Clinical Prediction

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Latest papers 202

30 papers in the last four weeks, up 30% on the four weeks before. 0.2% of all new papers.

Feb 28, 2026

Stroke outcome and evolution prediction from CT brain using a spatiotemporal diffusion autoencoder

Stroke is a major cause of death and disability worldwide. Accurate outcome and evolution prediction has the potential to revolutionize stroke care by individualizing clinical decision-making leading to better outcomes. However, despite a plethora of attempts and the rich data provided by neuroimaging, modelling the ultimate fate of brain tissue remains a challenging task. In this work, we apply recent ideas in the field of diffusion probabilistic models to generate a self-supervised semantically meaningful stroke representation from Computed Tomography (CT) images. We then improve this representation by extending the method to accommodate longitudinal images and the time from stroke onset. The effectiveness of our approach is evaluated on a dataset consisting of 5,824 CT images from 3,573 patients across two medical centers with minimal labels. Comparative experiments show that our method achieves the best performance for predicting next-day severity and functional outcome at discharge.

Adam Marcus, Paul Bentley, Daniel Rueckert

Imperial College London, London, UK · Technische Universität München, München, Germany

Clinical Outcome Prediction Clinical Prediction Medical Image Representation Learning Diffusion Models Longitudinal Medical Image Analysis

Feb 27, 2026

Pretty Good Measurement for Radiomics: A Quantum-Inspired Multi-Class Classifier for Lung Cancer Subtyping and Prostate Cancer Risk Stratification

We investigate a quantum-inspired approach to supervised multi-class classification based on the Pretty Good Measurement (PGM), viewed as an operator-valued decision rule derived from quantum state discrimination. The method associates each class with an encoded mixed state and performs classification through a single POVM construction, thus providing a genuinely multi-class strategy without reduction to pairwise or one-vs-rest schemes. In this perspective, classification is reformulated as the discrimination of a finite ensemble of class-dependent density operators, with performance governed by the geometry induced by the encoding map and by the overlap structure among classes. To assess the practical scope of this framework, we apply the PGM-based classifier to two biomedical radiomics case studies: histopathological subtyping of non-small-cell lung carcinoma (NSCLC) and prostate cancer (PCa) risk stratification. The evaluation is conducted under protocols aligned with previously reported radiomics studies, enabling direct comparison with established classical baselines. The results show that the PGM-based classifier is consistently competitive and, in several settings, improves upon standard methods. In particular, the method performs especially well in the NSCLC binary and three-class tasks, while remaining competitive in the four-class case, where increased class overlap yields a more demanding discrimination geometry. In the PCa study, the PGM classifier remains close to the strongest ensemble baseline and exhibits clinically relevant sensitivity--specificity trade-offs across feature-selection scenarios.

Giuseppe Sergioli, Carlo Cuccu, Giovanni Pasini +4

Università degli Studi di Cagliari, Via Is Mirrionis 1, Cagliari, 09123, Italy · Institute of Bioimaging and Complex Biological Systems - National Research Council (IBSBC - CNR), Cefalù, 90015, Italy · National Laboratory of South, National Institute for Nuclear Physics(LNS-INFN), Catania, 95125, Italy

Multiclass Classification Quantum-Inspired ML Clinical Prediction Radiomics Histopathology Image Classification

Feb 27, 2026

MINT: Multimodal Imaging-to-Speech Knowledge Transfer for Early Alzheimer's Screening

Alzheimer's disease is a progressive neurodegenerative disorder in which mild cognitive impairment (MCI) precedes dementia. Structural MRI provides biomarkers but requires costly infrastructure, limiting population-scale deployment. Speech offers a non-invasive alternative, yet speech-only classifiers are developed independently of neuroimaging and lack biological grounding for CN-versus-MCI classification. We propose MINT (Multimodal Imaging-to-Speech Knowledge Transfer), a three-stage framework that transfers MRI-derived biomarker structure to speech during training. An MRI teacher defines a compact embedding space for CN-versus-MCI classification, while a residual projection head aligns speech representations to this space using a combined geometric loss. The frozen MRI classifier enables imaging-free inference. On ADNI-4, aligned speech achieves performance comparable to speech baselines, while multimodal fusion improves over MRI alone. Ablations identify dropout regularization and self-supervised pretraining as important design choices. To our knowledge, MINT is the first demonstration of MRI-to-speech knowledge transfer for early Alzheimer's screening without imaging at inference.

Vrushank Ahire, Yogesh Kumar, Anouck Girard +1

Department of Computer Science and Engineering, Indian Institute of Technology Ropar, India · Embry-Riddle Aeronautical University, Florida, USA

Cross-Modal Knowledge Distillation Alzheimer's Disease Speech-Based Dementia Detection Clinical Prediction Alzheimer's Disease Classification

Feb 27, 2026

PREBA: Surgical Duration Prediction via PCA-Weighted Retrieval-Augmented LLMs and Bayesian Averaging Aggregation

Accurate prediction of surgical duration is pivotal for hospital resource management. Although recent supervised learning approaches-from machine learning (ML) to fine-tuned large language models (LLMs)-have shown strong performance, they remain constrained by the need for high-quality labeled data and computationally intensive training. In contrast, zero-shot LLM inference offers a promising training-free alternative but it lacks grounding in institution-specific clinical context (e.g., local demographics and case-mix distributions), making its predictions clinically misaligned and prone to instability. To address these limitations, we present PREBA, a retrieval-augmented framework that integrates PCA-weighted retrieval and Bayesian averaging aggregation to ground LLM predictions in institution-specific clinical evidence and statistical priors. The core of PREBA is to construct an evidence-based prompt for the LLM, comprising (1) the most clinically similar historical surgical cases and (2) clinical statistical priors. To achieve this, PREBA first encodes heterogeneous clinical features into a unified representation space enabling systematic retrieval. It then performs PCA-weighted retrieval to identify clinically relevant historical cases, which form the evidence context supplied to the LLM. Finally, PREBA applies Bayesian averaging to fuse multi-round LLM predictions with population-level statistical priors, yielding calibrated and clinically plausible duration estimates. We evaluate PREBA on two real-world clinical datasets using three state-of-the-art LLMs, including Qwen3, DeepSeek-R1, and HuatuoGPT-o1. PREBA significantly improves performance-for instance, reducing MAE by up to 40% and raising R^2 from -0.13 to 0.62 over zero-shot inference-and it achieves accuracy competitive with supervised ML methods, demonstrating strong effectiveness and generalization.

Wanyin Wu, Kanxue Li, Baosheng Yu +4

Wanyin Wu, Haoyun Zhao, and Dapeng Tao are with the School of Information Science and Engineering, Yunnan University, Kunming 650500, China. · Kanxue Li and Yibing Zhan are with the School of Computer Science, Wuhan University, Wuhan 430072, China. · Baosheng Yu is with the Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 639798. +1

Clinical Prediction Retrieval-Augmented Generation LLM Inference

Feb 26, 2026

Sample Size Calculations for Developing Clinical Prediction Models: Overview and pmsims R package

Background: Clinical prediction models are increasingly used to inform healthcare decisions, but determining the minimum sample size for their development remains a critical and unresolved challenge. Inadequate sample sizes can lead to overfitting, poor generalisability, and biased predictions. Existing approaches, such as heuristic rules, closed-form formulas, and simulation-based methods, vary in flexibility and accuracy, particularly for complex data structures and machine learning models. Methods: We review current methodologies for sample size estimation in prediction modelling and introduce a conceptual framework that distinguishes between mean-based and assurance-based criteria. Building on this, we propose a novel simulation-based approach that integrates learning curves, Gaussian Process optimisation, and assurance principles to identify sample sizes that achieve target performance with high probability. This approach is implemented in pmsims, an open-source, model-agnostic R package. Results: Through case studies, we demonstrate that sample size estimates vary substantially across methods, performance metrics, and modelling strategies. Compared to existing tools, pmsims provides flexible, efficient, and interpretable solutions that accommodate diverse models and user-defined metrics while explicitly accounting for variability in model performance. Conclusions: Our framework and software advance sample size methodology for clinical prediction modelling by combining flexibility with computational efficiency. Future work should extend these methods to hierarchical and multimodal data, incorporate fairness and stability metrics, and address challenges such as missing data and complex dependency structures.

Diana Shamsutdinova, Felix Zimmer, Oyebayo Ridwan Olaniran +4

Department of Biostatistics and Health Informatics, King’s College London · NIHR Biomedical Research Centre, Maudsley NHS Trust

Clinical Prediction Statistical Power Analysis

Feb 26, 2026

Global Interpretability via Automated Preprocessing: A Framework Inspired by Psychiatric Questionnaires

Psychiatric questionnaires are highly context sensitive and often only weakly predict subsequent symptom severity, which makes the prognostic relationship difficult to learn. Although flexible nonlinear models can improve predictive accuracy, their limited interpretability can erode clinical trust. In fields such as imaging and omics, investigators commonly address visit- and instrument-specific artifacts by extracting stable signal through preprocessing and then fitting an interpretable linear model. We adopt the same strategy for questionnaire data by decoupling preprocessing from prediction: REFINE (Redundancy-Exploiting Follow-up-Informed Nonlinear Enhancement) uses follow-up information to learn a nonlinear, item-aligned preprocessing of baseline measurements, and then maps these stabilized baseline items to future severity through a linear coefficient matrix. This construction constrains where nonlinearity enters rather than restricting the end-to-end predictive function class, allowing the prognostic relationship to remain globally interpretable through a single coefficient matrix rather than through post hoc local attributions. In the population, the resulting predictor recovers the Bayes-optimal conditional mean, so global linear interpretability does not require sacrificing nonlinear predictive flexibility. In experiments, REFINE outperforms other interpretable approaches while preserving clear global attribution of prognostic factors across psychiatric and non-psychiatric longitudinal prediction tasks.

Eric V. Strobl

Department of Biomedical Informatics, University of Pittsburgh.

Interpretable ML Clinical Outcome Prediction Clinical Prediction

Feb 26, 2026

An Explainable Ensemble Framework for Alzheimer's Disease Prediction Using Structured Clinical and Cognitive Data

Early and accurate detection of Alzheimer's disease (AD) remains a major challenge in medical diagnosis due to its subtle onset and progressive nature. This research introduces an explainable ensemble learning Framework designed to classify individuals as Alzheimer's or Non-Alzheimer's using structured clinical, lifestyle, metabolic, and lifestyle features. The workflow incorporates rigorous preprocessing, advanced feature engineering, SMOTE-Tomek hybrid class balancing, and optimized modeling using five ensemble algorithms-Random Forest, XGBoost, LightGBM, CatBoost, and Extra Trees-alongside a deep artificial neural network. Model selection was performed using stratified validation to prevent leakage, and the best-performing model was evaluated on a fully unseen test set. Ensemble methods achieved superior performance over deep learning, with XGBoost, Random Forest, and Soft Voting showing the strongest accuracy, sensitivity, and F1-score profiles. Explainability techniques, including SHAP and feature importance analysis, highlighted MMSE, Functional Assessment Age, and several engineered interaction features as the most influential determinants. The results demonstrate that the proposed framework provides a reliable and transparent approach to Alzheimer's disease prediction, offering strong potential for clinical decision support applications.

Nishan Mitra

Computer Science & Engineering (AI&ML), Institute of Engineering & Management, Kolkata, India

Alzheimer's Disease Classification Clinical Prediction Ensemble Learning

Feb 25, 2026

Predicting Multi-Drug Resistance in Bacterial Isolates Through Performance Comparison and LIME-based Interpretation of Classification Models

The rise of Antimicrobial Resistance, particularly Multi-Drug Resistance (MDR), presents a critical challenge for clinical decision-making due to limited treatment options and delays in conventional susceptibility testing. This study proposes an interpretable machine learning framework to predict MDR in bacterial isolates using clinical features and antibiotic susceptibility patterns. Five classification models were evaluated, including Logistic Regression, Random Forest, AdaBoost, XGBoost, and LightGBM. The models were trained on a curated dataset of 9,714 isolates, with resistance encoded at the antibiotic family level to capture cross-class resistance patterns consistent with MDR definitions. Performance assessment included accuracy, F1-score, AUC-ROC, and Matthews Correlation Coefficient. Ensemble models, particularly XGBoost and LightGBM, demonstrated superior predictive capability across all metrics. To address the clinical transparency gap, Local Interpretable Model-agnostic Explanations (LIME) was applied to generate instance-level explanations. LIME identified resistance to quinolones, Co-trimoxazole, Colistin, aminoglycosides, and Furanes as the strongest contributors to MDR predictions, aligning with known biological mechanisms. The results show that combining high-performing models with local interpretability provides both accuracy and actionable insights for antimicrobial stewardship. This framework supports earlier MDR identification and enhances trust in machine learning-assisted clinical decision support.

Santanam Wishal, Riad Sahara

Universitas Siber Asia

Clinical Prediction

Feb 25, 2026

Early Risk Stratification of Dosing Errors in Clinical Trials Using Machine Learning

Objective: The objective of this study is to develop a machine learning (ML)-based framework for early risk stratification of clinical trials (CTs) according to their likelihood of exhibiting a high rate of dosing errors, using information available prior to trial initiation. Materials and Methods: We constructed a dataset from ClinicalTrials.gov comprising 42,112 CTs. Structured, semi-structured trial data, and unstructured protocol-related free-text data were extracted. CTs were assigned binary labels indicating elevated dosing error rate, derived from adverse event reports, MedDRA terminology, and Wilson confidence intervals. We evaluated an XGBoost model trained on structured features, a ClinicalModernBERT model using textual data, and a simple late-fusion model combining both modalities. Post-hoc probability calibration was applied to enable interpretable, trial-level risk stratification. Results: The late-fusion model achieved the highest AUC-ROC (0.862). Beyond discrimination, calibrated outputs enabled robust stratification of CTs into predefined risk categories. The proportion of trials labeled as having an excessively high dosing error rate increased monotonically across higher predicted risk groups and aligned with the corresponding predicted probability ranges. Discussion: These findings indicate that dosing error risk can be anticipated at the trial level using pre-initiation information. Probability calibration was essential for translating model outputs into reliable and interpretable risk categories, while simple multimodal integration yielded performance gains without requiring complex architectures. Conclusion: This study introduces a reproducible and scalable ML framework for early, trial-level risk stratification of CTs at risk of high dosing error rates, supporting proactive, risk-based quality management in clinical research.

Félicien Hêche, Sohrab Ferdowsi, Anthony Yazdani +2

Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland · Actelion Pharmaceuticals Ltd, Basel, Switzerland

Clinical Risk Prediction Clinical Prediction

Feb 23, 2026

PaReGTA: A Temporally Aware LLM-Based Patient Representation Framework for EHR Analytics

Temporal information in structured electronic health records (EHRs) is often lost in sparse one-hot or count-based representations, while sequence models can be costly and data-hungry. We propose PaReGTA, an LLM-based encoding framework that (i) converts longitudinal EHR events into visit-level templated text with explicit temporal cues, (ii) learns domain-adapted visit embeddings via lightweight contrastive fine-tuning of a sentence-embedding model, and (iii) aggregates visit embeddings into a fixed-dimensional patient representation using hybrid temporal pooling that captures both recency and globally informative visits. The resulting fixed-dimensional patient representations can be used with conventional downstream machine-learning models. To examine factor-level sensitivity, we use PaReGTA-RSS (Representation Shift Score), a prespecified factor-removal analysis that recomputes patient representations after removing clinically defined factor groups and quantifies the resulting change in the fitted logit of a fixed logistic-regression model. We evaluated PaReGTA in a cohort of 39,088 patients with migraine from the All of Us Research Program (AoU) on a retrospective patient-level classification task with an EHR-derived target. In an exploratory comparison on the fixed held-out test cohort of 7,818 patients, PaReGTA-Gap + LightGBM, used as a post hoc analytical reference, had the highest reported AUC, accuracy, and F1 values among the evaluated sparse, BERT-based EHR, and recurrent approaches in this cohort.

Kihyuk Yoon, Lingchao Mao, Catherine Chong +3

Georgia Institute of Technology · Meta · Mayo Clinic

Longitudinal EHR Modeling Representation Learning Clinical Prediction

Feb 23, 2026

Human-Guided Agentic AI for Multimodal Clinical Prediction: Lessons from the AgentDS Healthcare Benchmark

Agentic AI systems are increasingly capable of autonomous data science workflows, yet clinical prediction tasks demand domain expertise that purely automated approaches struggle to provide. We investigate how human guidance of agentic AI can improve multimodal clinical prediction, presenting our approach to all three AgentDS Healthcare benchmark challenges: 30-day hospital readmission prediction (Macro-F1 = 0.8986), emergency department cost forecasting (MAE = $465.13), and discharge readiness assessment (Macro-F1 = 0.7939). Across these tasks, human analysts directed the agentic workflow at key decision points, multimodal feature engineering from clinical notes, scanned PDF billing receipts, and time-series vital signs; task-appropriate model selection; and clinically informed validation strategies. Our approach ranked 5th overall in the healthcare domain, with a 3rd-place finish on the discharge readiness task. Ablation studies reveal that human-guided decisions compounded to a cumulative gain of +0.065 F1 over automated baselines, with multimodal feature extraction contributing the largest single improvement (+0.041 F1). We distill three generalizable lessons: (1) domain-informed feature engineering at each pipeline stage yields compounding gains that outperform extensive automated search; (2) multimodal data integration requires task-specific human judgment that no single extraction strategy generalizes across clinical text, PDFs, and time-series; and (3) deliberate ensemble diversity with clinically motivated model configurations outperforms random hyperparameter search. These findings offer practical guidance for teams deploying agentic AI in healthcare settings where interpretability, reproducibility, and clinical validity are essential.

Lalitha Pranathi Pulavarthy, Raajitha Muthyala, Aravind V Kuruvikkattil +3

Dept. Biomedical Eng. & Informatics, Indiana University Indianapolis, Indianapolis, USA

Human-AI Collaboration Clinical Prediction LLM Agent Workflow Optimization

Feb 23, 2026

Making Conformal Predictors Robust in Healthcare Settings: a Case Study on EEG Classification

Quantifying uncertainty in clinical predictions is critical for high-stakes diagnosis tasks. Conformal prediction offers a principled approach by providing prediction sets with theoretical coverage guarantees. However, in practice, patient distribution shifts violate the i.i.d. assumptions underlying standard conformal methods, leading to poor coverage in healthcare settings. In this work, we evaluate several conformal prediction approaches on EEG seizure classification, a task with known distribution shift challenges and label uncertainty. We demonstrate that personalized calibration strategies can improve coverage by over 20 percentage points while maintaining comparable prediction set sizes. Our implementation is available via PyHealth, an open-source healthcare AI framework: https://github.com/sunlabuiuc/PyHealth.

Arjun Chatterjee, Sayeed Sajjad Razin, John Wu +3

University of Illinois Urbana-Champaign, Urbana, IL 61801, USA · PyHealth · Bangladesh University of Engineering and Technology

Conformal Prediction Clinical Prediction EEG Seizure Detection

Feb 19, 2026

Position: Evaluation of ECG Representations Must Be Fixed

This position paper argues that current benchmarking practice in 12-lead ECG representation learning must be fixed to ensure progress is reliable and aligned with clinically meaningful objectives. The field has largely converged on three public multi-label benchmarks (PTB-XL, CPSC2018, CSN) dominated by arrhythmia and waveform-morphology labels, even though the ECG is known to encode substantially broader clinical information. We argue that downstream evaluation should expand to include an assessment of structural heart disease and patient-level forecasting, in addition to other evolving ECG-related endpoints, as relevant clinical targets. Next, we outline evaluation best practices for multi-label, imbalanced settings, and show that when they are applied, the literature's current conclusion about which representations perform best is altered. Furthermore, we demonstrate the surprising result that a randomly initialized encoder with linear evaluation matches state-of-the-art pre-training on many tasks. This motivates the use of a random encoder as a reasonable baseline model. We substantiate our observations with an empirical evaluation of five representative ECG pre-training approaches across six evaluation settings: the three standard benchmarks, a structural disease dataset, hemodynamic inference, and patient forecasting.

Zachary Berger, Daniel Prakah-Asante, John Guttag +1

Massachusetts Institute of Technology, Cambridge, MA, USA · Massachusetts General Hospital, Boston, MA, USA

Representation Learning Electrocardiogram Classification Clinical Prediction Medical Diagnosis

Feb 10, 2026

MedFeat: Model-Aware and Explainability-Driven Feature Engineering with LLMs for Tabular Prediction

In clinical tabular prediction, classical machine learning models with feature engineering often outperform neural methods. LLMs are increasingly used to automate this process, acting as domain experts that propose diverse feature transformations to boost downstream performance. However, the feature generation process of existing LLM-based methods is agnostic to the downstream learner: the LLM receives no signal about which features currently drive predictions or where the model's representational capacity falls short, so proposals are neither targeted to promising regions of the feature space nor tailored to the learner's inductive bias. This shortcoming is amplified in healthcare data, which simultaneously exhibits class imbalance, heterogeneous feature spaces, and strict interpretability requirements. In this paper, we propose MedFeat, the first feature engineering framework inspired by the workflow of machine learning practitioners, leveraging model-awareness and feature importance signals to iteratively guide feature discovery for clinical tabular learning. We evaluate MedFeat on a broad range of challenging real-world clinical tasks and show that it statistically significantly outperforms state-of-the-art baselines, with an average F1 improvement of more than 10% over the baseline across models with distinct inductive biases.

Zizheng Zhang, Yiming Li, Justin Xu +6

Microsoft Research · University of Oxford

Interpretable ML Clinical Prediction Automated Feature Engineering Tabular Prediction

Jan 28, 2026

ECGFlowCMR: Pretraining with ECG-Generated Cine CMR Helps Cardiac Disease Classification and Phenotype Prediction

Cardiac Magnetic Resonance (CMR) imaging provides a comprehensive assessment of cardiac structure and function but remains constrained by high acquisition costs and reliance on expert annotations, limiting the availability of large-scale labeled datasets. In contrast, electrocardiograms (ECGs) are inexpensive, widely accessible, and offer a promising modality for conditioning the generative synthesis of cine CMR. To this end, we propose ECGFlowCMR, a novel ECG-to-CMR generative framework that integrates a Phase-Aware Masked Autoencoder (PA-MAE) and an Anatomy-Motion Disentangled Flow (AMDF) to address two fundamental challenges: (1) the cross-modal temporal mismatch between multi-beat ECG recordings and single-cycle CMR sequences, and (2) the anatomical observability gap due to the limited structural information inherent in ECGs. Extensive experiments on the UK Biobank and a proprietary clinical dataset demonstrate that ECGFlowCMR can generate realistic cine CMR sequences from ECG inputs, enabling scalable pretraining and improving performance on downstream cardiac disease classification and phenotype prediction tasks.

Xiaocheng Fang, Zhengyao Ding, Guangkun Nie +9

State Key Laboratory of General Artificial Intelligence, Peking University · School of Intelligence Science and Technology, Peking University, Beijing, China · Polytechnic Institute of Zhejiang University, Zhejiang University, Hangzhou, China +4

Synthetic Data Pretraining Medical Diagnosis Clinical Prediction Medical Image Synthesis Conditional Generative Modeling Cardiac MRI

Jan 8, 2026

ROOFS: RObust biOmarker Feature Selection

Feature selection (FS) is essential for biomarker discovery and clinical predictive modeling. Over the past decades, methodological literature on FS has become rich and mature, offering a wide spectrum of algorithmic approaches. However, much of this methodological progress has not fully translated into applied biomedical research. Moreover, challenges inherent in biomedical data, such as high-dimensional feature space, low sample size, multicollinearity, and missing values, make FS non-trivial. To help bridge this gap between methodological development and practical application, we propose ROOFS (RObust biOmarker Feature Selection), a Python package available at https://gitlab.inria.fr/compo/roofs, designed to help researchers in the choice of FS method adapted to their problem. ROOFS benchmarks multiple FS methods on the user's data and generates reports summarizing a comprehensive set of evaluation metrics, including downstream predictive performance estimated using optimism correction, stability, robustness of individual features, and true positive and false positive rates assessed on semi-synthetic data with a simulated outcome. We demonstrate the utility of ROOFS on data from the PIONeeR clinical trial, aimed at identifying predictors of resistance to anti-PD-(L)1 immunotherapy in lung cancer. Of the 34 FS methods gathered in ROOFS, we evaluated 23 in combination with 11 classifiers (253 models) and identified a filter based on the union of Benjamini-Hochberg false discovery rate-adjusted p-values from t-test and logistic regression as the optimal approach, outperforming other methods including widely used LASSO. We conclude that comprehensive benchmarking with ROOFS has the potential to improve the reproducibility of FS discoveries and increase the translational value of clinical models.

Anastasiia Bakhmach, Paul Dufossé, Simon Charpigny +4

1*COMPO Team (COMPutational Pharmacology and clinical Oncology), Inria Sophia Antipolis – Méditerranée, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France. · 2Veracyte SAS, Marseille, France. · 3Assistance Publique-Hôpitaux de Marseille (APHM), Marseille, France. +1

Scientific Discovery Clinical Prediction Feature Selection

Nov 22, 2025

Improving Forecasts of Suicide Attempts for Patients with Little Data

Ecological Momentary Assessment (EMA) studies provide real-time data on suicidal thoughts and behaviors, but forecasting suicide attempts remains challenging: attempts are rare, and the pathways patients take to them are heterogeneous. Here, we investigate a cohort of patients from an EMA study with recorded suicide-related events. We show that a single model fit to all patients forecasts poorly, while idiographic (per-patient) models show improvement but overfit for those with little data. Based on this result, one may hypothesize that patients should be partitioned into subgroups---this way, similar patients' data can be pooled together to improve forecasts. However, we show that grouping patients at random already improves forecasts, with performance increasing monotonically with the number of groups. Moreover, we show that grouping patients by demographics yields worse forecasts than random groupings. From these results, we hypothesize that patient similarity is continuous, rather than discrete, and must be inferred from the data. This motivated us to use Latent Variable Multiple Output Gaussian Processes (LVMOGPs), adapted to our data. Preliminary results show that, even without careful kernel design, LVMOGPs already match the strongest baseline models on most metrics, and their latent spaces yield a similarity between patients that we can inspect directly. Because the cohort is conditioned on the outcome and the splits are not temporal, we read these results as evidence that idiographic structure exists and can be recovered, not as deployable forecasting performance---an area for future work.

Genesis Hang, Annie Chen, Hope Neveux +2

Wellesley College · Harvard University

Latent Variable Models Gaussian Processes Clinical Prediction Suicide Risk Modeling Clinical Risk Prediction

Sep 9, 2025

General Demographic Pre-trained Models for Enhancing Predictive Performance Across Diseases and Population

Foundation models for healthcare require balancing robust generalization across heterogeneous clinical populations and disease settings with the architectural simplicity needed for deployment. We present a pre-trained model focused on demographic attributes that enhances feature utility across medical domains in a plug-and-play fashion. We introduce the General Demographic Pre-trained (GDP) model, designed to extract intrinsic representations of patient status based on age and sex, the two most ubiquitous clinical features. The composition of GDP was optimized by investigating various encoding methods and visit-reordering schemes. The model was pre-trained and transferability was validated by embedding the learned representations into diverse disease and geographic cohorts characterized by distinct demographic profiles. The optimal model configuration was subsequently validated against top-performing tabular foundation models (TabPFN, TabICL, and TabFM). Our findings demonstrate that concatenating GDP-derived embeddings with raw residual features consistently enhances predictive performance across classification tasks while elevating the relative importance of demographic attributes. The embedding transformation provides superior representational separability compared to the original data distribution, yielding competitive discrimination performance across metrics against all three general-purpose foundation models and tree-based algorithm. GDP has successfully served the purpose of a foundation model, which produce enriched representations that amplify the predictive insight of these features beyond their raw form. The generated embeddings can be directly concatenated with residual features, serving as an enhancement layer that maintains full compatibility with standard tabular classifiers.

Li-Chin Chen, Ji-Tian Sheu, Yuh-Jue Chuang

Data Analytics and Digital Transformation Research Center National Taiwan University Taipei, Taiwan · Department of Health Care Management Chang Gung University Taoyuan, Taiwan

Healthcare Representation Learning Clinical Prediction Tabular Foundation Models

Jul 18, 2025

Glucose-ML: A collection of longitudinal diabetes datasets for development of robust AI solutions

Artificial intelligence (AI) algorithms are a critical part of state-of-the-art digital health technology for diabetes management. Yet, access to large high-quality datasets is creating barriers that impede development of robust AI solutions. To accelerate development of transparent, reproducible, and robust AI solutions, we present Glucose-ML, a collection of 10 publicly available diabetes datasets, released within the last 7 years (i.e., 2018 - 2025). The Glucose-ML collection comprises over 300,000 days of continuous glucose monitor (CGM) data with a total of 38 million glucose samples collected from 2500+ people across 4 countries. Participants include persons living with type 1 diabetes, type 2 diabetes, prediabetes, and no diabetes. To support researchers and innovators with using this rich collection of diabetes datasets, we present a comparative analysis to guide algorithm developers with data selection. Additionally, we conduct a case study for the task of blood glucose prediction - one of the most common AI tasks within the field. Through this case study, we provide a benchmark for short-term blood glucose prediction across all 10 publicly available diabetes datasets within the Glucose-ML collection. We show that the same algorithm can have significantly different prediction results when developed/evaluated with different datasets. Findings from this study are then used to inform recommendations for developing robust AI solutions within the diabetes or broader health domain. We provide direct links to each longitudinal diabetes dataset and openly provide our code.

Temiloluwa Prioleau, Baiying Lu, Yanjun Cui

Department of Computer Science Emory University Atlanta, GA 30322 · Department of Computer Science Dartmouth College Hanover, NH 03755

Forecasting Benchmarks Blood Glucose Forecasting Clinical Prediction ML Reproducibility Wearable Health Monitoring Cross-Dataset Generalization

Jun 8, 2025

Discovering Hierarchy-Grounded Domains with Adaptive Granularity for Clinical Domain Generalization

Domain generalization has become a critical challenge in predictive healthcare, where different patient groups exhibit shifting data distributions that degrade model performance. Still, regular domain generalization approaches often struggle in clinical settings due to (1) the absence of domain labels and (2) the lack of clinical insight integration. To address these challenges in healthcare, we aim to explore how medical ontologies can be used to discover dynamic yet hierarchy-grounded patient domains, a partitioning strategy that remains under-explored in prior work. Hence, we introduce UdonCare, a hierarchy-pruning method that iteratively divides patients into latent domains and retrieves domain-invariant (label) information from patient data. On public datasets (MIMIC-III, MIMIC-IV, and eICU), UdonCare shows superiority over eight generalization baselines across four representative clinical prediction tasks with substantial domain gaps, highlighting the potential of medical knowledge for enhancing model generalization.

Pengfei Hu, Xiaoxue Han, Fei Wang +1

School of Computing Stevens Institute of Technology Hoboken, New Jersey, United States · Weill Cornell Medicine Cornell University New York, New York, United States

Healthcare Domain Generalization Clinical Prediction

Feb 4, 2025

Hierarchical Sparse Bayesian Multitask Learning for Disease Prediction in Pooled Microbiome Studies

This paper proposes a hierarchical Bayesian multitask learning model that is applicable to the general multi-task binary classification learning problem where the model assumes a shared sparsity structure across different tasks. We derive a computationally efficient inference algorithm based on variational inference to approximate the posterior distribution. We demonstrate the potential of the new approach on various synthetic datasets and for predicting human health status based on microbiome profile. Our analysis incorporates data pooled from multiple microbiome studies, along with a comprehensive comparison with other benchmark methods. Results in synthetic datasets show that the proposed approach has superior support recovery property when the underlying regression coefficients share a common sparsity structure across different tasks. Our experiments on microbiome classification demonstrate the utility of the method in extracting informative taxa while providing well-calibrated predictions with uncertainty quantification and achieving competitive performance in terms of prediction metrics. Notably, despite the heterogeneity of the pooled datasets (e.g., different experimental objectives, laboratory setups, sequencing equipment, patient demographics), our method delivers robust results.

Haonan Zhu, Andre R. Goncalves, Camilo Valdes +10

Lawrence Livermore National Laboratory · Electrical and Computer Engineering, University of Michigan

Clinical Outcome Prediction Multi-Task Learning Hierarchical Bayesian Modeling Binary Classification Clinical Prediction

Sep 30, 2023

Unveiling the Unborn: Advancing Fetal Health Classification through Machine Learning

Fetal health classification is a critical task in obstetrics, enabling early identification and management of potential health problems. However, it remains challenging due to data complexity and limited labeled samples. This research paper presents a novel machine-learning approach for fetal health classification, leveraging a LightGBM classifier trained on a comprehensive dataset. The proposed model achieves an impressive accuracy of 98.31% on a test set. Our findings demonstrate the potential of machine learning in enhancing fetal health classification, offering a more objective and accurate assessment. Notably, our approach combines various features, such as fetal heart rate, uterine contractions, and maternal blood pressure, to provide a comprehensive evaluation. This methodology holds promise for improving early detection and treatment of fetal health issues, ensuring better outcomes for both mothers and babies. Beyond the high accuracy achieved, the novelty of our approach lies in its comprehensive feature selection and assessment methodology. By incorporating multiple data points, our model offers a more holistic and reliable evaluation compared to traditional methods. This research has significant implications in the field of obstetrics, paving the way for advancements in early detection and intervention of fetal health concerns. Future work involves validating the model on a larger dataset and developing a clinical application. Ultimately, we anticipate that our research will revolutionize the assessment and management of fetal health, contributing to improved healthcare outcomes for expectant mothers and their babies.

Sujith K Mandala

Medical Diagnosis Clinical Prediction