Daily Papers

Hospitals and healthcare systems rely on operational decisions that determine patient flow, cost, and quality of care. Despite strong performance on medical knowledge and conversational benchmarks, foundation models trained on general text may lack the specialized knowledge required for these operational decisions. We introduce Lang1, a family of models (100M-7B parameters) pretrained on a specialized corpus blending 80B clinical tokens from NYU Langone Health's EHRs and 627B tokens from the internet. To rigorously evaluate Lang1 in real-world settings, we developed the REalistic Medical Evaluation (ReMedE), a benchmark derived from 668,331 EHR notes that evaluates five critical tasks: 30-day readmission prediction, 30-day mortality prediction, length of stay, comorbidity coding, and predicting insurance claims denial. In zero-shot settings, both general-purpose and specialized models underperform on four of five tasks (36.6%-71.7% AUROC), with mortality prediction being an exception. After finetuning, Lang1-1B outperforms finetuned generalist models up to 70x larger and zero-shot models up to 671x larger, improving AUROC by 3.64%-6.75% and 1.66%-23.66% respectively. We also observed cross-task scaling with joint finetuning on multiple tasks leading to improvement on other tasks. Lang1-1B effectively transfers to out-of-distribution settings, including other clinical tasks and an external health system. Our findings suggest that predictive capabilities for hospital operations require explicit supervised finetuning, and that this finetuning process is made more efficient by in-domain pretraining on EHR. Our findings support the emerging view that specialized LLMs can compete with generalist models in specialized tasks, and show that effective healthcare systems AI requires the combination of in-domain pretraining, supervised finetuning, and real-world evaluation beyond proxy benchmarks.

Clinical notes contain information about patients that goes beyond structured data like lab values and medications. However, clinical notes have been underused relative to structured data, because notes are high-dimensional and sparse. This work develops and evaluates representations of clinical notes using bidirectional transformers (ClinicalBERT). ClinicalBERT uncovers high-quality relationships between medical concepts as judged by humans. ClinicalBert outperforms baselines on 30-day hospital readmission prediction using both discharge summaries and the first few days of notes in the intensive care unit. Code and model parameters are available.

Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.

Decisions about managing patients on the heart transplant waitlist are currently made by committees of doctors who consider multiple factors, but the process remains largely ad-hoc. With the growing volume of longitudinal patient, donor, and organ data collected by the United Network for Organ Sharing (UNOS) since 2018, there is increasing interest in analytical approaches to support clinical decision-making at the time of organ availability. In this study, we benchmark machine learning models that leverage longitudinal waitlist history data for time-dependent, time-to-event modeling of waitlist mortality. We train on 23,807 patient records with 77 variables and evaluate both survival prediction and discrimination at a 1-year horizon. Our best model achieves a C-Index of 0.94 and AUROC of 0.89, significantly outperforming previous models. Key predictors align with known risk factors while also revealing novel associations. Our findings can support urgency assessment and policy refinement in heart transplant decision making.

This work proposes a framework for optimizing machine learning algorithms. The practicality of the framework is illustrated using an important case study from the healthcare domain, which is predicting the admission status of emergency department (ED) patients (e.g., admitted vs. discharged) using patient data at the time of triage. The proposed framework can mitigate the crowding problem by proactively planning the patient boarding process. A large retrospective dataset of patient records is obtained from the electronic health record database of all ED visits over three years from three major locations of a healthcare provider in the Midwest of the US. Three machine learning algorithms are proposed: T-XGB, T-ADAB, and T-MLP. T-XGB integrates extreme gradient boosting (XGB) and Tabu Search (TS), T-ADAB integrates Adaboost and TS, and T-MLP integrates multi-layer perceptron (MLP) and TS. The proposed algorithms are compared with the traditional algorithms: XGB, ADAB, and MLP, in which their parameters are tunned using grid search. The three proposed algorithms and the original ones are trained and tested using nine data groups that are obtained from different feature selection methods. In other words, 54 models are developed. Performance was evaluated using five measures: Area under the curve (AUC), sensitivity, specificity, F1, and accuracy. The results show that the newly proposed algorithms resulted in high AUC and outperformed the traditional algorithms. The T-ADAB performs the best among the newly developed algorithms. The AUC, sensitivity, specificity, F1, and accuracy of the best model are 95.4%, 99.3%, 91.4%, 95.2%, 97.2%, respectively.

Models that can predict the occurrence of events ahead of time with low false-alarm rates are critical to the acceptance of decision support systems in the medical community. This challenging task is typically treated as a simple binary classification, ignoring temporal dependencies between samples, whereas we propose to exploit this structure. We first introduce a common theoretical framework unifying dynamic survival analysis and early event prediction. Following an analysis of objectives from both fields, we propose Temporal Label Smoothing (TLS), a simpler, yet best-performing method that preserves prediction monotonicity over time. By focusing the objective on areas with a stronger predictive signal, TLS improves performance over all baselines on two large-scale benchmark tasks. Gains are particularly notable along clinically relevant measures, such as event recall at low false-alarm rates. TLS reduces the number of missed events by up to a factor of two over previously used approaches in early event prediction.

Urgent care clinics and emergency departments around the world periodically suffer from extended wait times beyond patient expectations due to inadequate staffing levels. These delays have been linked with adverse clinical outcomes. Previous research into forecasting demand this domain has mostly used a collection of statistical techniques, with machine learning approaches only now beginning to emerge in recent literature. The forecasting problem for this domain is difficult and has also been complicated by the COVID-19 pandemic which has introduced an additional complexity to this estimation due to typical demand patterns being disrupted. This study explores the ability of machine learning methods to generate accurate patient presentations at two large urgent care clinics located in Auckland, New Zealand. A number of machine learning algorithms were explored in order to determine the most effective technique for this problem domain, with the task of making forecasts of daily patient demand three months in advance. The study also performed an in-depth analysis into the model behaviour in respect to the exploration of which features are most effective at predicting demand and which features are capable of adaptation to the volatility caused by the COVID-19 pandemic lockdowns. The results showed that ensemble-based methods delivered the most accurate and consistent solutions on average, generating improvements in the range of 23%-27% over the existing in-house methods for estimating the daily demand.

In recent years, medical information technology has made it possible for electronic health record (EHR) to store fairly complete clinical data. This has brought health care into the era of "big data". However, medical data are often sparse and strongly correlated, which means that medical problems cannot be solved effectively. With the rapid development of deep learning in recent years, it has provided opportunities for the use of big data in healthcare. In this paper, we propose a temporal-saptial correlation attention network (TSCAN) to handle some clinical characteristic prediction problems, such as predicting death, predicting length of stay, detecting physiologic decline, and classifying phenotypes. Based on the design of the attention mechanism model, our approach can effectively remove irrelevant items in clinical data and irrelevant nodes in time according to different tasks, so as to obtain more accurate prediction results. Our method can also find key clinical indicators of important outcomes that can be used to improve treatment options. Our experiments use information from the Medical Information Mart for Intensive Care (MIMIC-IV) database, which is open to the public. Finally, we have achieved significant performance benefits of 2.0\% (metric) compared to other SOTA prediction methods. We achieved a staggering 90.7\% on mortality rate, 45.1\% on length of stay. The source code can be find: https://github.com/yuyuheintju/TSCAN.

This paper uses the MIMIC-IV dataset to examine the fairness and bias in an XGBoost binary classification model predicting the Intensive Care Unit (ICU) length of stay (LOS). Highlighting the critical role of the ICU in managing critically ill patients, the study addresses the growing strain on ICU capacity. It emphasizes the significance of LOS prediction for resource allocation. The research reveals class imbalances in the dataset across demographic attributes and employs data preprocessing and feature extraction. While the XGBoost model performs well overall, disparities across race and insurance attributes reflect the need for tailored assessments and continuous monitoring. The paper concludes with recommendations for fairness-aware machine learning techniques for mitigating biases and the need for collaborative efforts among healthcare professionals and data scientists.

The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.

Hospitals struggle to predict critical outcomes. Traditional early warning systems, like NEWS and MEWS, rely on static variables and fixed thresholds, limiting their adaptability, accuracy, and personalization. We previously developed the Enhanced Transformer for Health Outcome Simulation (ETHOS), an AI model that tokenizes patient health timelines (PHTs) from EHRs and uses transformer-based architectures to predict future PHTs. ETHOS is a versatile framework for developing a wide range of applications. In this work, we develop the Adaptive Risk Estimation System (ARES) that leverages ETHOS to compute dynamic, personalized risk probabilities for clinician-defined critical events. ARES also features a personalized explainability module that highlights key clinical factors influencing risk estimates. We evaluated ARES using the MIMIC-IV v2.2 dataset together with its Emergency Department (ED) extension and benchmarked performance against both classical early warning systems and contemporary machine learning models. The entire dataset was tokenized resulting in 285,622 PHTs, comprising over 360 million tokens. ETHOS outperformed benchmark models in predicting hospital admissions, ICU admissions, and prolonged stays, achieving superior AUC scores. Its risk estimates were robust across demographic subgroups, with calibration curves confirming model reliability. The explainability module provided valuable insights into patient-specific risk factors. ARES, powered by ETHOS, advances predictive healthcare AI by delivering dynamic, real-time, personalized risk estimation with patient-specific explainability. Although our results are promising, the clinical impact remains uncertain. Demonstrating ARES's true utility in real-world settings will be the focus of our future work. We release the source code to facilitate future research.

Adherence to prescribed treatments is crucial for individuals with chronic conditions to avoid costly or adverse health outcomes. For certain patient groups, intensive lifestyle interventions are vital for enhancing medication adherence. Accurate forecasting of treatment adherence can open pathways to developing an on-demand intervention tool, enabling timely and personalized support. With the increasing popularity of smartphones and wearables, it is now easier than ever to develop and deploy smart activity monitoring systems. However, effective forecasting systems for treatment adherence based on wearable sensors are still not widely available. We close this gap by proposing Adherence Forecasting and Intervention with Machine Intelligence (AIMI). AIMI is a knowledge-guided adherence forecasting system that leverages smartphone sensors and previous medication history to estimate the likelihood of forgetting to take a prescribed medication. A user study was conducted with 27 participants who took daily medications to manage their cardiovascular diseases. We designed and developed CNN and LSTM-based forecasting models with various combinations of input features and found that LSTM models can forecast medication adherence with an accuracy of 0.932 and an F-1 score of 0.936. Moreover, through a series of ablation studies involving convolutional and recurrent neural network architectures, we demonstrate that leveraging known knowledge about future and personalized training enhances the accuracy of medication adherence forecasting. Code available: https://github.com/ab9mamun/AIMI.

This study explores the potential of utilizing administrative claims data, combined with advanced machine learning and deep learning techniques, to predict the progression of Chronic Kidney Disease (CKD) to End-Stage Renal Disease (ESRD). We analyze a comprehensive, 10-year dataset provided by a major health insurance organization to develop prediction models for multiple observation windows using traditional machine learning methods such as Random Forest and XGBoost as well as deep learning approaches such as Long Short-Term Memory (LSTM) networks. Our findings demonstrate that the LSTM model, particularly with a 24-month observation window, exhibits superior performance in predicting ESRD progression, outperforming existing models in the literature. We further apply SHapley Additive exPlanations (SHAP) analysis to enhance interpretability, providing insights into the impact of individual features on predictions at the individual patient level. This study underscores the value of leveraging administrative claims data for CKD management and predicting ESRD progression.

Survival analysis, or time-to-event modelling, is a classical statistical problem that has garnered a lot of interest for its practical use in epidemiology, demographics or actuarial sciences. Recent advances on the subject from the point of view of machine learning have been concerned with precise per-individual predictions instead of population studies, driven by the rise of individualized medicine. We introduce here a conditional normalizing flow based estimate of the time-to-event density as a way to model highly flexible and individualized conditional survival distributions. We use a novel hierarchical formulation of normalizing flows to enable efficient fitting of flexible conditional distributions without overfitting and show how the normalizing flow formulation can be efficiently adapted to the censored setting. We experimentally validate the proposed approach on a synthetic dataset as well as four open medical datasets and an example of a common financial problem.

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

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

Over the past several years, across the globe, there has been an increase in people seeking care in emergency departments (EDs). ED resources, including nurse staffing, are strained by such increases in patient volume. Accurate forecasting of incoming patient volume in emergency departments (ED) is crucial for efficient utilization and allocation of ED resources. Working with a suburban ED in the Pacific Northwest, we developed a tool powered by machine learning models, to forecast ED arrivals and ED patient volume to assist end-users, such as ED nurses, in resource allocation. In this paper, we discuss the results from our predictive models, the challenges, and the learnings from users' experiences with the tool in active clinical deployment in a real world setting.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

Checklists are simple decision aids that are often used to promote safety and reliability in clinical applications. In this paper, we present a method to learn checklists for clinical decision support. We represent predictive checklists as discrete linear classifiers with binary features and unit weights. We then learn globally optimal predictive checklists from data by solving an integer programming problem. Our method allows users to customize checklists to obey complex constraints, including constraints to enforce group fairness and to binarize real-valued features at training time. In addition, it pairs models with an optimality gap that can inform model development and determine the feasibility of learning sufficiently accurate checklists on a given dataset. We pair our method with specialized techniques that speed up its ability to train a predictive checklist that performs well and has a small optimality gap. We benchmark the performance of our method on seven clinical classification problems, and demonstrate its practical benefits by training a short-form checklist for PTSD screening. Our results show that our method can fit simple predictive checklists that perform well and that can easily be customized to obey a rich class of custom constraints.

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP, they often lack structured reasoning capabilities critical for high-stakes decision support. We present a unified, multi-task learning framework that aligns autoregressive LLMs with clinical reasoning for outcome prediction on the MSK-CHORD dataset. Our models are trained to jointly perform binary survival classification, continuous survival time regression, and natural language rationale generation. We evaluate three alignment strategies: (1) standard supervised fine-tuning (SFT), (2) SFT with Chain-of-Thought (CoT) prompting to elicit step-by-step reasoning, and (3) Group Relative Policy Optimization (GRPO), a reinforcement learning method that aligns model outputs to expert-derived reasoning trajectories. Experiments with LLaMa3-8B and Med42-8B backbones demonstrate that CoT prompting improves F1 by +6.0 and reduces MAE by 12%, while GRPO achieves state-of-the-art interpretability and predictive performance across BLEU, ROUGE, and BERTScore. We further show that existing biomedical LLMs often fail to produce valid reasoning traces due to architectural constraints. Our findings underscore the importance of reasoning-aware alignment in multi-task clinical modeling and set a new benchmark for interpretable, trustworthy LLMs in precision oncology.

We present a foundation model-derived method to identify highly informative tokens and events in electronic health records. Our approach considers incoming data in the entire context of a patient's hospitalization and so can flag anomalous events that rule-based approaches would consider within a normal range. We demonstrate that the events our model flags are significant for predicting downstream patient outcomes and that a fraction of events identified as carrying little information can safely be dropped. Additionally, we show how informativeness can help interpret the predictions of prognostic models trained on foundation model-derived representations.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

We study multiple rule-based and machine learning (ML) models for sepsis detection. We report the first neural network detection and prediction results on three categories of sepsis. We have used the retrospective Medical Information Mart for Intensive Care (MIMIC)-III dataset, restricted to intensive care unit (ICU) patients. Features for prediction were created from only common vital sign measurements. We show significant improvement of AUC score using neural network based ensemble model compared to single ML and rule-based models. For the detection of sepsis, severe sepsis, and septic shock, our model achieves an AUC of 0.97, 0.96 and 0.91, respectively. Four hours before the positive hours, it predicts the same three categories with an AUC of 0.90, 0.91 and 0.90 respectively. Further, we ranked the features and found that using six vital signs consistently provides higher detection and prediction AUC for all the models tested. Our novel ensemble model achieves highest AUC in detecting and predicting sepsis, severe sepsis, and septic shock in the MIMIC-III ICU patients, and is amenable to deployment in hospital settings.

Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.

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.

Developing clinical prediction models (e.g., mortality prediction) based on electronic health records (EHRs) typically relies on expert opinion for feature selection and adjusting observation window size. This burdens experts and creates a bottleneck in the development process. We propose Retrieval-Enhanced Medical prediction model (REMed) to address such challenges. REMed can essentially evaluate an unlimited number of clinical events, select the relevant ones, and make predictions. This approach effectively eliminates the need for manual feature selection and enables an unrestricted observation window. We verified these properties through experiments on 27 clinical tasks and two independent cohorts from publicly available EHR datasets, where REMed outperformed other contemporary architectures that aim to handle as many events as possible. Notably, we found that the preferences of REMed align closely with those of medical experts. We expect our approach to significantly expedite the development of EHR prediction models by minimizing clinicians' need for manual involvement.

Sepsis is a life-threatening host response to infection associated with high mortality, morbidity, and health costs. Its management is highly time-sensitive since each hour of delayed treatment increases mortality due to irreversible organ damage. Meanwhile, despite decades of clinical research, robust biomarkers for sepsis are missing. Therefore, detecting sepsis early by utilizing the affluence of high-resolution intensive care records has become a challenging machine learning problem. Recent advances in deep learning and data mining promise to deliver a powerful set of tools to efficiently address this task. This empirical study proposes two novel approaches for the early detection of sepsis: a deep learning model and a lazy learner based on time series distances. Our deep learning model employs a temporal convolutional network that is embedded in a Multi-task Gaussian Process Adapter framework, making it directly applicable to irregularly-spaced time series data. Our lazy learner, by contrast, is an ensemble approach that employs dynamic time warping. We frame the timely detection of sepsis as a supervised time series classification task. For this, we derive the most recent sepsis definition in an hourly resolution to provide the first fully accessible early sepsis detection environment. Seven hours before sepsis onset, our methods improve area under the precision--recall curve from 0.25 to 0.35/0.40 over the state of the art. This demonstrates that they are well-suited for detecting sepsis in the crucial earlier stages when management is most effective.

Foundation models (FMs) trained on electronic health records (EHRs) have shown strong performance on a range of clinical prediction tasks. However, adapting these models to local health systems remains challenging due to limited data availability and resource constraints. In this study, we investigated what these models learn and evaluated the transferability of an FM trained on MIMIC-IV to an institutional EHR dataset at the University of Chicago Medical Center. We assessed their ability to identify outlier patients and examined representation-space patient trajectories in relation to future clinical outcomes. We also evaluated the performance of supervised fine-tuned classifiers on both source and target datasets. Our findings offer insights into the adaptability of FMs across different healthcare systems, highlight considerations for their effective implementation, and provide an empirical analysis of the underlying factors that contribute to their predictive performance.

Objective: We develop a deep learning framework based on the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model using unstructured clinical notes from electronic health records (EHRs) to predict the risk of disease progression from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD). Materials and Methods: We identified 3657 patients diagnosed with MCI together with their progress notes from Northwestern Medicine Enterprise Data Warehouse (NMEDW) between 2000-2020. The progress notes no later than the first MCI diagnosis were used for the prediction. We first preprocessed the notes by deidentification, cleaning and splitting, and then pretrained a BERT model for AD (AD-BERT) based on the publicly available Bio+Clinical BERT on the preprocessed notes. The embeddings of all the sections of a patient's notes processed by AD-BERT were combined by MaxPooling to compute the probability of MCI-to-AD progression. For replication, we conducted a similar set of experiments on 2563 MCI patients identified at Weill Cornell Medicine (WCM) during the same timeframe. Results: Compared with the 7 baseline models, the AD-BERT model achieved the best performance on both datasets, with Area Under receiver operating characteristic Curve (AUC) of 0.8170 and F1 score of 0.4178 on NMEDW dataset and AUC of 0.8830 and F1 score of 0.6836 on WCM dataset. Conclusion: We developed a deep learning framework using BERT models which provide an effective solution for prediction of MCI-to-AD progression using clinical note analysis.

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success in Natural Language Processing and Computer Vision domains. However, the development of PTMs on healthcare time-series data is lagging behind.This underscores the limitations of the existing transformer-based architectures, particularly their scalability to handle large-scale time series and ability to capture long-term temporal dependencies. In this study, we present Timely Generative Pre-trained Transformer (TimelyGPT). TimelyGPT employs an extrapolatable position (xPos) embedding to encode trend and periodic patterns into time-series representations. It also integrates recurrent attention and temporal convolution modules to effectively capture global-local temporal dependencies. We evaluated TimelyGPT on two large-scale healthcare time series datasets corresponding to continuous biosignals and irregularly-sampled time series, respectively. Our experiments show that during pre-training, TimelyGPT excels in learning time-series representations from continuously monitored biosignals and irregularly-sampled time series data commonly observed in longitudinal electronic health records (EHRs). In forecasting continuous biosignals, TimelyGPT achieves accurate extrapolation up to 6,000 timesteps of body temperature during the sleep stage transition, given a short look-up window (i.e., prompt) containing only 2,000 timesteps. For irregularly-sampled time series, TimelyGPT with a proposed time-specific inference demonstrates high top recall scores in predicting future diagnoses using early diagnostic records, effectively handling irregular intervals between clinical records. Together, we envision TimelyGPT to be useful in a broad spectrum of health domains, including long-term patient health state forecasting and patient risk trajectory prediction.

We developed an explainable artificial intelligence (AI) early warning score (xAI-EWS) system for early detection of acute critical illness. While maintaining a high predictive performance, our system explains to the clinician on which relevant electronic health records (EHRs) data the prediction is grounded. Acute critical illness is often preceded by deterioration of routinely measured clinical parameters, e.g., blood pressure and heart rate. Early clinical prediction is typically based on manually calculated screening metrics that simply weigh these parameters, such as Early Warning Scores (EWS). The predictive performance of EWSs yields a tradeoff between sensitivity and specificity that can lead to negative outcomes for the patient. Previous work on EHR-trained AI systems offers promising results with high levels of predictive performance in relation to the early, real-time prediction of acute critical illness. However, without insight into the complex decisions by such system, clinical translation is hindered. In this letter, we present our xAI-EWS system, which potentiates clinical translation by accompanying a prediction with information on the EHR data explaining it.

One straightforward metric to evaluate a survival prediction model is based on the Mean Absolute Error (MAE) -- the average of the absolute difference between the time predicted by the model and the true event time, over all subjects. Unfortunately, this is challenging because, in practice, the test set includes (right) censored individuals, meaning we do not know when a censored individual actually experienced the event. In this paper, we explore various metrics to estimate MAE for survival datasets that include (many) censored individuals. Moreover, we introduce a novel and effective approach for generating realistic semi-synthetic survival datasets to facilitate the evaluation of metrics. Our findings, based on the analysis of the semi-synthetic datasets, reveal that our proposed metric (MAE using pseudo-observations) is able to rank models accurately based on their performance, and often closely matches the true MAE -- in particular, is better than several alternative methods.

The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.

Almost 50% depression patients face the risk of going into relapse. The risk increases to 80% after the second episode of depression. Although, depression detection from social media has attained considerable attention, depression relapse detection has remained largely unexplored due to the lack of curated datasets and the difficulty of distinguishing relapse and non-relapse users. In this work, we present ReDepress, the first clinically validated social media dataset focused on relapse, comprising 204 Reddit users annotated by mental health professionals. Unlike prior approaches, our framework draws on cognitive theories of depression, incorporating constructs such as attention bias, interpretation bias, memory bias and rumination into both annotation and modeling. Through statistical analyses and machine learning experiments, we demonstrate that cognitive markers significantly differentiate relapse and non-relapse groups, and that models enriched with these features achieve competitive performance, with transformer-based temporal models attaining an F1 of 0.86. Our findings validate psychological theories in real-world textual data and underscore the potential of cognitive-informed computational methods for early relapse detection, paving the way for scalable, low-cost interventions in mental healthcare.

We introduce a novel machine learning model for credit risk by combining tree-boosting with a latent spatio-temporal Gaussian process model accounting for frailty correlation. This allows for modeling non-linearities and interactions among predictor variables in a flexible data-driven manner and for accounting for spatio-temporal variation that is not explained by observable predictor variables. We also show how estimation and prediction can be done in a computationally efficient manner. In an application to a large U.S. mortgage credit risk data set, we find that both predictive default probabilities for individual loans and predictive loan portfolio loss distributions obtained with our novel approach are more accurate compared to conventional independent linear hazard models and also linear spatio-temporal models. Using interpretability tools for machine learning models, we find that the likely reasons for this outperformance are strong interaction and non-linear effects in the predictor variables and the presence of large spatio-temporal frailty effects.

Missing values, irregularly collected samples, and multi-resolution signals commonly occur in multivariate time series data, making predictive tasks difficult. These challenges are especially prevalent in the healthcare domain, where patients' vital signs and electronic records are collected at different frequencies and have occasionally missing information due to the imperfections in equipment or patient circumstances. Researchers have handled each of these issues differently, often handling missing data through mean value imputation and then using sequence models over the multivariate signals while ignoring the different resolution of signals. We propose a unified model named Multi-resolution Flexible Irregular Time series Network (Multi-FIT). The building block for Multi-FIT is the FIT network. The FIT network creates an informative dense representation at each time step using signal information such as last observed value, time difference since the last observed time stamp and overall mean for the signal. Vertical FIT (FIT-V) is a variant of FIT which also models the relationship between different temporal signals while creating the informative dense representations for the signal. The multi-FIT model uses multiple FIT networks for sets of signals with different resolutions, further facilitating the construction of flexible representations. Our model has three main contributions: a.) it does not impute values but rather creates informative representations to provide flexibility to the model for creating task-specific representations b.) it models the relationship between different signals in the form of support signals c.) it models different resolutions in parallel before merging them for the final prediction task. The FIT, FIT-V and Multi-FIT networks improve upon the state-of-the-art models for three predictive tasks, including the forecasting of patient survival.

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

Conventional surveillance systems for monitoring infectious diseases, such as influenza, face challenges due to shortage of skilled healthcare professionals, remoteness of communities and absence of communication infrastructures. Internet-based approaches for surveillance are appealing logistically as well as economically. Search engine queries and Twitter have been the primarily used data sources in such approaches. The aim of this study is to assess the predictive power of an alternative data source, Instagram. By using 317 weeks of publicly available data from Instagram, we trained several machine learning algorithms to both nowcast and forecast the number of official influenza-like illness incidents in Finland where population-wide official statistics about the weekly incidents are available. In addition to date and hashtag count features of online posts, we were able to utilize also the visual content of the posted images with the help of deep convolutional neural networks. Our best nowcasting model reached a mean absolute error of 11.33 incidents per week and a correlation coefficient of 0.963 on the test data. Forecasting models for predicting 1 week and 2 weeks ahead showed statistical significance as well by reaching correlation coefficients of 0.903 and 0.862, respectively. This study demonstrates how social media and in particular, digital photographs shared in them, can be a valuable source of information for the field of infodemiology.

This study presents a hybrid framework for predicting movie success. The framework integrates multi-task learning (MTL), GPT-based sentiment analysis, and Susceptible-Infected-Recovered (SIR) propagation modeling. The study examines limitations in existing approaches. It models static production attributes, information dissemination, and audience sentiment at the same time. The framework uses 5,840 films from 2004 to 2024 and approximate 300,000 user reviews. It shows predictive performance with classification accuracy of 0.964 and regression metrics of MAE 0.388. Ablation analysis indicates component interactions. Selective feature combinations perform better than the comprehensive model. This result questions assumptions about feature integration. The model shows virality patterns between successful and unsuccessful films. Innovations include epidemiological modeling for information diffusion, multidimensional sentiment features from GPT-based analysis, and a shared representation architecture that optimizes multiple success metrics. The framework provides applications in the film production lifecycle. It also contributes to understanding how audience engagement leads to commercial outcomes.

Accurately forecasting patient arrivals at Urgent Care Clinics (UCCs) and Emergency Departments (EDs) is important for effective resourcing and patient care. However, correctly estimating patient flows is not straightforward since it depends on many drivers. The predictability of patient arrivals has recently been further complicated by the COVID-19 pandemic conditions and the resulting lockdowns. This study investigates how a suite of novel quasi-real-time variables like Google search terms, pedestrian traffic, the prevailing incidence levels of influenza, as well as the COVID-19 Alert Level indicators can both generally improve the forecasting models of patient flows and effectively adapt the models to the unfolding disruptions of pandemic conditions. This research also uniquely contributes to the body of work in this domain by employing tools from the eXplainable AI field to investigate more deeply the internal mechanics of the models than has previously been done. The Voting ensemble-based method combining machine learning and statistical techniques was the most reliable in our experiments. Our study showed that the prevailing COVID-19 Alert Level feature together with Google search terms and pedestrian traffic were effective at producing generalisable forecasts. The implications of this study are that proxy variables can effectively augment standard autoregressive features to ensure accurate forecasting of patient flows. The experiments showed that the proposed features are potentially effective model inputs for preserving forecast accuracies in the event of future pandemic outbreaks.

Machine learning (ML) holds great potential for accurately forecasting treatment outcomes over time, which could ultimately enable the adoption of more individualized treatment strategies in many practical applications. However, a significant challenge that has been largely overlooked by the ML literature on this topic is the presence of informative sampling in observational data. When instances are observed irregularly over time, sampling times are typically not random, but rather informative -- depending on the instance's characteristics, past outcomes, and administered treatments. In this work, we formalize informative sampling as a covariate shift problem and show that it can prohibit accurate estimation of treatment outcomes if not properly accounted for. To overcome this challenge, we present a general framework for learning treatment outcomes in the presence of informative sampling using inverse intensity-weighting, and propose a novel method, TESAR-CDE, that instantiates this framework using Neural CDEs. Using a simulation environment based on a clinical use case, we demonstrate the effectiveness of our approach in learning under informative sampling.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Large Language Models (LLMs) hold great promise to revolutionize current clinical systems for their superior capacities on medical text processing tasks and medical licensing exams. Meanwhile, traditional ML models such as SVM and XGBoost have still been mainly adopted in clinical prediction tasks. An emerging question is Can LLMs beat traditional ML models in clinical prediction? Thus, we build a new benchmark ClinicalBench to comprehensively study the clinical predictive modeling capacities of both general-purpose and medical LLMs, and compare them with traditional ML models. ClinicalBench embraces three common clinical prediction tasks, two databases, 14 general-purpose LLMs, 8 medical LLMs, and 11 traditional ML models. Through extensive empirical investigation, we discover that both general-purpose and medical LLMs, even with different model scales, diverse prompting or fine-tuning strategies, still cannot beat traditional ML models in clinical prediction yet, shedding light on their potential deficiency in clinical reasoning and decision-making. We call for caution when practitioners adopt LLMs in clinical applications. ClinicalBench can be utilized to bridge the gap between LLMs' development for healthcare and real-world clinical practice.

Many court systems are overwhelmed all over the world, leading to huge backlogs of pending cases. Effective triage systems, like those in emergency rooms, could ensure proper prioritization of open cases, optimizing time and resource allocation in the court system. In this work, we introduce the Criticality Prediction dataset, a novel resource for evaluating case prioritization. Our dataset features a two-tier labeling system: (1) the binary LD-Label, identifying cases published as Leading Decisions (LD), and (2) the more granular Citation-Label, ranking cases by their citation frequency and recency, allowing for a more nuanced evaluation. Unlike existing approaches that rely on resource-intensive manual annotations, we algorithmically derive labels leading to a much larger dataset than otherwise possible. We evaluate several multilingual models, including both smaller fine-tuned models and large language models in a zero-shot setting. Our results show that the fine-tuned models consistently outperform their larger counterparts, thanks to our large training set. Our results highlight that for highly domain-specific tasks like ours, large training sets are still valuable.

Pretrained time series models have enabled inference-only forecasting systems that produce accurate predictions without task-specific training. However, existing approaches largely focus on univariate forecasting, limiting their applicability in real-world scenarios where multivariate data and covariates play a crucial role. We present Chronos-2, a pretrained model capable of handling univariate, multivariate, and covariate-informed forecasting tasks in a zero-shot manner. Chronos-2 employs a group attention mechanism that facilitates in-context learning (ICL) through efficient information sharing across multiple time series within a group, which may represent sets of related series, variates of a multivariate series, or targets and covariates in a forecasting task. These general capabilities are achieved through training on synthetic datasets that impose diverse multivariate structures on univariate series. Chronos-2 delivers state-of-the-art performance across three comprehensive benchmarks: fev-bench, GIFT-Eval, and Chronos Benchmark II. On fev-bench, which emphasizes multivariate and covariate-informed forecasting, Chronos-2's universal ICL capabilities lead to substantial improvements over existing models. On tasks involving covariates, it consistently outperforms baselines by a wide margin. Case studies in the energy and retail domains further highlight its practical advantages. The in-context learning capabilities of Chronos-2 establish it as a general-purpose forecasting model that can be used "as is" in real-world forecasting pipelines.

A significant body of recent research in the field of Learning Analytics has focused on leveraging machine learning approaches for predicting at-risk students in order to initiate timely interventions and thereby elevate retention and completion rates. The overarching feature of the majority of these research studies has been on the science of prediction only. The component of predictive analytics concerned with interpreting the internals of the models and explaining their predictions for individual cases to stakeholders has largely been neglected. Additionally, works that attempt to employ data-driven prescriptive analytics to automatically generate evidence-based remedial advice for at-risk learners are in their infancy. eXplainable AI is a field that has recently emerged providing cutting-edge tools which support transparent predictive analytics and techniques for generating tailored advice for at-risk students. This study proposes a novel framework that unifies both transparent machine learning as well as techniques for enabling prescriptive analytics, while integrating the latest advances in large language models. This work practically demonstrates the proposed framework using predictive models for identifying at-risk learners of programme non-completion. The study then further demonstrates how predictive modelling can be augmented with prescriptive analytics on two case studies in order to generate human-readable prescriptive feedback for those who are at risk using ChatGPT.

Machine learning models in modern mass-market applications are often updated over time. One of the foremost challenges faced is that, despite increasing overall performance, these updates may flip specific model predictions in unpredictable ways. In practice, researchers quantify the number of unstable predictions between models pre and post update -- i.e., predictive churn. In this paper, we study this effect through the lens of predictive multiplicity -- i.e., the prevalence of conflicting predictions over the set of near-optimal models (the Rashomon set). We show how traditional measures of predictive multiplicity can be used to examine expected churn over this set of prospective models -- i.e., the set of models that may be used to replace a baseline model in deployment. We present theoretical results on the expected churn between models within the Rashomon set from different perspectives. And we characterize expected churn over model updates via the Rashomon set, pairing our analysis with empirical results on real-world datasets -- showing how our approach can be used to better anticipate, reduce, and avoid churn in consumer-facing applications. Further, we show that our approach is useful even for models enhanced with uncertainty awareness.

The long-term effects of Postacute Sequelae of SARS-CoV-2, known as PASC, pose a significant challenge to healthcare systems worldwide. Accurate identification of progression events, such as hospitalization and reinfection, is essential for effective patient management and resource allocation. However, traditional models trained on structured data struggle to capture the nuanced progression of PASC. In this study, we introduce the first publicly available cohort of 18 PASC patients, with text time series features based on Large Language Model Llama-3.1-70B-Instruct and clinical risk annotated by clinical expert. We propose an Active Attention Network to predict the clinical risk and identify progression events related to the risk. By integrating human expertise with active learning, we aim to enhance clinical risk prediction accuracy and enable progression events identification with fewer number of annotation. The ultimate goal is to improves patient care and decision-making for SARS-CoV-2 patient.

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

Machine learning models are often used to inform real world risk assessment tasks: predicting consumer default risk, predicting whether a person suffers from a serious illness, or predicting a person's risk to appear in court. Given multiple models that perform almost equally well for a prediction task, to what extent do predictions vary across these models? If predictions are relatively consistent for similar models, then the standard approach of choosing the model that optimizes a penalized loss suffices. But what if predictions vary significantly for similar models? In machine learning, this is referred to as predictive multiplicity i.e. the prevalence of conflicting predictions assigned by near-optimal competing models. In this paper, we present a framework for measuring predictive multiplicity in probabilistic classification (predicting the probability of a positive outcome). We introduce measures that capture the variation in risk estimates over the set of competing models, and develop optimization-based methods to compute these measures efficiently and reliably for convex empirical risk minimization problems. We demonstrate the incidence and prevalence of predictive multiplicity in real-world tasks. Further, we provide insight into how predictive multiplicity arises by analyzing the relationship between predictive multiplicity and data set characteristics (outliers, separability, and majority-minority structure). Our results emphasize the need to report predictive multiplicity more widely.

Identifying patient cohorts is fundamental to numerous healthcare tasks, including clinical trial recruitment and retrospective studies. Current cohort retrieval methods in healthcare organizations rely on automated queries of structured data combined with manual curation, which are time-consuming, labor-intensive, and often yield low-quality results. Recent advancements in large language models (LLMs) and information retrieval (IR) offer promising avenues to revolutionize these systems. Major challenges include managing extensive eligibility criteria and handling the longitudinal nature of unstructured Electronic Medical Records (EMRs) while ensuring that the solution remains cost-effective for real-world application. This paper introduces a new task, Automatic Cohort Retrieval (ACR), and evaluates the performance of LLMs and commercial, domain-specific neuro-symbolic approaches. We provide a benchmark task, a query dataset, an EMR dataset, and an evaluation framework. Our findings underscore the necessity for efficient, high-quality ACR systems capable of longitudinal reasoning across extensive patient databases.

Transformers have significantly advanced the modeling of Electronic Health Records (EHR), yet their deployment in real-world healthcare is limited by several key challenges. Firstly, the quadratic computational cost and insufficient context length of these models pose significant obstacles for hospitals in processing the extensive medical histories typical in EHR data. Additionally, existing models employ separate finetuning for each clinical task, complicating maintenance in healthcare environments. Moreover, these models focus exclusively on either clinical prediction or EHR forecasting, lacking the flexibility to perform well across both. To overcome these limitations, we introduce EHRMamba, a robust foundation model built on the Mamba architecture. EHRMamba can process sequences up to four times longer than previous models due to its linear computational cost. We also introduce a novel approach to Multitask Prompted Finetuning (MTF) for EHR data, which enables EHRMamba to simultaneously learn multiple clinical tasks in a single finetuning phase, significantly enhancing deployment and cross-task generalization. Furthermore, our model leverages the HL7 FHIR data standard to simplify integration into existing hospital systems. Alongside EHRMamba, we open-source Odyssey, a toolkit designed to support the development and deployment of EHR foundation models, with an emphasis on data standardization and interpretability. Our evaluations on the MIMIC-IV dataset demonstrate that EHRMamba advances state-of-the-art performance across 6 major clinical tasks and excels in EHR forecasting, marking a significant leap forward in the field.

In medical applications, deep learning methods are built to automate diagnostic tasks. However, a clinically relevant question that practitioners usually face, is how to predict the future trajectory of a disease (prognosis). Current methods for such a problem often require domain knowledge, and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many forecasting problem from multimodal data. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner, we model a prognosis prediction problem with two transformer-based components that share information between each other. The first block in this model aims to analyze the imaging data, and the second block leverages the internal representations of the first one as inputs, also fusing them with auxiliary patient data. We show the effectiveness of our method in predicting the development of structural knee osteoarthritis changes over time. Our results show that the proposed method outperforms the state-of-the-art baselines in terms of various performance metrics. In addition, we empirically show that the existence of the multi-agent transformers with depths of 2 is sufficient to achieve good performances. Our code is publicly available at https://github.com/MIPT-Oulu/CLIMAT.

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p < 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

A unified foundation model for medical time series -- pretrained on open access and ethics board-approved medical corpora -- offers the potential to reduce annotation burdens, minimize model customization, and enable robust transfer across clinical institutions, modalities, and tasks, particularly in data-scarce or privacy-constrained environments. However, existing generalist time series foundation models struggle to handle medical time series data due to their inherent challenges, including irregular intervals, heterogeneous sampling rates, and frequent missing values. To address these challenges, we introduce MIRA, a unified foundation model specifically designed for medical time series forecasting. MIRA incorporates a Continuous-Time Rotary Positional Encoding that enables fine-grained modeling of variable time intervals, a frequency-specific mixture-of-experts layer that routes computation across latent frequency regimes to further promote temporal specialization, and a Continuous Dynamics Extrapolation Block based on Neural ODE that models the continuous trajectory of latent states, enabling accurate forecasting at arbitrary target timestamps. Pretrained on a large-scale and diverse medical corpus comprising over 454 billion time points collect from publicly available datasets, MIRA achieves reductions in forecasting errors by an average of 10% and 7% in out-of-distribution and in-distribution scenarios, respectively, when compared to other zero-shot and fine-tuned baselines. We also introduce a comprehensive benchmark spanning multiple downstream clinical tasks, establishing a foundation for future research in medical time series modeling.

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

In today's digital age, conspiracies and information campaigns can emerge rapidly and erode social and democratic cohesion. While recent deep learning approaches have made progress in modeling engagement through language and propagation models, they struggle with irregularly sampled data and early trajectory assessment. We present IC-Mamba, a novel state space model that forecasts social media engagement by modeling interval-censored data with integrated temporal embeddings. Our model excels at predicting engagement patterns within the crucial first 15-30 minutes of posting (RMSE 0.118-0.143), enabling rapid assessment of content reach. By incorporating interval-censored modeling into the state space framework, IC-Mamba captures fine-grained temporal dynamics of engagement growth, achieving a 4.72% improvement over state-of-the-art across multiple engagement metrics (likes, shares, comments, and emojis). Our experiments demonstrate IC-Mamba's effectiveness in forecasting both post-level dynamics and broader narrative patterns (F1 0.508-0.751 for narrative-level predictions). The model maintains strong predictive performance across extended time horizons, successfully forecasting opinion-level engagement up to 28 days ahead using observation windows of 3-10 days. These capabilities enable earlier identification of potentially problematic content, providing crucial lead time for designing and implementing countermeasures. Code is available at: https://github.com/ltian678/ic-mamba. An interactive dashboard demonstrating our results is available at: https://ic-mamba.behavioral-ds.science.

We present a self-supervised, time-to-event (TTE) foundation model called MOTOR (Many Outcome Time Oriented Representations) which is pretrained on timestamped sequences of events in electronic health records (EHR) and health insurance claims. TTE models are used for estimating the probability distribution of the time until a specific event occurs, which is an important task in medical settings. TTE models provide many advantages over classification using fixed time horizons, including naturally handling censored observations, but are challenging to train with limited labeled data. MOTOR addresses this challenge by pretraining on up to 55M patient records (9B clinical events). We evaluate MOTOR's transfer learning performance on 19 tasks, across 3 patient databases (a private EHR system, MIMIC-IV, and Merative claims data). Task-specific models adapted from MOTOR improve time-dependent C statistics by 4.6% over state-of-the-art, improve label efficiency by up to 95% ,and are more robust to temporal distributional shifts. We further evaluate cross-site portability by adapting our MOTOR foundation model for six prediction tasks on the MIMIC-IV dataset, where it outperforms all baselines. MOTOR is the first foundation model for medical TTE predictions and we release a 143M parameter pretrained model for research use at [redacted URL].

Self-supervision may boost model performance in downstream tasks. However, there is no principled way of selecting the self-supervised objectives that yield the most adaptable models. Here, we study this problem on daily time-series data generated from wearable sensors used to detect onset of influenza-like illness (ILI). We first show that using self-supervised learning to predict next-day time-series values allows us to learn rich representations which can be adapted to perform accurate ILI prediction. Second, we perform an empirical analysis of three different self-supervised objectives to assess their adaptability to ILI prediction. Our results show that predicting the next day's resting heart rate or time-in-bed during sleep provides better representations for ILI prediction. These findings add to previous work demonstrating the practical application of self-supervised learning from activity data to improve health predictions.

Databases of electronic health records (EHRs) are increasingly used to inform clinical decisions. Machine learning methods can find patterns in EHRs that are predictive of future adverse outcomes. However, statistical models may be built upon patterns of health-seeking behavior that vary across patient subpopulations, leading to poor predictive performance when training on one patient population and predicting on another. This note proposes two tests to better measure and understand model generalization. We use these tests to compare models derived from two data sources: (i) historical medical records, and (ii) electrocardiogram (EKG) waveforms. In a predictive task, we show that EKG-based models can be more stable than EHR-based models across different patient populations.

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.

Background: This study aimed to evaluate and compare the performance of classical machine learning models (CMLs) and large language models (LLMs) in predicting mortality associated with COVID-19 by utilizing a high-dimensional tabular dataset. Materials and Methods: We analyzed data from 9,134 COVID-19 patients collected across four hospitals. Seven CML models, including XGBoost and random forest (RF), were trained and evaluated. The structured data was converted into text for zero-shot classification by eight LLMs, including GPT-4 and Mistral-7b. Additionally, Mistral-7b was fine-tuned using the QLoRA approach to enhance its predictive capabilities. Results: Among the CML models, XGBoost and RF achieved the highest accuracy, with F1 scores of 0.87 for internal validation and 0.83 for external validation. In the LLM category, GPT-4 was the top performer with an F1 score of 0.43. Fine-tuning Mistral-7b significantly improved its recall from 1% to 79%, resulting in an F1 score of 0.74, which was stable during external validation. Conclusion: While LLMs show moderate performance in zero-shot classification, fine-tuning can significantly enhance their effectiveness, potentially aligning them closer to CML models. However, CMLs still outperform LLMs in high-dimensional tabular data tasks.

Accurately predicting the criticalness of ICU patients (such as in-ICU mortality risk) is vital for early intervention in critical care. However, conventional models often treat each patient in isolation and struggle to exploit the relational structure in Electronic Health Records (EHR). We propose a Similarity-Based Self-Construct Graph Model (SBSCGM) that dynamically builds a patient similarity graph from multi-modal EHR data, and a HybridGraphMedGNN architecture that operates on this graph to predict patient mortality and a continuous criticalness score. SBSCGM uses a hybrid similarity measure (combining feature-based and structural similarities) to connect patients with analogous clinical profiles in real-time. The HybridGraphMedGNN integrates Graph Convolutional Network (GCN), GraphSAGE, and Graph Attention Network (GAT) layers to learn robust patient representations, leveraging both local and global graph patterns. In experiments on 6,000 ICU stays from the MIMIC-III dataset, our model achieves state-of-the-art performance (AUC-ROC 0.94) outperforming baseline classifiers and single-type GNN models. We also demonstrate improved precision/recall and show that the attention mechanism provides interpretable insights into model predictions. Our framework offers a scalable and interpretable solution for critical care risk prediction, with potential to support clinicians in real-world ICU deployment.

Sepsis requires urgent diagnosis, but research is predominantly focused on Western datasets. In this study, we perform a comparative analysis of two ensemble learning methods, LightGBM and XGBoost, using the public eICU-CRD dataset and a private South Korean St. Mary's Hospital's dataset. Our analysis reveals the effectiveness of these methods in addressing healthcare data imbalance and enhancing sepsis detection. Specifically, LightGBM shows a slight edge in computational efficiency and scalability. The study paves the way for the broader application of machine learning in critical care, thereby expanding the reach of predictive analytics in healthcare globally.

Given the clinical notes written in electronic health records (EHRs), it is challenging to predict the diagnostic codes which is formulated as a multi-label classification task. The large set of labels, the hierarchical dependency, and the imbalanced data make this prediction task extremely hard. Most existing work built a binary prediction for each label independently, ignoring the dependencies between labels. To address this problem, we propose a two-stage framework to improve automatic ICD coding by capturing the label correlation. Specifically, we train a label set distribution estimator to rescore the probability of each label set candidate generated by a base predictor. This paper is the first attempt at learning the label set distribution as a reranking module for medical code prediction. In the experiments, our proposed framework is able to improve upon best-performing predictors on the benchmark MIMIC datasets. The source code of this project is available at https://github.com/MiuLab/ICD-Correlation.

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

The impact of person-job fit on job satisfaction and performance is widely acknowledged, which highlights the importance of providing workers with next steps at the right time in their career. This task of predicting the next step in a career is known as career path prediction, and has diverse applications such as turnover prevention and internal job mobility. Existing methods to career path prediction rely on large amounts of private career history data to model the interactions between job titles and companies. We propose leveraging the unexplored textual descriptions that are part of work experience sections in resumes. We introduce a structured dataset of 2,164 anonymized career histories, annotated with ESCO occupation labels. Based on this dataset, we present a novel representation learning approach, CareerBERT, specifically designed for work history data. We develop a skill-based model and a text-based model for career path prediction, which achieve 35.24% and 39.61% recall@10 respectively on our dataset. Finally, we show that both approaches are complementary as a hybrid approach achieves the strongest result with 43.01% recall@10.

Time series foundation models excel in zero-shot forecasting, handling diverse tasks without explicit training. However, the advancement of these models has been hindered by the lack of comprehensive benchmarks. To address this gap, we introduce the General Time Series Forecasting Model Evaluation, GIFT-Eval, a pioneering benchmark aimed at promoting evaluation across diverse datasets. GIFT-Eval encompasses 28 datasets over 144,000 time series and 177 million data points, spanning seven domains, 10 frequencies, multivariate inputs, and prediction lengths ranging from short to long-term forecasts. To facilitate the effective pretraining and evaluation of foundation models, we also provide a non-leaking pretraining dataset containing approximately 230 billion data points. Additionally, we provide a comprehensive analysis of 17 baselines, which includes statistical models, deep learning models, and foundation models. We discuss each model in the context of various benchmark characteristics and offer a qualitative analysis that spans both deep learning and foundation models. We believe the insights from this analysis, along with access to this new standard zero-shot time series forecasting benchmark, will guide future developments in time series foundation models. The codebase, datasets, and a leaderboard showing all the results in detail will be available soon.

Surgical future prediction, driven by real-time AI analysis of surgical video, is critical for operating room safety and efficiency. It provides actionable insights into upcoming events, their timing, and risks-enabling better resource allocation, timely instrument readiness, and early warnings for complications (e.g., bleeding, bile duct injury). Despite this need, current surgical AI research focuses on understanding what is happening rather than predicting future events. Existing methods target specific tasks in isolation, lacking unified approaches that span both short-term (action triplets, events) and long-term horizons (remaining surgery duration, phase transitions). These methods rely on coarse-grained supervision while fine-grained surgical action triplets and steps remain underexplored. Furthermore, methods based only on future feature prediction struggle to generalize across different surgical contexts and procedures. We address these limits by reframing surgical future prediction as state-change learning. Rather than forecasting raw observations, our approach classifies state transitions between current and future timesteps. We introduce SurgFUTR, implementing this through a teacher-student architecture. Video clips are compressed into state representations via Sinkhorn-Knopp clustering; the teacher network learns from both current and future clips, while the student network predicts future states from current videos alone, guided by our Action Dynamics (ActDyn) module. We establish SFPBench with five prediction tasks spanning short-term (triplets, events) and long-term (remaining surgery duration, phase and step transitions) horizons. Experiments across four datasets and three procedures show consistent improvements. Cross-procedure transfer validates generalizability.

The rapid advancements in computing dramatically increase the scale and cost of training Large Language Models (LLMs). Accurately predicting downstream task performance prior to model training is crucial for efficient resource allocation, yet remains challenging due to two primary constraints: (1) the "emergence phenomenon", wherein downstream performance metrics become meaningful only after extensive training, which limits the ability to use smaller models for prediction; (2) Uneven task difficulty distributions and the absence of consistent scaling laws, resulting in substantial metric variability. Existing performance prediction methods suffer from limited accuracy and reliability, thereby impeding the assessment of potential LLM capabilities. To address these challenges, we propose a Clustering-On-Difficulty (COD) downstream performance prediction framework. COD first constructs a predictable support subset by clustering tasks based on difficulty features, strategically excluding non-emergent and non-scalable clusters. The scores on the selected subset serve as effective intermediate predictors of downstream performance on the full evaluation set. With theoretical support, we derive a mapping function that transforms performance metrics from the predictable subset to the full evaluation set, thereby ensuring accurate extrapolation of LLM downstream performance. The proposed method has been applied to predict performance scaling for a 70B LLM, providing actionable insights for training resource allocation and assisting in monitoring the training process. Notably, COD achieves remarkable predictive accuracy on the 70B LLM by leveraging an ensemble of small models, demonstrating an absolute mean deviation of 1.36% across eight important LLM evaluation benchmarks.

User churn, characterized by customers ending their relationship with a business, has profound economic consequences across various Business-to-Customer scenarios. For numerous system-to-user actions, such as promotional discounts and retention campaigns, predicting potential churners stands as a primary objective. In volatile sectors like fantasy sports, unpredictable factors such as international sports events can influence even regular spending habits. Consequently, while transaction history and user-product interaction are valuable in predicting churn, they demand deep domain knowledge and intricate feature engineering. Additionally, feature development for churn prediction systems can be resource-intensive, particularly in production settings serving 200m+ users, where inference pipelines largely focus on feature engineering. This paper conducts an exhaustive study on predicting user churn using historical data. We aim to create a model forecasting customer churn likelihood, facilitating businesses in comprehending attrition trends and formulating effective retention plans. Our approach treats churn prediction as multivariate time series classification, demonstrating that combining user activity and deep neural networks yields remarkable results for churn prediction in complex business-to-customer contexts.

Risk scores are simple classification models that let users make quick risk predictions by adding and subtracting a few small numbers. These models are widely used in medicine and criminal justice, but are difficult to learn from data because they need to be calibrated, sparse, use small integer coefficients, and obey application-specific operational constraints. In this paper, we present a new machine learning approach to learn risk scores. We formulate the risk score problem as a mixed integer nonlinear program, and present a cutting plane algorithm for non-convex settings to efficiently recover its optimal solution. We improve our algorithm with specialized techniques to generate feasible solutions, narrow the optimality gap, and reduce data-related computation. Our approach can fit risk scores in a way that scales linearly in the number of samples, provides a certificate of optimality, and obeys real-world constraints without parameter tuning or post-processing. We benchmark the performance benefits of this approach through an extensive set of numerical experiments, comparing to risk scores built using heuristic approaches. We also discuss its practical benefits through a real-world application where we build a customized risk score for ICU seizure prediction in collaboration with the Massachusetts General Hospital.

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

Clinical notes contain rich data, which is unexploited in predictive modeling compared to structured data. In this work, we developed a new text representation Clinical XLNet for clinical notes which also leverages the temporal information of the sequence of the notes. We evaluated our models on prolonged mechanical ventilation prediction problem and our experiments demonstrated that Clinical XLNet outperforms the best baselines consistently.

Summarization of clinical narratives is a long-standing research problem. Here, we introduce the task of hospital-course summarization. Given the documentation authored throughout a patient's hospitalization, generate a paragraph that tells the story of the patient admission. We construct an English, text-to-text dataset of 109,000 hospitalizations (2M source notes) and their corresponding summary proxy: the clinician-authored "Brief Hospital Course" paragraph written as part of a discharge note. Exploratory analyses reveal that the BHC paragraphs are highly abstractive with some long extracted fragments; are concise yet comprehensive; differ in style and content organization from the source notes; exhibit minimal lexical cohesion; and represent silver-standard references. Our analysis identifies multiple implications for modeling this complex, multi-document summarization task.

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Surgical site infection (SSI) is one of the most common and costly healthcare-associated infections and and surgical wound care remains a significant clinical challenge in preventing SSIs and improving patient outcomes. While recent studies have explored the use of deep learning for preliminary surgical wound screening, progress has been hindered by concerns over data privacy and the high costs associated with expert annotation. Currently, no publicly available dataset or benchmark encompasses various types of surgical wounds, resulting in the absence of an open-source Surgical-Wound screening tool. To address this gap: (1) we present SurgWound, the first open-source dataset featuring a diverse array of surgical wound types. It contains 697 surgical wound images annotated by 3 professional surgeons with eight fine-grained clinical attributes. (2) Based on SurgWound, we introduce the first benchmark for surgical wound diagnosis, which includes visual question answering (VQA) and report generation tasks to comprehensively evaluate model performance. (3) Furthermore, we propose a three-stage learning framework, WoundQwen, for surgical wound diagnosis. In the first stage, we employ five independent MLLMs to accurately predict specific surgical wound characteristics. In the second stage, these predictions serve as additional knowledge inputs to two MLLMs responsible for diagnosing outcomes, which assess infection risk and guide subsequent interventions. In the third stage, we train a MLLM that integrates the diagnostic results from the previous two stages to produce a comprehensive report. This three-stage framework can analyze detailed surgical wound characteristics and provide subsequent instructions to patients based on surgical images, paving the way for personalized wound care, timely intervention, and improved patient outcomes.

Our motivation is to shed light the performance of the widely popular "R-Learner." Like many other methods for estimating conditional average treatment effects (CATEs), R-Learning can be expressed as a weighted pseudo-outcome regression (POR). Previous comparisons of POR techniques have paid careful attention to the choice of pseudo-outcome transformation. However, we argue that the dominant driver of performance is actually the choice of weights. Specifically, we argue that R-Learning implicitly performs an inverse-variance weighted form of POR. These weights stabilize the regression and allow for convenient simplifications of bias terms.

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Objective: Using natural language processing (NLP) to find sentences that state treatment plans in a clinical note, would automate plan extraction and would further enable their use in tools that help providers and care managers. However, as in the most NLP tasks on clinical text, creating gold standard to train and test NLP models is tedious and expensive. Fortuitously, sometimes but not always clinical notes contain sections with a heading that identifies the section as a plan. Leveraging contents of such labeled sections as a noisy training data, we assessed accuracy of NLP models trained with the data. Methods: We used common variations of plan headings and rule-based heuristics to find plan sections with headings in clinical notes, and we extracted sentences from them and formed a noisy training data of plan sentences. We trained Support Vector Machine (SVM) and Convolutional Neural Network (CNN) models with the data. We measured accuracy of the trained models on the noisy dataset using ten-fold cross validation and separately on a set-aside manually annotated dataset. Results: About 13% of 117,730 clinical notes contained treatment plans sections with recognizable headings in the 1001 longitudinal patient records that were obtained from Cleveland Clinic under an IRB approval. We were able to extract and create a noisy training data of 13,492 plan sentences from the clinical notes. CNN achieved best F measures, 0.91 and 0.97 in the cross-validation and set-aside evaluation experiments respectively. SVM slightly underperformed with F measures of 0.89 and 0.96 in the same experiments. Conclusion: Our study showed that the training supervised learning models using noisy plan sentences was effective in identifying them in all clinical notes. More broadly, sections with informal headings in clinical notes can be a good source for generating effective training data.

Customer Lifetime Value (CLTV) prediction is a critical task in business applications. Accurately predicting CLTV is challenging in real-world business scenarios, as the distribution of CLTV is complex and mutable. Firstly, there is a large number of users without any consumption consisting of a long-tailed part that is too complex to fit. Secondly, the small set of high-value users spent orders of magnitude more than a typical user leading to a wide range of the CLTV distribution which is hard to capture in a single distribution. Existing approaches for CLTV estimation either assume a prior probability distribution and fit a single group of distribution-related parameters for all samples, or directly learn from the posterior distribution with manually predefined buckets in a heuristic manner. However, all these methods fail to handle complex and mutable distributions. In this paper, we propose a novel optimal distribution selection model OptDist for CLTV prediction, which utilizes an adaptive optimal sub-distribution selection mechanism to improve the accuracy of complex distribution modeling. Specifically, OptDist trains several candidate sub-distribution networks in the distribution learning module (DLM) for modeling the probability distribution of CLTV. Then, a distribution selection module (DSM) is proposed to select the sub-distribution for each sample, thus making the selection automatically and adaptively. Besides, we design an alignment mechanism that connects both modules, which effectively guides the optimization. We conduct extensive experiments on both two public and one private dataset to verify that OptDist outperforms state-of-the-art baselines. Furthermore, OptDist has been deployed on a large-scale financial platform for customer acquisition marketing campaigns and the online experiments also demonstrate the effectiveness of OptDist.

Many empirical studies of labor market questions rely on estimating relatively simple predictive models using small, carefully constructed longitudinal survey datasets based on hand-engineered features. Large Language Models (LLMs), trained on massive datasets, encode vast quantities of world knowledge and can be used for the next job prediction problem. However, while an off-the-shelf LLM produces plausible career trajectories when prompted, the probability with which an LLM predicts a particular job transition conditional on career history will not, in general, align with the true conditional probability in a given population. Recently, Vafa et al. (2024) introduced a transformer-based "foundation model", CAREER, trained using a large, unrepresentative resume dataset, that predicts transitions between jobs; it further demonstrated how transfer learning techniques can be used to leverage the foundation model to build better predictive models of both transitions and wages that reflect conditional transition probabilities found in nationally representative survey datasets. This paper considers an alternative where the fine-tuning of the CAREER foundation model is replaced by fine-tuning LLMs. For the task of next job prediction, we demonstrate that models trained with our approach outperform several alternatives in terms of predictive performance on the survey data, including traditional econometric models, CAREER, and LLMs with in-context learning, even though the LLM can in principle predict job titles that are not allowed in the survey data. Further, we show that our fine-tuned LLM-based models' predictions are more representative of the career trajectories of various workforce subpopulations than off-the-shelf LLM models and CAREER. We conduct experiments and analyses that highlight the sources of the gains in the performance of our models for representative predictions.

Social and collaborative platforms emit multivariate time-series traces in which early interactions-such as views, likes, or downloads-are followed, sometimes months or years later, by higher impact like citations, sales, or reviews. We formalize this setting as Lead-Lag Forecasting (LLF): given an early usage channel (the lead), predict a correlated but temporally shifted outcome channel (the lag). Despite the ubiquity of such patterns, LLF has not been treated as a unified forecasting problem within the time-series community, largely due to the absence of standardized datasets. To anchor research in LLF, here we present two high-volume benchmark datasets-arXiv (accesses -> citations of 2.3M papers) and GitHub (pushes/stars -> forks of 3M repositories)-and outline additional domains with analogous lead-lag dynamics, including Wikipedia (page views -> edits), Spotify (streams -> concert attendance), e-commerce (click-throughs -> purchases), and LinkedIn profile (views -> messages). Our datasets provide ideal testbeds for lead-lag forecasting, by capturing long-horizon dynamics across years, spanning the full spectrum of outcomes, and avoiding survivorship bias in sampling. We documented all technical details of data curation and cleaning, verified the presence of lead-lag dynamics through statistical and classification tests, and benchmarked parametric and non-parametric baselines for regression. Our study establishes LLF as a novel forecasting paradigm and lays an empirical foundation for its systematic exploration in social and usage data. Our data portal with downloads and documentation is available at https://lead-lag-forecasting.github.io/.

A ventilator simulation system can make mechanical ventilation easier and more effective. As a result, predicting a patient's ventilator pressure is essential when designing a simulation ventilator. We suggested a hybrid deep learning-based approach to forecast required ventilator pressure for patients. This system is made up of Bi-LSTM and Bi-GRU networks. The SELU activation function was used in our proposed model. MAE and MSE were used to examine the accuracy of the proposed model so that our proposed methodology can be applied to real-world problems. The model performed well against test data and created far too few losses. Major parts of our research were data collection, data analysis, data cleaning, building hybrid Bi-LSTM and Bi-GRU model, training the model, model evaluation, and result analysis. We compared the results of our research with some contemporary works, and our proposed model performed better than those models.

Recent advances in large language models have led to renewed interest in natural language processing in healthcare using the free text of clinical notes. One distinguishing characteristic of clinical notes is their long time span over multiple long documents. The unique structure of clinical notes creates a new design choice: when the context length for a language model predictor is limited, which part of clinical notes should we choose as the input? Existing studies either choose the inputs with domain knowledge or simply truncate them. We propose a framework to analyze the sections with high predictive power. Using MIMIC-III, we show that: 1) predictive power distribution is different between nursing notes and discharge notes and 2) combining different types of notes could improve performance when the context length is large. Our findings suggest that a carefully selected sampling function could enable more efficient information extraction from clinical notes.

Forecasting multiple future events within a given time horizon is essential for applications in finance, retail, social networks, and healthcare. Marked Temporal Point Processes (MTPP) provide a principled framework to model both the timing and labels of events. However, most existing research focuses on predicting only the next event, leaving long-horizon forecasting largely underexplored. To address this gap, we introduce HoTPP, the first benchmark specifically designed to rigorously evaluate long-horizon predictions. We identify shortcomings in widely used evaluation metrics, propose a theoretically grounded T-mAP metric, present strong statistical baselines, and offer efficient implementations of popular models. Our empirical results demonstrate that modern MTPP approaches often underperform simple statistical baselines. Furthermore, we analyze the diversity of predicted sequences and find that most methods exhibit mode collapse. Finally, we analyze the impact of autoregression and intensity-based losses on prediction quality, and outline promising directions for future research. The HoTPP source code, hyperparameters, and full evaluation results are available at GitHub.

Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n = 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

This paper presents a comprehensive study on resume classification to reduce the time and labor needed to screen an overwhelming number of applications significantly, while improving the selection of suitable candidates. A total of 6,492 resumes are extracted from 24,933 job applications for 252 positions designated into four levels of experience for Clinical Research Coordinators (CRC). Each resume is manually annotated to its most appropriate CRC position by experts through several rounds of triple annotation to establish guidelines. As a result, a high Kappa score of 61% is achieved for inter-annotator agreement. Given this dataset, novel transformer-based classification models are developed for two tasks: the first task takes a resume and classifies it to a CRC level (T1), and the second task takes both a resume and a job description to apply and predicts if the application is suited to the job T2. Our best models using section encoding and multi-head attention decoding give results of 73.3% to T1 and 79.2% to T2. Our analysis shows that the prediction errors are mostly made among adjacent CRC levels, which are hard for even experts to distinguish, implying the practical value of our models in real HR platforms.

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

Estimating the impact of continuous treatment variables (e.g., dosage amount) on binary outcomes presents significant challenges in modeling and estimation because many existing approaches make strong assumptions that do not hold for certain continuous treatment variables. For instance, traditional logistic regression makes strong linearity assumptions that do not hold for continuous treatment variables like time of initiation. In this work, we propose a semiparametric regression framework that decomposes effects into two interpretable components: a prognostic score that captures baseline outcome risk based on a combination of clinical, genetic, and sociodemographic features, and a treatment-interaction score that flexibly models the optimal treatment level via a nonparametric link function. By connecting these two parametric scores with Nadaraya-Watson regression, our approach is both interpretable and flexible. The potential of our approach is demonstrated through numerical simulations that show empirical estimation convergence. We conclude by applying our approach to a real-world case study using the International Warfarin Pharmacogenomics Consortium (IWPC) dataset to show our approach's clinical utility by deriving personalized warfarin dosing recommendations that integrate both genetic and clinical data, providing insights towards enhancing patient safety and therapeutic efficacy in anticoagulation therapy.

LLMs have emerged as powerful tools for interpreting multimodal data. In medicine, they hold particular promise for synthesizing large volumes of clinical information into actionable insights and digital health applications. Yet, a major limitation remains their inability to handle time series. To overcome this gap, we present OpenTSLM, a family of Time Series Language Models (TSLMs) created by integrating time series as a native modality to pretrained LLMs, enabling reasoning over multiple time series of any length. We investigate two architectures for OpenTSLM. The first, OpenTSLM-SoftPrompt, models time series implicitly by concatenating learnable time series tokens with text tokens via soft prompting. Although parameter-efficient, we hypothesize that explicit time series modeling scales better and outperforms implicit approaches. We thus introduce OpenTSLM-Flamingo, which integrates time series with text via cross-attention. We benchmark both variants against baselines that treat time series as text tokens or plots, across a suite of text-time-series Chain-of-Thought (CoT) reasoning tasks. We introduce three datasets: HAR-CoT, Sleep-CoT, and ECG-QA-CoT. Across all, OpenTSLM models outperform baselines, reaching 69.9 F1 in sleep staging and 65.4 in HAR, compared to 9.05 and 52.2 for finetuned text-only models. Notably, even 1B-parameter OpenTSLM models surpass GPT-4o (15.47 and 2.95). OpenTSLM-Flamingo matches OpenTSLM-SoftPrompt in performance and outperforms on longer sequences, while maintaining stable memory requirements. By contrast, SoftPrompt grows exponentially in memory with sequence length, requiring around 110 GB compared to 40 GB VRAM when training on ECG-QA with LLaMA-3B. Expert reviews by clinicians find strong reasoning capabilities exhibited by OpenTSLMs on ECG-QA. To facilitate further research, we provide all code, datasets, and models open-source.

Watch time prediction (WTP) has emerged as a pivotal task in short video recommendation systems, designed to quantify user engagement through continuous interaction modeling. Predicting users' watch times on videos often encounters fundamental challenges, including wide value ranges and imbalanced data distributions, which can lead to significant estimation bias when directly applying regression techniques. Recent studies have attempted to address these issues by converting the continuous watch time estimation into an ordinal regression task. While these methods demonstrate partial effectiveness, they exhibit notable limitations: (1) the discretization process frequently relies on bucket partitioning, inherently reducing prediction flexibility and accuracy and (2) the interdependencies among different partition intervals remain underutilized, missing opportunities for effective error correction. Inspired by language modeling paradigms, we propose a novel Generative Regression (GR) framework that reformulates WTP as a sequence generation task. Our approach employs structural discretization to enable nearly lossless value reconstruction while maintaining prediction fidelity. Through carefully designed vocabulary construction and label encoding schemes, each watch time is bijectively mapped to a token sequence. To mitigate the training-inference discrepancy caused by teacher-forcing, we introduce a curriculum learning with embedding mixup strategy that gradually transitions from guided to free-generation modes. We evaluate our method against state-of-the-art approaches on two public datasets and one industrial dataset. We also perform online A/B testing on the Kuaishou App to confirm the real-world effectiveness. The results conclusively show that GR outperforms existing techniques significantly.

The absence of transparency and explainability hinders the clinical adoption of Machine learning (ML) algorithms. Although various methods of explainable artificial intelligence (XAI) have been suggested, there is a lack of literature that delves into their practicality and assesses them based on criteria that could foster trust in clinical environments. To address this gap this study evaluates two popular XAI methods used for explaining predictive models in the healthcare context in terms of whether they (i) generate domain-appropriate representation, i.e. coherent with respect to the application task, (ii) impact clinical workflow and (iii) are consistent. To that end, explanations generated at the cohort and patient levels were analysed. The paper reports the first benchmarking of the XAI methods applied to risk prediction models obtained by evaluating the concordance between generated explanations and the trigger of a future clinical deterioration episode recorded by the data collection system. We carried out an analysis using two Electronic Medical Records (EMR) datasets sourced from Australian major hospitals. The findings underscore the limitations of state-of-the-art XAI methods in the clinical context and their potential benefits. We discuss these limitations and contribute to the theoretical development of trustworthy XAI solutions where clinical decision support guides the choice of intervention by suggesting the pattern or drivers for clinical deterioration in the future.

Predictive coding networks are neuroscience-inspired models with roots in both Bayesian statistics and neuroscience. Training such models, however, is quite inefficient and unstable. In this work, we show how by simply changing the temporal scheduling of the update rule for the synaptic weights leads to an algorithm that is much more efficient and stable than the original one, and has theoretical guarantees in terms of convergence. The proposed algorithm, that we call incremental predictive coding (iPC) is also more biologically plausible than the original one, as it it fully automatic. In an extensive set of experiments, we show that iPC constantly performs better than the original formulation on a large number of benchmarks for image classification, as well as for the training of both conditional and masked language models, in terms of test accuracy, efficiency, and convergence with respect to a large set of hyperparameters.

To build a French national electronic injury surveillance system based on emergency room visits, we aim to develop a coding system to classify their causes from clinical notes in free-text. Supervised learning techniques have shown good results in this area but require a large amount of expert annotated dataset which is time consuming and costly to obtain. We hypothesize that the Natural Language Processing Transformer model incorporating a generative self-supervised pre-training step can significantly reduce the required number of annotated samples for supervised fine-tuning. In this preliminary study, we test our hypothesis in the simplified problem of predicting whether a visit is the consequence of a traumatic event or not from free-text clinical notes. Using fully re-trained GPT-2 models (without OpenAI pre-trained weights), we assess the gain of applying a self-supervised pre-training phase with unlabeled notes prior to the supervised learning task. Results show that the number of data required to achieve a ginve level of performance (AUC>0.95) was reduced by a factor of 10 when applying pre-training. Namely, for 16 times more data, the fully-supervised model achieved an improvement <1% in AUC. To conclude, it is possible to adapt a multi-purpose neural language model such as the GPT-2 to create a powerful tool for classification of free-text notes with only a small number of labeled samples.

We introduce NeuralProphet, a successor to Facebook Prophet, which set an industry standard for explainable, scalable, and user-friendly forecasting frameworks. With the proliferation of time series data, explainable forecasting remains a challenging task for business and operational decision making. Hybrid solutions are needed to bridge the gap between interpretable classical methods and scalable deep learning models. We view Prophet as a precursor to such a solution. However, Prophet lacks local context, which is essential for forecasting the near-term future and is challenging to extend due to its Stan backend. NeuralProphet is a hybrid forecasting framework based on PyTorch and trained with standard deep learning methods, making it easy for developers to extend the framework. Local context is introduced with auto-regression and covariate modules, which can be configured as classical linear regression or as Neural Networks. Otherwise, NeuralProphet retains the design philosophy of Prophet and provides the same basic model components. Our results demonstrate that NeuralProphet produces interpretable forecast components of equivalent or superior quality to Prophet on a set of generated time series. NeuralProphet outperforms Prophet on a diverse collection of real-world datasets. For short to medium-term forecasts, NeuralProphet improves forecast accuracy by 55 to 92 percent.

Missing values are common in real-world time series, and multivariate time series forecasting with missing values (MTSF-M) has become a crucial area of research for ensuring reliable predictions. To address the challenge of missing data, current approaches have developed an imputation-then-prediction framework that uses imputation modules to fill in missing values, followed by forecasting on the imputed data. However, this framework overlooks a critical issue: there is no ground truth for the missing values, making the imputation process susceptible to errors that can degrade prediction accuracy. In this paper, we conduct a systematic empirical study and reveal that imputation without direct supervision can corrupt the underlying data distribution and actively degrade prediction accuracy. To address this, we propose a paradigm shift that moves away from imputation and directly predicts from the partially observed time series. We introduce Consistency-Regularized Information Bottleneck (CRIB), a novel framework built on the Information Bottleneck principle. CRIB combines a unified-variate attention mechanism with a consistency regularization scheme to learn robust representations that filter out noise introduced by missing values while preserving essential predictive signals. Comprehensive experiments on four real-world datasets demonstrate the effectiveness of CRIB, which predicts accurately even under high missing rates. Our code is available in https://github.com/Muyiiiii/CRIB.

Many existing evaluation benchmarks for Large Language Models (LLMs) quickly become outdated due to the emergence of new models and training data. These benchmarks also fall short in assessing how LLM performance changes over time, as they consist of static questions without a temporal dimension. To address these limitations, we propose using future event prediction as a continuous evaluation method to assess LLMs' temporal generalization and forecasting abilities. Our benchmark, Daily Oracle, automatically generates question-answer (QA) pairs from daily news, challenging LLMs to predict "future" event outcomes. Our findings reveal that as pre-training data becomes outdated, LLM performance degrades over time. While Retrieval Augmented Generation (RAG) has the potential to enhance prediction accuracy, the performance degradation pattern persists, highlighting the need for continuous model updates.

Time series research has gathered lots of interests in the last decade, especially for Time Series Classification (TSC) and Time Series Forecasting (TSF). Research in TSC has greatly benefited from the University of California Riverside and University of East Anglia (UCR/UEA) Time Series Archives. On the other hand, the advancement in Time Series Forecasting relies on time series forecasting competitions such as the Makridakis competitions, NN3 and NN5 Neural Network competitions, and a few Kaggle competitions. Each year, thousands of papers proposing new algorithms for TSC and TSF have utilized these benchmarking archives. These algorithms are designed for these specific problems, but may not be useful for tasks such as predicting the heart rate of a person using photoplethysmogram (PPG) and accelerometer data. We refer to this problem as Time Series Extrinsic Regression (TSER), where we are interested in a more general methodology of predicting a single continuous value, from univariate or multivariate time series. This prediction can be from the same time series or not directly related to the predictor time series and does not necessarily need to be a future value or depend heavily on recent values. To the best of our knowledge, research into TSER has received much less attention in the time series research community and there are no models developed for general time series extrinsic regression problems. Most models are developed for a specific problem. Therefore, we aim to motivate and support the research into TSER by introducing the first TSER benchmarking archive. This archive contains 19 datasets from different domains, with varying number of dimensions, unequal length dimensions, and missing values. In this paper, we introduce the datasets in this archive and did an initial benchmark on existing models.

Deep Learning based models are currently dominating most state-of-the-art solutions for disease prediction. Existing works employ RNNs along with multiple levels of attention mechanisms to provide interpretability. These deep learning models, with trainable parameters running into millions, require huge amounts of compute and data to train and deploy. These requirements are sometimes so huge that they render usage of such models as unfeasible. We address these challenges by developing a simpler yet interpretable non-deep learning based model for application to EHR data. We model and showcase our work's results on the task of predicting first occurrence of a diagnosis, often overlooked in existing works. We push the capabilities of a tree based model and come up with a strong baseline for more sophisticated models. Its performance shows an improvement over deep learning based solutions (both, with and without the first-occurrence constraint) all the while maintaining interpretability.

Time series forecasting holds significant importance in many real-world dynamic systems and has been extensively studied. Unlike natural language process (NLP) and computer vision (CV), where a single large model can tackle multiple tasks, models for time series forecasting are often specialized, necessitating distinct designs for different tasks and applications. While pre-trained foundation models have made impressive strides in NLP and CV, their development in time series domains has been constrained by data sparsity. Recent studies have revealed that large language models (LLMs) possess robust pattern recognition and reasoning abilities over complex sequences of tokens. However, the challenge remains in effectively aligning the modalities of time series data and natural language to leverage these capabilities. In this work, we present Time-LLM, a reprogramming framework to repurpose LLMs for general time series forecasting with the backbone language models kept intact. We begin by reprogramming the input time series with text prototypes before feeding it into the frozen LLM to align the two modalities. To augment the LLM's ability to reason with time series data, we propose Prompt-as-Prefix (PaP), which enriches the input context and directs the transformation of reprogrammed input patches. The transformed time series patches from the LLM are finally projected to obtain the forecasts. Our comprehensive evaluations demonstrate that Time-LLM is a powerful time series learner that outperforms state-of-the-art, specialized forecasting models. Moreover, Time-LLM excels in both few-shot and zero-shot learning scenarios.

Recent advances in Large Language Models (LLMs) have demonstrated new possibilities for accurate and efficient time series analysis, but prior work often required heavy fine-tuning and/or ignored inter-series correlations. In this work, we explore simple and flexible prompt-based strategies that enable LLMs to perform time series forecasting without extensive retraining or the use of a complex external architecture. Through the exploration of specialized prompting methods that leverage time series decomposition, patch-based tokenization, and similarity-based neighbor augmentation, we find that it is possible to enhance LLM forecasting quality while maintaining simplicity and requiring minimal preprocessing of data. To this end, we propose our own method, PatchInstruct, which enables LLMs to make precise and effective predictions.

Bronchopulmonary dysplasia (BPD) is a chronic lung disease affecting 35% of extremely low birth weight infants. Defined by oxygen dependence at 36 weeks postmenstrual age, it causes lifelong respiratory complications. However, preventive interventions carry severe risks, including neurodevelopmental impairment, ventilator-induced lung injury, and systemic complications. Therefore, early BPD prognosis and prediction of BPD outcome is crucial to avoid unnecessary toxicity in low risk infants. Admission radiographs of extremely preterm infants are routinely acquired within 24h of life and could serve as a non-invasive prognostic tool. In this work, we developed and investigated a deep learning approach using chest X-rays from 163 extremely low-birth-weight infants (leq32 weeks gestation, 401-999g) obtained within 24 hours of birth. We fine-tuned a ResNet-50 pretrained specifically on adult chest radiographs, employing progressive layer freezing with discriminative learning rates to prevent overfitting and evaluated a CutMix augmentation and linear probing. For moderate/severe BPD outcome prediction, our best performing model with progressive freezing, linear probing and CutMix achieved an AUROC of 0.78 pm 0.10, balanced accuracy of 0.69 pm 0.10, and an F1-score of 0.67 pm 0.11. In-domain pre-training significantly outperformed ImageNet initialization (p = 0.031) which confirms domain-specific pretraining to be important for BPD outcome prediction. Routine IRDS grades showed limited prognostic value (AUROC 0.57 pm 0.11), confirming the need of learned markers. Our approach demonstrates that domain-specific pretraining enables accurate BPD prediction from routine day-1 radiographs. Through progressive freezing and linear probing, the method remains computationally feasible for site-level implementation and future federated learning deployments.

Recruiting patients to participate in clinical trials can be challenging and time-consuming. Usually, participation in a clinical trial is initiated by a healthcare professional and proposed to the patient. Promoting clinical trials directly to patients via online recruitment might help to reach them more efficiently. In this study, we address the case where a patient is initiating their own recruitment process and wants to determine whether they are eligible for a given clinical trial, using their own language to describe their medical profile. To study whether this creates difficulties in the patient trial matching process, we design a new dataset and task, Natural Language Inference for Patient Recruitment (NLI4PR), in which patient language profiles must be matched to clinical trials. We create it by adapting the TREC 2022 Clinical Trial Track dataset, which provides patients' medical profiles, and rephrasing them manually using patient language. We also use the associated clinical trial reports where the patients are either eligible or excluded. We prompt several open-source Large Language Models on our task and achieve from 56.5 to 71.8 of F1 score using patient language, against 64.7 to 73.1 for the same task using medical language. When using patient language, we observe only a small loss in performance for the best model, suggesting that having the patient as a starting point could be adopted to help recruit patients for clinical trials. The corpus and code bases are all freely available on our Github and HuggingFace repositories.

In light of recent work on scheduling with predicted job sizes, we consider the effect of the cost of predictions in queueing systems, removing the assumption in prior research that predictions are external to the system's resources and/or cost-free. In particular, we introduce a novel approach to utilizing predictions, SkipPredict, designed to address their inherent cost. Rather than uniformly applying predictions to all jobs, we propose a tailored approach that categorizes jobs based on their prediction requirements. To achieve this, we employ one-bit "cheap predictions" to classify jobs as either short or long. SkipPredict prioritizes predicted short jobs over long jobs, and for the latter, SkipPredict applies a second round of more detailed "expensive predictions" to approximate Shortest Remaining Processing Time for these jobs. Our analysis takes into account the cost of prediction. We examine the effect of this cost for two distinct models. In the external cost model, predictions are generated by some external method without impacting job service times but incur a cost. In the server time cost model, predictions themselves require server processing time, and are scheduled on the same server as the jobs.

Financial market predictions utilize historical data to anticipate future stock prices and market trends. Traditionally, these predictions have focused on the statistical analysis of quantitative factors, such as stock prices, trading volumes, inflation rates, and changes in industrial production. Recent advancements in large language models motivate the integrated financial analysis of both sentiment data, particularly market news, and numerical factors. Nonetheless, this methodology frequently encounters constraints due to the paucity of extensive datasets that amalgamate both quantitative and qualitative sentiment analyses. To address this challenge, we introduce a large-scale financial dataset, namely, Financial News and Stock Price Integration Dataset (FNSPID). It comprises 29.7 million stock prices and 15.7 million time-aligned financial news records for 4,775 S&P500 companies, covering the period from 1999 to 2023, sourced from 4 stock market news websites. We demonstrate that FNSPID excels existing stock market datasets in scale and diversity while uniquely incorporating sentiment information. Through financial analysis experiments on FNSPID, we propose: (1) the dataset's size and quality significantly boost market prediction accuracy; (2) adding sentiment scores modestly enhances performance on the transformer-based model; (3) a reproducible procedure that can update the dataset. Completed work, code, documentation, and examples are available at github.com/Zdong104/FNSPID. FNSPID offers unprecedented opportunities for the financial research community to advance predictive modeling and analysis.

Chronotype compares individuals' circadian phase to others. It contextualizes mental health risk assessments and detection of social jet lag, which can hamper mental health and cognitive performance. Existing ways of determining chronotypes, such as Dim Light Melatonin Onset (DLMO) or the Morningness-Eveningness Questionnaire (MEQ), are limited by being discrete in time and time-intensive to update, meaning they rarely capture real-world variability across time. Chronotyping users based on a daily planner app might augment existing methods to enable assessment continuously and at scale. This paper reports the construction of a supervised binary classifier that attempts to demonstrate the feasibility of this approach. 1,460 registered users from the Owaves app opted in by filling out the MEQ survey between July 14, 2022, and May 1, 2023. 142 met the eligibility criteria. We used multimodal app data from individuals identified as morning and evening types from MEQ data, basing the classifier on app time series data. This included daily timing for 8 main lifestyle activity types: exercise, sleep, social interactions, meal times, relaxation, work, play, and miscellaneous, as defined in the app. The timing of activities showed substantial change across time, as well as heterogeneity by activity type. Our novel chronotyping classifier was able to predict the morningness and eveningness of its users with an ROC AUC of 0.70. Our findings demonstrate the feasibility of chronotype classification from multimodal, real-world app data, while highlighting fundamental challenges to applying discrete and fixed labels to complex, dynamic, multimodal behaviors. Our findings suggest a potential for real-time monitoring of shifts in chronotype specific to different causes (i.e. types of activity), which could feasibly be used to support future, prospective mental health support research.

Postprandial hyperglycemia, marked by the blood glucose level exceeding the normal range after meals, is a critical indicator of progression toward type 2 diabetes in prediabetic and healthy individuals. A key metric for understanding blood glucose dynamics after eating is the postprandial area under the curve (PAUC). Predicting PAUC in advance based on a person's diet and activity level and explaining what affects postprandial blood glucose could allow an individual to adjust their lifestyle accordingly to maintain normal glucose levels. In this paper, we propose GlucoLens, an explainable machine learning approach to predict PAUC and hyperglycemia from diet, activity, and recent glucose patterns. We conducted a five-week user study with 10 full-time working individuals to develop and evaluate the computational model. Our machine learning model takes multimodal data including fasting glucose, recent glucose, recent activity, and macronutrient amounts, and provides an interpretable prediction of the postprandial glucose pattern. Our extensive analyses of the collected data revealed that the trained model achieves a normalized root mean squared error (NRMSE) of 0.123. On average, GlucoLense with a Random Forest backbone provides a 16% better result than the baseline models. Additionally, GlucoLens predicts hyperglycemia with an accuracy of 74% and recommends different options to help avoid hyperglycemia through diverse counterfactual explanations. Code available: https://github.com/ab9mamun/GlucoLens.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

Predicting in-hospital mortality for intensive care unit (ICU) patients is key to final clinical outcomes. AI has shown advantaged accuracy but suffers from the lack of explainability. To address this issue, this paper proposes an eXplainable Multimodal Mortality Predictor (X-MMP) approaching an efficient, explainable AI solution for predicting in-hospital mortality via multimodal ICU data. We employ multimodal learning in our framework, which can receive heterogeneous inputs from clinical data and make decisions. Furthermore, we introduce an explainable method, namely Layer-Wise Propagation to Transformer, as a proper extension of the LRP method to Transformers, producing explanations over multimodal inputs and revealing the salient features attributed to prediction. Moreover, the contribution of each modality to clinical outcomes can be visualized, assisting clinicians in understanding the reasoning behind decision-making. We construct a multimodal dataset based on MIMIC-III and MIMIC-III Waveform Database Matched Subset. Comprehensive experiments on benchmark datasets demonstrate that our proposed framework can achieve reasonable interpretation with competitive prediction accuracy. In particular, our framework can be easily transferred to other clinical tasks, which facilitates the discovery of crucial factors in healthcare research.

Run-time steering strategies like Medprompt are valuable for guiding large language models (LLMs) to top performance on challenging tasks. Medprompt demonstrates that a general LLM can be focused to deliver state-of-the-art performance on specialized domains like medicine by using a prompt to elicit a run-time strategy involving chain of thought reasoning and ensembling. OpenAI's o1-preview model represents a new paradigm, where a model is designed to do run-time reasoning before generating final responses. We seek to understand the behavior of o1-preview on a diverse set of medical challenge problem benchmarks. Following on the Medprompt study with GPT-4, we systematically evaluate the o1-preview model across various medical benchmarks. Notably, even without prompting techniques, o1-preview largely outperforms the GPT-4 series with Medprompt. We further systematically study the efficacy of classic prompt engineering strategies, as represented by Medprompt, within the new paradigm of reasoning models. We found that few-shot prompting hinders o1's performance, suggesting that in-context learning may no longer be an effective steering approach for reasoning-native models. While ensembling remains viable, it is resource-intensive and requires careful cost-performance optimization. Our cost and accuracy analysis across run-time strategies reveals a Pareto frontier, with GPT-4o representing a more affordable option and o1-preview achieving state-of-the-art performance at higher cost. Although o1-preview offers top performance, GPT-4o with steering strategies like Medprompt retains value in specific contexts. Moreover, we note that the o1-preview model has reached near-saturation on many existing medical benchmarks, underscoring the need for new, challenging benchmarks. We close with reflections on general directions for inference-time computation with LLMs.

Bone density prediction via CT scans to estimate T-scores is crucial, providing a more precise assessment of bone health compared to traditional methods like X-ray bone density tests, which lack spatial resolution and the ability to detect localized changes. However, CT-based prediction faces two major challenges: the high computational complexity of transformer-based architectures, which limits their deployment in portable and clinical settings, and the imbalanced, long-tailed distribution of real-world hospital data that skews predictions. To address these issues, we introduce MedConv, a convolutional model for bone density prediction that outperforms transformer models with lower computational demands. We also adapt Bal-CE loss and post-hoc logit adjustment to improve class balance. Extensive experiments on our AustinSpine dataset shows that our approach achieves up to 21% improvement in accuracy and 20% in ROC AUC over previous state-of-the-art methods.

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

We study short-horizon forecasting of weekly terrorism incident counts using the Global Terrorism Database (GTD, 1970--2016). We build a reproducible pipeline with fixed time-based splits and evaluate a Bidirectional LSTM (BiLSTM) against strong classical anchors (seasonal-naive, linear/ARIMA) and a deep LSTM-Attention baseline. On the held-out test set, the BiLSTM attains RMSE 6.38, outperforming LSTM-Attention (9.19; +30.6\%) and a linear lag-regression baseline (+35.4\% RMSE gain), with parallel improvements in MAE and MAPE. Ablations varying temporal memory, training-history length, spatial grain, lookback size, and feature groups show that models trained on long historical data generalize best; a moderate lookback (20--30 weeks) provides strong context; and bidirectional encoding is critical for capturing both build-up and aftermath patterns within the window. Feature-group analysis indicates that short-horizon structure (lagged counts and rolling statistics) contributes most, with geographic and casualty features adding incremental lift. We release code, configs, and compact result tables, and provide a data/ethics statement documenting GTD licensing and research-only use. Overall, the study offers a transparent, baseline-beating reference for GTD incident forecasting.

Health conditions among patients in intensive care units (ICUs) are monitored via electronic health records (EHRs), composed of numerical time series and lengthy clinical note sequences, both taken at irregular time intervals. Dealing with such irregularity in every modality, and integrating irregularity into multimodal representations to improve medical predictions, is a challenging problem. Our method first addresses irregularity in each single modality by (1) modeling irregular time series by dynamically incorporating hand-crafted imputation embeddings into learned interpolation embeddings via a gating mechanism, and (2) casting a series of clinical note representations as multivariate irregular time series and tackling irregularity via a time attention mechanism. We further integrate irregularity in multimodal fusion with an interleaved attention mechanism across temporal steps. To the best of our knowledge, this is the first work to thoroughly model irregularity in multimodalities for improving medical predictions. Our proposed methods for two medical prediction tasks consistently outperforms state-of-the-art (SOTA) baselines in each single modality and multimodal fusion scenarios. Specifically, we observe relative improvements of 6.5\%, 3.6\%, and 4.3\% in F1 for time series, clinical notes, and multimodal fusion, respectively. These results demonstrate the effectiveness of our methods and the importance of considering irregularity in multimodal EHRs.

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance.