Objective: Electronic health records (EHR) are widely available to complement administrative data-based disease surveillance and healthcare performance evaluation. Defining conditions from EHR is labour-intensive and requires extensive manual labelling of disease outcomes. This study developed an efficient strategy based on advanced large language models to identify multiple conditions from EHR clinical notes. Methods: We linked a cardiac registry cohort in 2015 with an EHR system in Alberta, Canada. We developed a pipeline that leveraged a generative large language model (LLM) to analyze, understand, and interpret EHR notes by prompts based on specific diagnosis, treatment management, and clinical guidelines. The pipeline was applied to detect acute myocardial infarction (AMI), diabetes, and hypertension. The performance was compared against clinician-validated diagnoses as the reference standard and widely adopted International Classification of Diseases (ICD) codes-based methods. Results: The study cohort accounted for 3,088 patients and 551,095 clinical notes. The prevalence was 55.4%, 27.7%, 65.9% and for AMI, diabetes, and hypertension, respectively. The performance of the LLM-based pipeline for detecting conditions varied: AMI had 88% sensitivity, 63% specificity, and 77% positive predictive value (PPV); diabetes had 91% sensitivity, 86% specificity, and 71% PPV; and hypertension had 94% sensitivity, 32% specificity, and 72% PPV. Compared with ICD codes, the LLM-based method demonstrated improved sensitivity and negative predictive value across all conditions. The monthly percentage trends from the detected cases by LLM and reference standard showed consistent patterns.

Ensuring fairness in machine learning is a critical and challenging task, as biased data representations often lead to unfair predictions. To address this, we propose Deep Fair Learning, a framework that integrates nonlinear sufficient dimension reduction with deep learning to construct fair and informative representations. By introducing a novel penalty term during fine-tuning, our method enforces conditional independence between sensitive attributes and learned representations, addressing bias at its source while preserving predictive performance. Unlike prior methods, it supports diverse sensitive attributes, including continuous, discrete, binary, or multi-group types. Experiments on various types of data structure show that our approach achieves a superior balance between fairness and utility, significantly outperforming state-of-the-art baselines.

Computational phenotyping is essential for biomedical research but often requires significant time and resources, especially since traditional methods typically involve extensive manual data review. While machine learning and natural language processing advancements have helped, further improvements are needed. Few studies have explored using Large Language Models (LLMs) for these tasks despite known advantages of LLMs for text-based tasks. T o facilitate further research in this area, we developed an evaluation framework, Evaluation of PHEnotyping for Observational Health Data (PHEONA), that outlines context-specific considerations. W e applied and demonstrated PHEONA on concept classification, a specific task within a broader phenotyping process for Acute Respiratory Failure (ARF) respiratory support therapies. From the sample concepts tested, we achieved high classification accuracy, suggesting the potential for LLM-based methods to improve computational phenotyping processes.

We propose a neural-network based survival model (SurvSurf) specifically designed for direct and simultaneous probabilistic prediction of the first hitting time of sequential events from baseline. Unlike existing models, SurvSurf is theoretically guaranteed to never violate the monotonic relationship between the cumulative incidence functions of sequential events, while allowing nonlinear influence from predictors. It also incorporates implicit truths for unobserved intermediate events in model fitting, and supports both discrete and continuous time and events. We also identified a variant of the Integrated Brier Score (IBS) that showed robust correlation with the mean squared error (MSE) between the true and predicted probabilities by accounting for implied truths about the missing intermediate events. We demonstrated the superiority of SurvSurf compared to modern and traditional predictive survival models in two simulated datasets and two real-world datasets, using MSE, the more robust IBS and by measuring the extent of monotonicity violation.

This paper explores transfer learning in heterogeneous multi-source environments with distributional divergence between target and auxiliary domains. To address challenges in statistical bias and computational efficiency, we propose a Sparse Optimization for Transfer Learning (SOTL) framework based on L0-regularization. The method extends the Joint Estimation Transferred from Strata (JETS) paradigm with two key innovations: (1) L0-constrained exact sparsity for parameter space compression and complexity reduction, and (2) refining optimization focus to emphasize target parameters over redundant ones. Simulations show that SOTL significantly improves both estimation accuracy and computational speed, especially under adversarial auxiliary domain conditions. Empirical validation on the Community and Crime benchmarks demonstrates the statistical robustness of the SOTL method in cross-domain transfer.

ML-supported decisions, such as ordering tests or determining preventive custody, often involve binary classification based on probabilistic forecasts. Evaluation frameworks for such forecasts typically consider whether to prioritize independent-decision metrics (e.g., Accuracy) or top-K metrics (e.g., Precision@K), and whether to focus on fixed thresholds or threshold-agnostic measures like AUC-ROC. We highlight that a consequentialist perspective, long advocated by decision theorists, should naturally favor evaluations that support independent decisions using a mixture of thresholds given their prevalence, such as Brier scores and Log loss. However, our empirical analysis reveals a strong preference for top-K metrics or fixed thresholds in evaluations at major conferences like ICML, FAccT, and CHIL. To address this gap, we use this decision-theoretic framework to map evaluation metrics to their optimal use cases, along with a Python package, briertools, to promote the broader adoption of Brier scores. In doing so, we also uncover new theoretical connections, including a reconciliation between the Brier Score and Decision Curve Analysis, which clarifies and responds to a longstanding critique by (Assel, et al. 2017) regarding the clinical utility of proper scoring rules.

The opioid overdose epidemic remains a critical public health crisis, particularly in the United States, leading to significant mortality and societal costs. Social media platforms like Reddit provide vast amounts of unstructured data that offer insights into public perceptions, discussions, and experiences related to opioid use. This study leverages Natural Language Processing (NLP), specifically Opioid Named Entity Recognition (ONER-2025), to extract actionable information from these platforms. Our research makes four key contributions. First, we created a unique, manually annotated dataset sourced from Reddit, where users share self-reported experiences of opioid use via different administration routes. This dataset contains 331,285 tokens and includes eight major opioid entity categories. Second, we detail our annotation process and guidelines while discussing the challenges of labeling the ONER-2025 dataset. Third, we analyze key linguistic challenges, including slang, ambiguity, fragmented sentences, and emotionally charged language, in opioid discussions. Fourth, we propose a real-time monitoring system to process streaming data from social media, healthcare records, and emergency services to identify overdose events. Using 5-fold cross-validation in 11 experiments, our system integrates machine learning, deep learning, and transformer-based language models with advanced contextual embeddings to enhance understanding. Our transformer-based models (bert-base-NER and roberta-base) achieved 97% accuracy and F1-score, outperforming baselines by 10.23% (RF=0.88).

Complex systems with intricate causal dependencies challenge accurate prediction. Effective modeling requires precise physical process representation, integration of interdependent factors, and incorporation of multi-resolution observational data. These systems manifest in both static scenarios with instantaneous causal chains and temporal scenarios with evolving dynamics, complicating modeling efforts. Current methods struggle to simultaneously handle varying resolutions, capture physical relationships, model causal dependencies, and incorporate temporal dynamics, especially with inconsistently sampled data from diverse sources. We introduce Temporal-SVGDM: Score-based Variational Graphical Diffusion Model for Multi-resolution observations. Our framework constructs individual SDEs for each variable at its native resolution, then couples these SDEs through a causal score mechanism where parent nodes inform child nodes' evolution. This enables unified modeling of both immediate causal effects in static scenarios and evolving dependencies in temporal scenarios. In temporal models, state representations are processed through a sequence prediction model to predict future states based on historical patterns and causal relationships. Experiments on real-world datasets demonstrate improved prediction accuracy and causal understanding compared to existing methods, with robust performance under varying levels of background knowledge. Our model exhibits graceful degradation across different disaster types, successfully handling both static earthquake scenarios and temporal hurricane and wildfire scenarios, while maintaining superior performance even with limited data.

Out-of-Distribution (OOD) detection is a critical task in machine learning, particularly in safety-sensitive applications where model failures can have serious consequences. However, current OOD detection methods often suffer from restrictive distributional assumptions, limited scalability, and a lack of interpretability. To address these challenges, we propose STOOD-X, a two-stage methodology that combines a Statistical nonparametric Test for OOD Detection with eXplainability enhancements. In the first stage, STOOD-X uses feature-space distances and a Wilcoxon-Mann-Whitney test to identify OOD samples without assuming a specific feature distribution. In the second stage, it generates user-friendly, concept-based visual explanations that reveal the features driving each decision, aligning with the BLUE XAI paradigm. Through extensive experiments on benchmark datasets and multiple architectures, STOOD-X achieves competitive performance against state-of-the-art post hoc OOD detectors, particularly in high-dimensional and complex settings. In addition, its explainability framework enables human oversight, bias detection, and model debugging, fostering trust and collaboration between humans and AI systems. The STOOD-X methodology therefore offers a robust, explainable, and scalable solution for real-world OOD detection tasks.

The behavior of the random feature model in the high-dimensional regression framework has become a popular issue of interest in the machine learning literature}. This model is generally considered for feature vectors $x_i = \Sigma^{1/2} x_i'$, where $x_i'$ is a random vector made of independent and identically distributed (iid) entries, and $\Sigma$ is a positive definite matrix representing the covariance of the features. In this paper, we move beyond {\CB this standard assumption by studying the performances of the random features model in the setting of non-iid feature vectors}. Our approach is related to the analysis of the spectrum of large random matrices through random matrix theory (RMT) {\CB and free probability} results. We turn to the analysis of non-iid data by using the notion of variance profile {\CB which} is {\CB well studied in RMT.} Our main contribution is then the study of the limits of the training and {\CB prediction} risks associated to the ridge estimator in the random features model when its dimensions grow. We provide asymptotic equivalents of these risks that capture the behavior of ridge regression with random features in a {\CB high-dimensional} framework. These asymptotic equivalents, {\CB which prove to be sharp in numerical experiments}, are retrieved by adapting, to our setting, established results from operator-valued free probability theory. Moreover, {\CB for various classes of random feature vectors that have not been considered so far in the literature}, our approach allows to show the appearance of the double descent phenomenon when the ridge regularization parameter is small enough.