving collaboration. Structured data, one of the most prevalent forms of clinical data, has experienced significant growth in volume concurrently, notably with the widespread adoption of electronic health records in clinical practice. This review examines FL applications on structured medical data, identifies contemporary limitations and discusses potential innovations. We searched five databases, SCOPUS, MEDLINE, Web of Science, Embase, and CINAHL, to identify articles that applied FL to structured medical data and reported results following the PRISMA guidelines. Each selected publication was evaluated from three primary perspectives, including data quality, modeling strategies, and FL frameworks. Out of the 1160 papers screened, 34 met the inclusion criteria, with each article consisting of one or more studies that used FL to handle structured clinical/medical data. Of these, 24 utilized data acquired from electronic health records, with clinical predictions and association studies being the most common clinical research tasks that FL was applied to. Only one article exclusively explored the vertical FL setting, while the remaining 33 explored the horizontal FL setting, with only 14 discussing comparisons between single-site (local) and FL (global) analysis. The existing FL applications on structured medical data lack sufficient evaluations of clinically meaningful benefits, particularly when compared to single-site analyses. Therefore, it is crucial for future FL applications to prioritize clinical motivations and develop designs and methodologies that can effectively support and aid clinical practice and research.

Siqi Li, Yilin Ning, Marcus Eng Hock Ong et al.

We propose FedScore, a privacy-preserving federated learning framework for scoring system generation across multiple sites to facilitate cross-institutional collaborations. The FedScore framework includes five modules: federated variable ranking, federated variable transformation, federated score derivation, federated model selection and federated model evaluation. To illustrate usage and assess FedScore's performance, we built a hypothetical global scoring system for mortality prediction within 30 days after a visit to an emergency department using 10 simulated sites divided from a tertiary hospital in Singapore. We employed a pre-existing score generator to construct 10 local scoring systems independently at each site and we also developed a scoring system using centralized data for comparison. We compared the acquired FedScore model's performance with that of other scoring models using the receiver operating characteristic (ROC) analysis. The FedScore model achieved an average area under the curve (AUC) value of 0.763 across all sites, with a standard deviation (SD) of 0.020. We also calculated the average AUC values and SDs for each local model, and the FedScore model showed promising accuracy and stability with a high average AUC value which was closest to the one of the pooled model and SD which was lower than that of most local models. This study demonstrates that FedScore is a privacy-preserving scoring system generator with potentially good generalizability.

David Durst, Feng Xie, Vishnu Sarukkai et al.

In multiplayer, first-person shooter games like Counter-Strike: Global Offensive (CS:GO), coordinated movement is a critical component of high-level strategic play. However, the complexity of team coordination and the variety of conditions present in popular game maps make it impractical to author hand-crafted movement policies for every scenario. We show that it is possible to take a data-driven approach to creating human-like movement controllers for CS:GO. We curate a team movement dataset comprising 123 hours of professional game play traces, and use this dataset to train a transformer-based movement model that generates human-like team movement for all players in a "Retakes" round of the game. Importantly, the movement prediction model is efficient. Performing inference for all players takes less than 0.5 ms per game step (amortized cost) on a single CPU core, making it plausible for use in commercial games today. Human evaluators assess that our model behaves more like humans than both commercially-available bots and procedural movement controllers scripted by experts (16% to 59% higher by TrueSkill rating of "human-like"). Using experiments involving in-game bot vs. bot self-play, we demonstrate that our model performs simple forms of teamwork, makes fewer common movement mistakes, and yields movement distributions, player lifetimes, and kill locations similar to those observed in professional CS:GO match play.

Feng Xie, Zhong Zhang, Liang Li et al.

Epidemic forecasting is the key to effective control of epidemic transmission and helps the world mitigate the crisis that threatens public health. To better understand the transmission and evolution of epidemics, we propose EpiGNN, a graph neural network-based model for epidemic forecasting. Specifically, we design a transmission risk encoding module to characterize local and global spatial effects of regions in epidemic processes and incorporate them into the model. Meanwhile, we develop a Region-Aware Graph Learner (RAGL) that takes transmission risk, geographical dependencies, and temporal information into account to better explore spatial-temporal dependencies and makes regions aware of related regions' epidemic situations. The RAGL can also combine with external resources, such as human mobility, to further improve prediction performance. Comprehensive experiments on five real-world epidemic-related datasets (including influenza and COVID-19) demonstrate the effectiveness of our proposed method and show that EpiGNN outperforms state-of-the-art baselines by 9.48% in RMSE.

Feng Xie, Zhong Zhang, Xuechen Zhao et al.

The ongoing COVID-19 pandemic has caused immeasurable losses for people worldwide. To contain the spread of the virus and further alleviate the crisis, various health policies (e.g., stay-at-home orders) have been issued which spark heated discussions as users turn to share their attitudes on social media. In this paper, we consider a more realistic scenario on stance detection (i.e., cross-target and zero-shot settings) for the pandemic and propose an adversarial learning-based stance classifier to automatically identify the public's attitudes toward COVID-19-related health policies. Specifically, we adopt adversarial learning that allows the model to train on a large amount of labeled data and capture transferable knowledge from source topics, so as to enable generalize to the emerging health policies with sparse labeled data. To further enhance the model's deeper understanding, we incorporate policy descriptions as external knowledge into the model. Meanwhile, a GeoEncoder is designed which encourages the model to capture unobserved background factors specified by each region and then represent them as non-text information. We evaluate the performance of a broad range of baselines on the stance detection task for COVID-19-related health policies, and experimental results show that our proposed method achieves state-of-the-art performance in both cross-target and zero-shot settings.

Feng Xie, Xiang Zeng, Bin Zhou et al.

Entity alignment (EA) which links equivalent entities across different knowledge graphs (KGs) plays a crucial role in knowledge fusion. In recent years, graph neural networks (GNNs) have been successfully applied in many embedding-based EA methods. However, existing GNN-based methods either suffer from the structural heterogeneity issue that especially appears in the real KG distributions or ignore the heterogeneous representation learning for unseen (unlabeled) entities, which would lead the model to overfit on few alignment seeds (i.e., training data) and thus cause unsatisfactory alignment performance. To enhance the EA ability, we propose GAEA, a novel EA approach based on graph augmentation. In this model, we design a simple Entity-Relation (ER) Encoder to generate latent representations for entities via jointly modeling comprehensive structural information and rich relation semantics. Moreover, we use graph augmentation to create two graph views for margin-based alignment learning and contrastive entity representation learning, thus mitigating structural heterogeneity and further improving the model's alignment performance. Extensive experiments conducted on benchmark datasets demonstrate the effectiveness of our method.

Xuechen Zhao, Jiaying Zou, Zhong Zhang et al.

Zero-shot stance detection is challenging because it requires detecting the stance of previously unseen targets in the inference phase. The ability to learn transferable target-invariant features is critical for zero-shot stance detection. In this work, we propose a stance detection approach that can efficiently adapt to unseen targets, the core of which is to capture target-invariant syntactic expression patterns as transferable knowledge. Specifically, we first augment the data by masking the topic words of sentences, and then feed the augmented data to an unsupervised contrastive learning module to capture transferable features. Then, to fit a specific target, we encode the raw texts as target-specific features. Finally, we adopt an attention mechanism, which combines syntactic expression patterns with target-specific features to obtain enhanced features for predicting previously unseen targets. Experiments demonstrate that our model outperforms competitive baselines on four benchmark datasets.

Feng Xie, Zhong Zhang, Xuechen Zhao et al.

The accurate forecasting of infectious epidemic diseases is the key to effective control of the epidemic situation in a region. Most existing methods ignore potential dynamic dependencies between regions or the importance of temporal dependencies and inter-dependencies between regions for prediction. In this paper, we propose an Inter- and Intra-Series Embeddings Fusion Network (SEFNet) to improve epidemic prediction performance. SEFNet consists of two parallel modules, named Inter-Series Embedding Module and Intra-Series Embedding Module. In Inter-Series Embedding Module, a multi-scale unified convolution component called Region-Aware Convolution is proposed, which cooperates with self-attention to capture dynamic dependencies between time series obtained from multiple regions. The Intra-Series Embedding Module uses Long Short-Term Memory to capture temporal relationships within each time series. Subsequently, we learn the influence degree of two embeddings and fuse them with the parametric-matrix fusion method. To further improve the robustness, SEFNet also integrates a traditional autoregressive component in parallel with nonlinear neural networks. Experiments on four real-world epidemic-related datasets show SEFNet is effective and outperforms state-of-the-art baselines.

Shuang Zhou, Kai Yu, Song Wang et al.

Heart diseases remain a leading cause of morbidity and mortality worldwide, necessitating accurate and trustworthy differential diagnosis. However, existing artificial intelligence-based diagnostic methods are often limited by insufficient cardiology knowledge, inadequate support for complex reasoning, and poor interpretability. Here we present HeartAgent, a cardiology-specific agent system designed to support a reliable and explainable differential diagnosis. HeartAgent integrates customized tools and curated data resources and orchestrates multiple specialized sub-agents to perform complex reasoning while generating transparent reasoning trajectories and verifiable supporting references. Evaluated on the MIMIC dataset and a private electronic health records cohort, HeartAgent achieved over 36% and 20% improvements over established comparative methods, in top-3 diagnostic accuracy, respectively. Additionally, clinicians assisted by HeartAgent demonstrated gains of 26.9% in diagnostic accuracy and 22.7% in explanatory quality compared with unaided experts. These results demonstrate that HeartAgent provides reliable, explainable, and clinically actionable decision support for cardiovascular care.

Zeyu Liu, Zheng Li, Feng Xie et al.

We study the problem of selecting covariates for unbiased estimation of the total causal effect.Existing approaches typically rely on global causal structure learning over all variables, or on strong assumptions such as causal sufficiency - where observed variables share no latent confounders - or the pretreatment assumption, which limits covariates to those unaffected by the treatment or outcome. These requirements are often unrealistic in practice, and global learning becomes computationally prohibitive in high-dimensional settings.To address these challenges, we propose a novel local learning method for covariate selection in nonparametric causal effect estimation that avoids both the pretreatment and causal sufficiency assumptions. We first characterize a local boundary that contains at least one valid adjustment set whenever one exists for identifying the causal effect, and then develop local identification procedures to efficiently search within this boundary.We prove that the proposed method is sound and complete. Experiments on multiple synthetic datasets and two real-world datasets show that our approach achieves accurate causal effect estimation while substantially improving computational efficiency.

Shuang Zhou, Kai Yu, Zaifu Zhan et al.

Epilepsy and psychogenic non-epileptic seizures often present with similar seizure-like manifestations but require fundamentally different management strategies. Misdiagnosis is common and can lead to prolonged diagnostic delays, unnecessary treatments, and substantial patient morbidity. Although prolonged video-electroencephalography is the diagnostic gold standard, its high cost and limited accessibility hinder timely diagnosis. Here, we developed a low-cost, effective approach, EpiScreen, for early epilepsy detection by utilizing routinely collected clinical notes from electronic health records. Through fine-tuning large language models on labeled notes, EpiScreen achieved an AUC of up to 0.875 on the MIMIC-IV dataset and 0.980 on a private cohort of the University of Minnesota. In a clinician-AI collaboration setting, EpiScreen-assisted neurologists outperformed unaided experts by up to 10.9%. Overall, this study demonstrates that EpiScreen supports early epilepsy detection, facilitating timely and cost-effective screening that may reduce diagnostic delays and avoid unnecessary interventions, particularly in resource-limited regions.

Feng Xie, Xin Song, Xiang Zeng et al.

Semi-supervised entity alignment (EA) is a practical and challenging task because of the lack of adequate labeled mappings as training data. Most works address this problem by generating pseudo mappings for unlabeled entities. However, they either suffer from the erroneous (noisy) pseudo mappings or largely ignore the uncertainty of pseudo mappings. In this paper, we propose a novel semi-supervised EA method, termed as MixTEA, which guides the model learning with an end-to-end mixture teaching of manually labeled mappings and probabilistic pseudo mappings. We firstly train a student model using few labeled mappings as standard. More importantly, in pseudo mapping learning, we propose a bi-directional voting (BDV) strategy that fuses the alignment decisions in different directions to estimate the uncertainty via the joint matching confidence score. Meanwhile, we also design a matching diversity-based rectification (MDR) module to adjust the pseudo mapping learning, thus reducing the negative influence of noisy mappings. Extensive results on benchmark datasets as well as further analyses demonstrate the superiority and the effectiveness of our proposed method.

Kai Yu, Shuang Zhou, Yiran Song et al.

Multimodal self-supervised pretraining offers a promising route to cancer prognosis by integrating histopathology whole-slide images, gene expression, and pathology reports, yet most existing approaches require fully paired and complete inputs. In practice, clinical cohorts are fragmented and often miss one or more modalities, limiting both supervised fusion and scalable multimodal pretraining. We propose PRIME, a missing-aware multimodal self-supervised pretraining framework that learns robust and transferable representations from partially observed cohorts. PRIME maps heterogeneous modality embeddings into a unified token space and introduces a shared prototype memory bank for latent-space semantic imputation via patient-level consensus retrieval, producing structurally aligned tokens without reconstructing raw signals. Two complementary pretraining objectives: inter-modality alignment and post-fusion consistency under structured missingness augmentation, jointly learn representations that remain predictive under arbitrary modality subsets. We evaluate PRIME on The Cancer Genome Atlas with label-free pretraining on 32 cancer types and downstream 5-fold evaluation on five cohorts across overall survival prediction, 3-year mortality classification, and 3-year recurrence classification. PRIME achieves the best macro-average performance among all compared methods, reaching 0.653 C-index, 0.689 AUROC, and 0.637 AUROC on the three tasks, respectively, while improving robustness under test-time missingness and supporting parameter-efficient and label-efficient adaptation. These results support missing-aware multimodal pretraining as a practical strategy for prognosis modeling in fragmented clinical data settings.

Zheng Li, Feng Xie, Shenglan Nie et al.

Constraint-based causal discovery is widely used for learning causal structures, but heavy reliance on conditional independence (CI) testing makes it computationally expensive in high-dimensional settings. To mitigate this limitation, many divide-and-conquer frameworks have been proposed, but most assume causal sufficiency, i.e., no latent variables. In this paper, we show that divide-and-conquer strategies can be theoretically generalized beyond causal sufficiency to settings with latent variables. Specifically, we propose a recursive decomposition framework, termed DiCoLa, that enables divide-and-conquer causal discovery in the presence of latent variables. It recursively decomposes the global learning task into smaller subproblems and integrates their solutions through a principled reconstruction step to recover the global structure. We theoretically establish the soundness and completeness of the proposed framework. Extensive experiments on synthetic data demonstrate that our approach significantly improves computational efficiency across a range of causal discovery algorithms, while experiments on a real-world dataset further illustrate its practical effectiveness.

Feng Xie, Jun Zhou, Jin Wee Lee et al.

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

Feng Xie, Zhen Yao, Lin Xie et al.

We consider the challenging problem of estimating causal effects from purely observational data in the bi-directional Mendelian randomization (MR), where some invalid instruments, as well as unmeasured confounding, usually exist. To address this problem, most existing methods attempt to find proper valid instrumental variables (IVs) for the target causal effect by expert knowledge or by assuming that the causal model is a one-directional MR model. As such, in this paper, we first theoretically investigate the identification of the bi-directional MR from observational data. In particular, we provide necessary and sufficient conditions under which valid IV sets are correctly identified such that the bi-directional MR model is identifiable, including the causal directions of a pair of phenotypes (i.e., the treatment and outcome). Moreover, based on the identification theory, we develop a cluster fusion-like method to discover valid IV sets and estimate the causal effects of interest. We theoretically demonstrate the correctness of the proposed algorithm. Experimental results show the effectiveness of our method for estimating causal effects in bi-directional MR.

Ziwen Wang, Jin Wee Lee, Tanujit Chakraborty et al.

Survival analysis is essential for studying time-to-event outcomes and providing a dynamic understanding of the probability of an event occurring over time. Various survival analysis techniques, from traditional statistical models to state-of-the-art machine learning algorithms, support healthcare intervention and policy decisions. However, there remains ongoing discussion about their comparative performance. We conducted a comparative study of several survival analysis methods, including Cox proportional hazards (CoxPH), stepwise CoxPH, elastic net penalized Cox model, Random Survival Forests (RSF), Gradient Boosting machine (GBM) learning, AutoScore-Survival, DeepSurv, time-dependent Cox model based on neural network (CoxTime), and DeepHit survival neural network. We applied the concordance index (C-index) for model goodness-of-fit, and integral Brier scores (IBS) for calibration, and considered the model interpretability. As a case study, we performed a retrospective analysis of patients admitted through the emergency department of a tertiary hospital from 2017 to 2019, predicting 90-day all-cause mortality based on patient demographics, clinicopathological features, and historical data. The results of the C-index indicate that deep learning achieved comparable performance, with DeepSurv producing the best discrimination (DeepSurv: 0.893; CoxTime: 0.892; DeepHit: 0.891). The calibration of DeepSurv (IBS: 0.041) performed the best, followed by RSF (IBS: 0.042) and GBM (IBS: 0.0421), all using the full variables. Moreover, AutoScore-Survival, using a minimal variable subset, is easy to interpret, and can achieve good discrimination and calibration (C-index: 0.867; IBS: 0.044). While all models were satisfactory, DeepSurv exhibited the best discrimination and calibration. In addition, AutoScore-Survival offers a more parsimonious model and excellent interpretability.

Xichen Guo, Zheng Li, Biwei Huang et al.

We address the issue of the testability of instrumental variables derived from observational data. Most existing testable implications are centered on scenarios where the treatment is a discrete variable, e.g., instrumental inequality (Pearl, 1995), or where the effect is assumed to be constant, e.g., instrumental variables condition based on the principle of independent mechanisms (Burauel, 2023). However, treatments can often be continuous variables, such as drug dosages or nutritional content levels, and non-constant effects may occur in many real-world scenarios. In this paper, we consider an additive nonlinear, non-constant effects model with unmeasured confounders, in which treatments can be either discrete or continuous, and propose an Auxiliary-based Independence Test (AIT) condition to test whether a variable is a valid instrument. We first show that if the candidate instrument is valid, then the AIT condition holds. Moreover, we illustrate the implications of the AIT condition and demonstrate that, in certain conditions, AIT conditions are necessary and sufficient to detect all invalid IVs. We also extend the AIT condition to include covariates and introduce a practical testing algorithm. Experimental results on both synthetic and three different real-world datasets show the effectiveness of our proposed condition.

Yan Zeng, Shenglan Nie, Feng Xie et al.

Imitation learning from demonstrations usually suffers from the confounding effects of unmeasured variables (i.e., unmeasured confounders) on the states and actions. If ignoring them, a biased estimation of the policy would be entailed. To break up this confounding gap, in this paper, we take the best of the strong power of instrumental variables (IV) and propose a Confounded Causal Imitation Learning (C2L) model. This model accommodates confounders that influence actions across multiple timesteps, rather than being restricted to immediate temporal dependencies. We develop a two-stage imitation learning framework for valid IV identification and policy optimization. In particular, in the first stage, we construct a testing criterion based on the defined pseudo-variable, with which we achieve identifying a valid IV for the C2L models. Such a criterion entails the sufficient and necessary identifiability conditions for IV validity. In the second stage, with the identified IV, we propose two candidate policy learning approaches: one is based on a simulator, while the other is offline. Extensive experiments verified the effectiveness of identifying the valid IV as well as learning the policy.

Jie Peng, Shuang Zhou, Longwei Yang et al.

Cancer prognosis is a critical task that involves predicting patient outcomes and survival rates. To enhance prediction accuracy, previous studies have integrated diverse data modalities, such as clinical notes, medical images, and genomic data, leveraging their complementary information. However, existing approaches face two major limitations. First, they struggle to incorporate newly arrived data with varying distributions into training, such as patient records from different hospitals, thus rendering sub-optimal generalizability and limited utility in real-world applications. Second, most multimodal integration methods rely on simplistic concatenation or task-specific pipelines, which fail to capture the complex interdependencies across modalities. To address these, we propose a continually evolving multi-modal foundation model. Extensive experiments on the TCGA dataset demonstrate the effectiveness of our approach, highlighting its potential to advance cancer prognosis by enabling robust and adaptive multimodal integration.

Zheng Li, Xichen Guo, Feng Xie et al.

Estimating causal effects from nonexperimental data is a fundamental problem in many fields of science. A key component of this task is selecting an appropriate set of covariates for confounding adjustment to avoid bias. Most existing methods for covariate selection often assume the absence of latent variables and rely on learning the global network structure among variables. However, identifying the global structure can be unnecessary and inefficient, especially when our primary interest lies in estimating the effect of a treatment variable on an outcome variable. To address this limitation, we propose a novel local learning approach for covariate selection in nonparametric causal effect estimation, which accounts for the presence of latent variables. Our approach leverages testable independence and dependence relationships among observed variables to identify a valid adjustment set for a target causal relationship, ensuring both soundness and completeness under standard assumptions. We validate the effectiveness of our algorithm through extensive experiments on both synthetic and real-world data.

Zhengming Chen, Ruichu Cai, Feng Xie et al.

Unobserved discrete data are ubiquitous in many scientific disciplines, and how to learn the causal structure of these latent variables is crucial for uncovering data patterns. Most studies focus on the linear latent variable model or impose strict constraints on latent structures, which fail to address cases in discrete data involving non-linear relationships or complex latent structures. To achieve this, we explore a tensor rank condition on contingency tables for an observed variable set $\mathbf{X}_p$, showing that the rank is determined by the minimum support of a specific conditional set (not necessary in $\mathbf{X}_p$) that d-separates all variables in $\mathbf{X}_p$. By this, one can locate the latent variable through probing the rank on different observed variables set, and further identify the latent causal structure under some structure assumptions. We present the corresponding identification algorithm and conduct simulated experiments to verify the effectiveness of our method. In general, our results elegantly extend the identification boundary for causal discovery with discrete latent variables and expand the application scope of causal discovery with latent variables.

Peng Wu, Ziyu Shen, Feng Xie et al.

Empirical researchers and decision-makers spanning various domains frequently seek profound insights into the long-term impacts of interventions. While the significance of long-term outcomes is undeniable, an overemphasis on them may inadvertently overshadow short-term gains. Motivated by this, this paper formalizes a new framework for learning the optimal policy that effectively balances both long-term and short-term rewards, where some long-term outcomes are allowed to be missing. In particular, we first present the identifiability of both rewards under mild assumptions. Next, we deduce the semiparametric efficiency bounds, along with the consistency and asymptotic normality of their estimators. We also reveal that short-term outcomes, if associated, contribute to improving the estimator of the long-term reward. Based on the proposed estimators, we develop a principled policy learning approach and further derive the convergence rates of regret and estimation errors associated with the learned policy. Extensive experiments are conducted to validate the effectiveness of the proposed method, demonstrating its practical applicability.

Yilin Ning, Siqi Li, Marcus Eng Hock Ong et al.

Risk scores are widely used for clinical decision making and commonly generated from logistic regression models. Machine-learning-based methods may work well for identifying important predictors, but such 'black box' variable selection limits interpretability, and variable importance evaluated from a single model can be biased. We propose a robust and interpretable variable selection approach using the recently developed Shapley variable importance cloud (ShapleyVIC) that accounts for variability across models. Our approach evaluates and visualizes overall variable contributions for in-depth inference and transparent variable selection, and filters out non-significant contributors to simplify model building steps. We derive an ensemble variable ranking from variable contributions, which is easily integrated with an automated and modularized risk score generator, AutoScore, for convenient implementation. In a study of early death or unplanned readmission, ShapleyVIC selected 6 of 41 candidate variables to create a well-performing model, which had similar performance to a 16-variable model from machine-learning-based ranking.

Feng Xie, Han Yuan, Yilin Ning et al.

Objective: Temporal electronic health records (EHRs) can be a wealth of information for secondary uses, such as clinical events prediction or chronic disease management. However, challenges exist for temporal data representation. We therefore sought to identify these challenges and evaluate novel methodologies for addressing them through a systematic examination of deep learning solutions. Methods: We searched five databases (PubMed, EMBASE, the Institute of Electrical and Electronics Engineers [IEEE] Xplore Digital Library, the Association for Computing Machinery [ACM] digital library, and Web of Science) complemented with hand-searching in several prestigious computer science conference proceedings. We sought articles that reported deep learning methodologies on temporal data representation in structured EHR data from January 1, 2010, to August 30, 2020. We summarized and analyzed the selected articles from three perspectives: nature of time series, methodology, and model implementation. Results: We included 98 articles related to temporal data representation using deep learning. Four major challenges were identified, including data irregularity, data heterogeneity, data sparsity, and model opacity. We then studied how deep learning techniques were applied to address these challenges. Finally, we discuss some open challenges arising from deep learning. Conclusion: Temporal EHR data present several major challenges for clinical prediction modeling and data utilization. To some extent, current deep learning solutions can address these challenges. Future studies can consider designing comprehensive and integrated solutions. Moreover, researchers should incorporate additional clinical domain knowledge into study designs and enhance the interpretability of the model to facilitate its implementation in clinical practice.

Han Yuan, Feng Xie, Marcus Eng Hock Ong et al.

Background: Medical decision-making impacts both individual and public health. Clinical scores are commonly used among a wide variety of decision-making models for determining the degree of disease deterioration at the bedside. AutoScore was proposed as a useful clinical score generator based on machine learning and a generalized linear model. Its current framework, however, still leaves room for improvement when addressing unbalanced data of rare events. Methods: Using machine intelligence approaches, we developed AutoScore-Imbalance, which comprises three components: training dataset optimization, sample weight optimization, and adjusted AutoScore. All scoring models were evaluated on the basis of their area under the curve (AUC) in the receiver operating characteristic analysis and balanced accuracy (i.e., mean value of sensitivity and specificity). By utilizing a publicly accessible dataset from Beth Israel Deaconess Medical Center, we assessed the proposed model and baseline approaches in the prediction of inpatient mortality. Results: AutoScore-Imbalance outperformed baselines in terms of AUC and balanced accuracy. The nine-variable AutoScore-Imbalance sub-model achieved the highest AUC of 0.786 (0.732-0.839) while the eleven-variable original AutoScore obtained an AUC of 0.723 (0.663-0.783), and the logistic regression with 21 variables obtained an AUC of 0.743 (0.685-0.800). The AutoScore-Imbalance sub-model (using down-sampling algorithm) yielded an AUC of 0. 0.771 (0.718-0.823) with only five variables, demonstrating a good balance between performance and variable sparsity. Conclusions: The AutoScore-Imbalance tool has the potential to be applied to highly unbalanced datasets to gain further insight into rare medical events and to facilitate real-world clinical decision-making.

Feng Xie, Yilin Ning, Han Yuan et al.

Scoring systems are highly interpretable and widely used to evaluate time-to-event outcomes in healthcare research. However, existing time-to-event scores are predominantly created ad-hoc using a few manually selected variables based on clinician's knowledge, suggesting an unmet need for a robust and efficient generic score-generating method. AutoScore was previously developed as an interpretable machine learning score generator, integrated both machine learning and point-based scores in the strong discriminability and accessibility. We have further extended it to time-to-event data and developed AutoScore-Survival, for automatically generating time-to-event scores with right-censored survival data. Random survival forest provides an efficient solution for selecting variables, and Cox regression was used for score weighting. We illustrated our method in a real-life study of 90-day mortality of patients in intensive care units and compared its performance with survival models (i.e., Cox) and the random survival forest. The AutoScore-Survival-derived scoring model was more parsimonious than survival models built using traditional variable selection methods (e.g., penalized likelihood approach and stepwise variable selection), and its performance was comparable to survival models using the same set of variables. Although AutoScore-Survival achieved a comparable integrated area under the curve of 0.782 (95% CI: 0.767-0.794), the integer-valued time-to-event scores generated are favorable in clinical applications because they are easier to compute and interpret. Our proposed AutoScore-Survival provides an automated, robust and easy-to-use machine learning-based clinical score generator to studies of time-to-event outcomes. It provides a systematic guideline to facilitate the future development of time-to-event scores for clinical applications.

Feng Xie, Ruichu Cai, Biwei Huang et al.

Causal discovery aims to recover causal structures or models underlying the observed data. Despite its success in certain domains, most existing methods focus on causal relations between observed variables, while in many scenarios the observed ones may not be the underlying causal variables (e.g., image pixels), but are generated by latent causal variables or confounders that are causally related. To this end, in this paper, we consider Linear, Non-Gaussian Latent variable Models (LiNGLaMs), in which latent confounders are also causally related, and propose a Generalized Independent Noise (GIN) condition to estimate such latent variable graphs. Specifically, for two observed random vectors $\mathbf{Y}$ and $\mathbf{Z}$, GIN holds if and only if $ω^{\intercal}\mathbf{Y}$ and $\mathbf{Z}$ are statistically independent, where $ω$ is a parameter vector characterized from the cross-covariance between $\mathbf{Y}$ and $\mathbf{Z}$. From the graphical view, roughly speaking, GIN implies that causally earlier latent common causes of variables in $\mathbf{Y}$ d-separate $\mathbf{Y}$ from $\mathbf{Z}$. Interestingly, we find that the independent noise condition, i.e., if there is no confounder, causes are independent from the error of regressing the effect on the causes, can be seen as a special case of GIN. Moreover, we show that GIN helps locate latent variables and identify their causal structure, including causal directions. We further develop a recursive learning algorithm to achieve these goals. Experimental results on synthetic and real-world data demonstrate the effectiveness of our method.

Yan Zeng, Shohei Shimizu, Ruichu Cai et al.

Discovering causal structures among latent factors from observed data is a particularly challenging problem. Despite some efforts for this problem, existing methods focus on the single-domain data only. In this paper, we propose Multi-Domain Linear Non-Gaussian Acyclic Models for Latent Factors (MD-LiNA), where the causal structure among latent factors of interest is shared for all domains, and we provide its identification results. The model enriches the causal representation for multi-domain data. We propose an integrated two-phase algorithm to estimate the model. In particular, we first locate the latent factors and estimate the factor loading matrix. Then to uncover the causal structure among shared latent factors of interest, we derive a score function based on the characterization of independence relations between external influences and the dependence relations between multi-domain latent factors and latent factors of interest. We show that the proposed method provides locally consistent estimators. Experimental results on both synthetic and real-world data demonstrate the efficacy and robustness of our approach.

Dong-dong Zhang, Lei Zhang, Vladimir Zaborovsky et al.

During the rapid urbanization construction of China, acquisition of urban geographic information and timely data updating are important and fundamental tasks for the refined management of cities. With the development of domestic remote sensing technology, the application of Gaofen-2 (GF-2) high-resolution remote sensing images can greatly improve the accuracy of information extraction. This paper introduces an approach using object-oriented classification methods for urban feature extraction based on GF-2 satellite data. A combination of spectral, spatial attributes and membership functions was employed for mapping the urban features of Qinhuai District, Nanjing. The data preprocessing is carried out by ENVI software, and the subsequent data is exported into the eCognition software for object-oriented classification and extraction of urban feature information. Finally, the obtained raster image classification results are vectorized using the ARCGIS software, and the vector graphics are stored in the library, which can be used for further analysis and modeling. Accuracy assessment was performed using ground truth data acquired by visual interpretation and from other reliable secondary data sources. Compared with the result of pixel-based supervised (neural net) classification, the developed object-oriented method can significantly improve extraction accuracy, and after manual interpretation, an overall accuracy of 95.44% can be achieved, with a Kappa coefficient of 0.9405, which objectively confirmed the superiority of the object-oriented method and the feasibility of the utilization of GF-2 satellite data.