Clinical Outcome Prediction

Follow this topic Ask about this topic

Momentum

18 papers in the last four weeks, up 157% on the four weeks before. 0.2% of all new papers.

Jul 13Week of Sep 28

Latest papers 174

May 18, 2026eess.IV

From Division to Decision: Leveraging Temporal Cell-Stage Segmentation for Embryo Transferability Prediction

Accurate selection of bovine embryos is a challenging task, as current practice relies on a single expert assessment on the seventh day after insemination, resulting in high rates of pregnancy loss. Time-lapse videomicroscopy provides detailed information on early development, but is difficult to exploit because of complex motion patterns and time-consuming analysis. We propose TransFACT, a transformer-based framework for modeling early developmental stages and embryo transferability using 2D time-lapse videos from the first four days of development. TransFACT combines frame-level temporal features with stage-level representations, using developmental stages as auxiliary supervision to predict transferability on day four. Our experiments demonstrate that TransFACT, by leveraging an existing method designed for action recognition, achieves superior performance than its competitor in predicting embryo transferability.

Yasmine Hachani, Patrick Bouthemy, Elisa Fromont +3

MALT · Inria center at Rennes University, France · University of Rennes, IRISA France +4

Clinical Outcome Prediction

May 17, 2026q-bio.OT

A Logistic Regression Model to Predict Malaria Severity in Children

One of the main causes of death around the globe is malaria. Researchers have sought to develop predictive models for malaria outbreaks based on meteorological data, climate data and the breeding cycle of Plasmodium, the causative agent of malaria. This study predicts the severity of malaria based on environmental and biological factors. A logistic regression model was developed in this study to predict the severity of malaria based on such factors as sickle cell disease, stagnant water, garbage dump, wet lawns, and the use of treated mosquito nets, with an 83.3% accuracy rate. The study was carried out in the Bosomtwe District of Ghana with 417 respondents. It was deduced that although children in the District are highly prone to malaria infection, the severity is very low. The study recommends that not just having a good sample size alone is important during machine learning model development, but also having a good sample representation of the various class labels is equally important.

Mary Opokua Ansong, Asare Yaw Obeng, Samuel King Opoku

Logistic Regression Clinical Outcome Prediction

May 16, 2026cs.AI

From Static Risk to Dynamic Trajectories: Toward World-Model-Inspired Clinical Prediction

Clinical decision-making is a feedback system where risk estimates influence treatment, which in turn changes disease trajectories, and both shape clinicians' measurement practices. Static prediction often fails clinically: models trained on observational care logs conflate disease biology with clinician behavior, particularly under treatment confounder feedback and irregular or informative observation. This Review focuses on intervention-aware disease trajectory modeling in clinical AI--methods estimating patient-specific longitudinal disease evolution and assessing trajectory changes under alternative treatments. We organize the field around six linked components: three decision tasks (factual forecasting, counterfactual estimation, policy evaluation) and three data-generating mechanisms (disease evolution, treatment assignment, observation process) that determine identifiability. We present the first unified framework bridging forecasting, counterfactual trajectories, and policy evaluation across discrete/continuous time, explicitly addressing treatment assignment, time-varying confounding, and observation bias. We synthesize key method families (multistate/joint models, temporal point-process, deep sequence architectures, longitudinal causal inference), map them to relevant components, and align evaluation with claim strength via overlap diagnostics, uncertainty quantification, off-policy robustness, and target-trial validation. This synthesis advances benchmark prediction to decision-grade clinical evidence, enabling treatment-sensitive individualized futures, pre-deployment policy stress-testing, and safer closed-loop learning health systems that adapt/abstain when evidence is insufficient.

Pujun Feng, Xiaoyu Guo, Seyed Ehsan Saffari +10

Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR 999078, China. · Medin.ai, Beijing 100871, China. · School of Software & Microelectronics, Peking University, Beijing 100871, China. +8

Causal Effect Estimation Off-Policy Evaluation Healthcare Clinical Outcome Prediction Counterfactual Prediction Causal Inference+2

May 16, 2026eess.SP

Prognostic Value of Lung Ultrasound Biomarkers for Readmission Risk in Congestive Heart Failure: A Pilot Data-Driven Analysis

Hospital readmission within 30 days of discharge is a leading driver of morbidity, mortality, and avoidable healthcare expenditure in congestive heart failure (CHF). Current clinical risk stratification tools rely primarily on non-imaging data and exhibit limited predictive performance. Point-of-care lung ultrasound (LUS) offers a sensitive, noninvasive window into the pulmonary congestion that characterizes CHF decompensation, yet its prognostic utility for readmission prediction remains largely unexplored. We present a pilot feasibility study, the first systematic machine learning study using B-mode LUS acquired during hospitalization to predict 30-day CHF readmission. Quantitative spatiotemporal embeddings are extracted from a pretrained Temporal Shift Module (TSM) ResNet-18 encoder, and interpretable biomarker features are separately evaluated. Through structured ablations over lung view, temporal representation, multi-view fusion, and cross-lung augmentation, we identify the key imaging factors driving readmission risk. Our findings reveal that (1) dependent lower-lung regions (Left-3, Right-3) carry the strongest prognostic signal, consistent with their greater susceptibility to hydrostatic congestion; (2) temporal difference features between sequential examinations substantially outperform single-timepoint representations, highlighting the importance of capturing disease trajectory; and (3) multi-view feature concatenation yields the best overall performance, with our top MLP model achieving an F1 score of 0.80 (95% CI: 0.62-0.96). Biomarker analysis further reveals that pleural-line abnormalities, including breaks and indentations, are as informative as the canonical A-line and B-line markers. These results support POCUS-derived biomarkers as practical, interpretable tools for noninvasive CHF risk stratification.

Jana Armouti, Laura Hutchins, Jacob Duplantis +12

Carnegie Mellon University, Pittsburgh, USA · LSUHSC Internal Medicine, New Orleans, USA · Cosmetic Surgery Facility LLC, Baltimore, MD 21093, USA

Longitudinal Medical Image Analysis Clinical Outcome Prediction Ultrasound Imaging

May 14, 2026cs.CV

Predicting Response to Neoadjuvant Chemotherapy in Ovarian Cancer from CT Baseline Using Multi-Loss Deep Learning

Ovarian cancer is the most lethal gynecologic malignancy: around 60% of patients are diagnosed at an advanced stage, with an associated 5-year survival rate of about 30%. Early identification of non-responders to neoadjuvant chemotherapy remains a key unmet need, as it could prevent ineffective therapy and avoid delays in optimal surgical management. This work proposes a non-invasive deep learning framework to predict neoadjuvant chemotherapy response from pre-treatment contrast-enhanced CT by leveraging automatically derived 3D lesion masks. The approach encodes axial slices with a partially fine-tuned pretrained image encoder and aggregates slice-level representations into a volumetric embedding through an attention-based module. Training combines classification loss with supervised contrastive regularization and hard-negative mining to improve separation between ambiguous responders and non-responders. The method was developed on a retrospective single-center cohort from the European Institute of Oncology (Milan, IT), including 280 eligible patients (147 responder, 133 non-responder). On the test cohort, the model achieved a ROC-AUC of 0.73 (95% CI: 0.58-0.86) and an F1-score of 0.70 (95% CI: 0.56-0.82). Overall, these results suggest that the proposed architecture learns clinically relevant predictive patterns and provides a robust foundation for an imaging-based stratification tool.

Francesco Pastori, Francesca Fati, Marina Rosanu +8

Department of Gynecologic Oncology, European Institute of Oncology, IEO, IRCCS, Milan, Italy · Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy · Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, USA +2

Clinical Outcome Prediction Oncology

May 14, 2026cs.CV

Vision-Core Guided Contrastive Learning for Balanced Multi-modal Prognosis Prediction of Stroke

Deep learning and multi-modal fusion have demonstrated transformative potential in medical diagnosis by integrating diverse data sources. However, accurate prognosis for ischemic stroke remains challenging due to limitations in existing multi-modal approaches. First, current methods are predominantly confined to dual-modal fusion, lacking a framework that effectively integrates the trifecta of medical images, structured clinical data, and unstructured text. Second, they often fail to establish deep bidirectional interactions between modalities; To address these critical gaps, this paper proposes a novel tri-modal fusion model for ischemic stroke prognosis. Our approach first enriches the data representation by employing a Large Language Model (LLM) to automatically generate semi-structured diagnostic text from brain MRIs. This process not only addresses the scarcity of expert annotations but also serves as a regularized semantic enhancement, improving multimodal fusion robustness. Furthermore, we design a core component termed the Vision-Conditioned Dual Alignment Fusion Module (VDAFM), which strategically uses visual features as a conditional prior to guide fine-grained interaction with the generated text. This module achieves a dynamic and profound fusion through a dual semantic alignment loss, effectively mitigating modal heterogeneity. Extensive experiments on a real-world clinical dataset demonstrate that our model achieves state-of-the-art performance.

Liren Chen, Lidong Sun, Mingyan Huang +5

School of Information Science and Engineering, East China University of Science and Technology, Shanghai, 200237, PR China

Cross-Modal Alignment Clinical Outcome Prediction Multimodal Contrastive Learning Multimodal Fusion

May 13, 2026cs.LG

MILM: Large Language Models for Multimodal Irregular Time Series with Informative Sampling

Multimodal irregular time series (MITS) consist of asynchronous and irregularly sampled observations from heterogeneous numerical and textual channels. In healthcare, for example, patients' electronic health records (EHR) include irregular lab measurements and clinical notes. The irregular timing and channel patterns of observations carry predictive signal alongside the numerical values and textual content. LLMs are natural candidates for processing such heterogeneous data, given their extensive pretrained knowledge spanning textual and numerical domains. We introduce MILM (Multimodal Irregular time series Language Model), which represents MITS as time-ordered triplets in Extensible Markup Language (XML) format and fine-tunes an LLM through a two-stage strategy for MITS classification. The first stage trains on value-redacted MITS to predict from sampling patterns alone, and the second stage trains on full MITS to jointly model sampling patterns and observed values. Our two-stage model (MILM-2S) and its single-stage counterpart (MILM-Direct) achieve the best and second-best average performance on multiple EHR datasets. Further value redaction evaluations confirm that sampling patterns carry predictive signal and that MILM-2S learns to exploit them. In the value pending evaluation we introduce, where some values are unavailable at prediction time, MILM-2S outperforms MILM-Direct by a larger margin compared to standard evaluation. For MILM-2S, preserving the time and channel of value-pending observations as additional sampling information further improves in-hospital mortality prediction.

Hsing-Huan Chung, Shijun Li, Yoav Wald +3

University of Texas at Austin · Technion-IIT · Johns Hopkins University

Irregular Time-Series Modeling Healthcare Time Series Classification Multimodal Large Language Models Clinical Outcome Prediction

May 13, 2026cs.LG

Dynamical Predictive Modelling of Cardiovascular Disease Progression Post-Myocardial Infarction via ECG-Trained Artificial Intelligence Model

Myocardial infarction (MI) is a leading cause of death, and its adverse outcomes are urgent to predict. Yet ECG-based prognostic models underperform because deep learning requires large, labelled datasets, which are scarce in medicine. Foundation models can learn from unlabelled ECGs via selfsupervision, but medically relevant training strategies remain underexplored. We propose a pretrained artificial intelligence model that combines patient-specific temporal information using contrastive learning with supervised multitask heads, then fine-tunes on post-MI outcome prediction. The proposed model outperformed a model trained from scratch (0.794 vs 0.608 AUC) showing that clinically structured ECG modelling improves classification in limited data regimes.

Riccardo Cavarra, Lupo Lovatelli, Shaheim Ogbomo-Harmitt +4

King’s College London, St Thomas’ Hospital, London, UK · North Bristol NHS Trust, Bristol, UK

Electrocardiography Clinical Outcome Prediction Electrocardiogram Foundation Models Time-Series Foundation Models

May 13, 2026cs.CV

Prediction of Rectal Cancer Regrowth from Longitudinal Endoscopy

Clinical trial studies indicate benefit of watch-and-wait (WW) surveillance for patients with rectal cancer showing a complete or near clinical response (CR) directly after treatment (restaging). However, there are no objectively accurate methods to early detect local tumor regrowth (LR) in patients undergoing WW from follow-up exams. Hence, we developed Temporal Rectal Endoscopy Cross-attention (TREX), a longitudinal deep learning approach that combines pairs of images acquired at restaging and follow-up to distinguish CR from LR. TREX uses pretrained Swin Transformers in a siamese setting to extract features from longitudinal images and dual cross-attention to combine the features without spatial co-registration between image pairs. TREX and Swin-based baselines were trained under two settings: (a) detecting LR or CR at the last available follow-up and (b) early detection of LR at 3--6, 6--12, and 12--24 months before clinical confirmation. TREX achieved the highest accuracy in detecting LR with a high sensitivity of 97%

\pm

6% and a balanced accuracy of 90%

\pm

3%, and outperformed all baselines in early detection at both 3--6 (74%

\pm

1%) and 6--12 months (62%

\pm

4%) prior to clinical detection. Clinical validation via a surgeon survey showed that TREX matched attending-level overall accuracy (TREX: 86.21% vs.\ Clinicians: 87.84%

\pm

1.28%). Finally, we explored TREX's ability to predict treatment response by combining pre-treatment (pre-TNT) and restaging endoscopies, achieving a balanced accuracy of 73%

\pm

12%. These results show that longitudinal deep learning analysis of endoscopy may improve surveillance and enable earlier identification of rectal cancer regrowth.

Jorge Tapias Gomez, Despoina Kanata, Aneesh Rangnekar +8

School of Computer Science, Cornell University and Cornell Tech, New York, NY · Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center, New York, NY · Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY +3

Endoscopy Medical Image Analysis Longitudinal Medical Image Analysis Clinical Outcome Prediction Medical Image Classification Oncology

May 11, 2026cs.LG

ReTAMamba: Reliability-Aware Temporal Aggregation with Mamba for Irregular Clinical Time Series Prediction

Clinical time-series data are difficult to model with methods designed for regular sequences because they exhibit irregular sampling, frequent missing values, and heterogeneous observation patterns across variables. Existing approaches commonly use observation masks and time-gap information, but they do not continuously capture the decaying reliability of past observations or consistently organize multi-resolution information within a coherent temporal context during aggregation. To address these limitations, we propose Reliability-aware Temporal Aggregation with Mamba (ReTAMamba), which reconstructs clinical time series as time-variable token sequences, estimates observation reliability from missingness and elapsed time, and augments interval summaries with statistical descriptors. Chronological Weaving is used to integrate short- and long-term temporal information within a coherent temporal context, and a budgeted token router is applied to constrain sequence length while preserving informative summaries. Experiments on MIMIC-IV, eICU, and PhysioNet 2012 show that ReTAMamba consistently improves AUPRC over strong baselines, with average relative gains of 7.51%, 7.80%, and 10.15%, respectively. Cohort-level and patient-level analyses on eICU further showed that the learned mean decay for more dynamic signals, such as heart rate and blood pressure, was 24.3% larger than that for relatively static signals, such as laboratory test variables. These findings suggest that effective prediction in irregular clinical time series requires modeling not only what was measured, but also when and how it was observed, including information freshness and observation timeliness.

Jinwoong Kim, Sangjin Park

Department of Industrial Data Engineering Hanyang University Seoul, Republic of Korea

Irregular Time-Series Modeling Clinical Outcome Prediction Longitudinal EHR Modeling Multiscale Time-Series Modeling

May 11, 2026cs.CL

The Association of Transformer-based Sentiment Analysis with Symptom Distress and Deterioration in Routine Psychotherapy Care

Sentiment analysis has been of long-standing interest in psychotherapy research. Recently, the Transformer deep learning architecture has produced text-based sentiment analysis models that are highly accurate and context-aware. These models have been explored as proxies for emotion measurement instruments in psychotherapy, but not investigated as stand-alone psychometric tools. Using proposed utterance-level and session-level sentiment features derived from a fine-grained sentiment model on a large corpus of psychotherapy sessions (N = 751), we investigate the distribution of session aggregated sentiment scores. Further, we characterize the relationship of these features to individual components and the overall score of the OQ-45 instrument and find that this sentiment feature is most strongly correlated to components related to emotional valence in directionally intuitive ways. Finally, we report that there are statistically significant differences between the sentiment distributions for patients flagged as at risk of deterioration or dropping out of care via either the OQ Rational or Empirical outcome models. These correlations to a fully-validated psychometric instrument demonstrate that these proposed sentiment features are, at least, adjunctive measures of client distress and deterioration.

Douglas K. Faust, Peter Awad, Alexandre Vaz +1

Sentio University, Torrance, CA, USA · Western Washington University, Department of Mathematics, Bellingham, WA, USA

Sentiment Analysis Clinical Outcome Prediction Psychometric Validation Clinical NLP

May 8, 2026cs.CV

Multimodal Stepwise Clinically-Guided Attention Learning for Pathological Complete Response Prediction in Breast Cancer

Pathological complete response (pCR) is a key prognostic factor in breast cancer patients undergoing neoadjuvant therapy, strongly associated with long-term survival and treatment personalization. However, accurate pre-treatment pCR prediction remains challenging due to severe class imbalance and limited generalizability across diverse clinical settings. In this work, we propose a multimodal stepwise clinically-guided attention learning framework for pCR prediction from breast magnetic resonance imaging (MRI), designed to address these limitations through medically grounded spatial guidance and multimodal integration. The approach follows a stepwise training strategy inspired by physician reasoning: the model first learns global discriminative imaging patterns, then attention mechanisms are introduced to constrain the network toward tumor regions, and finally clinical variables are integrated to refine decision-making. This guidance strategy encourages prioritization of task-relevant features, improving identification of responders despite their limited representation in the dataset. Moreover, grounding attention in anatomically consistent tumor regions reduces reliance on dataset-specific patterns, thereby enhancing cross-institutional generalization. The framework is evaluated through external validation across heterogeneous MRI cohorts. Compared to non-guided single-stage baselines, the proposed approach improves sensitivity while maintaining competitive specificity, and produces anatomically coherent attention maps that support interpretation of the model's predictions. These findings highlight the potential of clinically-guided multimodal attention learning for robust and generalizable pCR prediction in breast cancer.

Alice Natalina Caragliano, Valerio Guarrasi, Michela Gravina +2

Unit of Artificial Intelligence and Computer Systems, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy · Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy · Department of Diagnostics and Intervention, Radiation Physics, Biomedical Engineering, Umeå University, Umeå, Sweden

Breast Cancer Clinical Outcome Prediction Multimodal Classification Oncology Explainable Medical Image Analysis

May 5, 2026cs.AI

Actionable Real-Time Modeling of Surgical Team Dynamics via Time-Expanded Interaction Graphs

Surgical team performance arises from complex interactions between technical execution and non-technical skills, including communication and coordination dynamics. However, current surgical AI systems predominantly model visual workflow signals, lacking structured representations of intraoperative team interactions over time. We propose a real-time actionable approach for modeling surgical team dynamics using time-expanded interaction graphs, where team members are modeled as time-indexed nodes and communication exchanges define directed edges. This spatio-temporal expansion enables dynamic interaction modeling, while allowing efficient inference with a static graph neural network. The model predicts procedural efficiency as the deviation from the expected duration and supports real-time deployment. Beyond prediction, we perform a counterfactual analysis to identify minimal changes in communication structure and interpretable behavioral variables associated with improved predicted outcomes. Experiments on recorded surgical procedures show that structured modeling of team interactions improves early identification of prolonged interventions and provides coherent, actionable explanations. This work advances surgical AI toward real-time, team-aware, and actionable decision support in the operating room.

Vincenzo Marco De Luca, Antonio Longa, Giovanna Varni +1

a University of Trento · b UiT the Arctic University of Norway

Clinical Outcome Prediction Dynamic Graph Learning Spatiotemporal GNNs

May 5, 2026cs.LG

A Domain Incremental Continual Learning Benchmark for ICU Time Series Model Transportability

In recent years, machine learning has made significant progress in clinical outcome prediction, demonstrating increasingly accurate results. However, the substantial resources required for hospitals to train these models, such as data collection, labeling, and computational power, limit the feasibility for smaller hospitals to develop their own models. An alternative approach involves transferring a machine learning model trained by a large hospital to smaller hospitals, allowing them to fine-tune the model on their specific patient data. However, these models are often trained and validated on data from a single hospital, raising concerns about their generalizability to new data. Our research shows that there are notable differences in measurement distributions and frequencies across various regions in the United States. To address this, we propose a benchmark that tests a machine learning model's ability to transfer from a source domain to different regions across the country. This benchmark assesses a model's capacity to learn meaningful information about each new domain while retaining key features from the original domain. Using this benchmark, we frame the transfer of a machine learning model from one region to another as a domain incremental learning problem. While the task of patient outcome prediction remains the same, the input data distribution varies, necessitating a model that can effectively manage these shifts. We evaluate two popular domain incremental learning methods: data replay, which stores examples from previous data sources for fine-tuning on the current source, and Elastic Weight Consolidation (EWC), a model parameter regularization method that maintains features important for both data sources.

Ryan King, Conrad Krueger, Ethan Veselka +2

Computer Science & Engineering, Texas A&M University, College Station, United States

Clinical Outcome Prediction Domain-Incremental Learning Replay-Based Continual Learning Cross-Dataset Generalization

May 5, 2026q-bio.QM

A Machine Learning Framework for EEG-Based Prediction of Treatment Efficacy in Chronic Neck Pain

Chronic neck pain is a leading cause of disability worldwide, and current treatment selection remains largely trial and error. We present a machine learning framework that uses electroencephalography to predict treatment efficacy in patients with chronic neck pain, with the goal of supporting individualized therapy and reducing the burden on healthcare systems. The framework centers on a rigorous data preprocessing stage tailored to the characteristics of each EEG recording type. For resting-state EEG, the preprocessing pipeline comprises baseline signal removal, bad channel identification and exclusion, re-referencing, bandpass and notch filtering, Independent Component Analysis, and power spectral density analysis. For motor execution and motor imagery recordings, the same initial steps are applied, after which signals are aligned to trigger events so that event-related desynchronization (ERD) and event-related synchronization (ERS) can be quantified. Synchronously recorded electromyography data are bandpass filtered and smoothed with a moving average, then correlated with the corresponding EEG channels to characterize the EEG EMG relationship during attempted movement. In parallel, we performed an extensive literature review of machine learning models applied to clinical EEG (763 records initially screened, 16 patient and 47 healthy-control studies retained), to inform the post-processing strategy. Through this combined preprocessing and review effort, we aim to develop a robust predictive model that can support personalized healthcare strategies in chronic pain management.

Xiru Wang, Aiden Li, Hongzhao Tan +3

Department of Kinesiology, Faculty of Science, McMaster University, Hamilton, ON, Canada · W Booth School of Engineering Practice and Technology, Faculty of Engineering, McMaster University, Hamilton, ON, Canada

Clinical Outcome Prediction

May 5, 2026cs.LG

Disentangling Shared and Task-Specific Representations from Multi-Modal Clinical Data

Real-world clinical data is inherently multimodal, providing complementary evidence that mirrors the practical necessity of jointly assessing multiple related outcomes. Although multi-task learning can improve efficiency by sharing information across outcomes, existing approaches often fail to balance shared representation learning with outcome-specific modeling. Hard parameter sharing can trigger negative transfer when task gradients conflict, while flexible sharing may still entangle shared and task-specific signals. To address this, we propose a multi-task framework built on a unified Transformer for multimodal fusion, augmented with Orthogonal Task Decomposition (OrthTD) to split patient representations into shared and task-specific subspaces and impose a geometric orthogonality constraint to reduce redundancy and isolate task-specific signals. We evaluated OrthTD on a real-world cohort of 12,430 surgical patients for predicting four outcomes. OrthTD achieved average AUC (area under the receiver operating characteristic curve) of 87.5% and average AUPRC (area under the precision-recall curve) of 37.2%, consistently outperformed advanced tabular and multi-task methods. Notably, OrthTD achieves substantial gains in AUPRC, indicating superior performance in identifying rare events within imbalanced clinical data. These results suggest that enforcing non-redundant shared and task-specific representations can improve multi-outcome prediction from multimodal clinical data.

He Lyu, Huolin Zeng, Junren Wang +7

Department of Anesthesiology and West China Biomedical Big Data Center West China Hospital, Sichuan University, Chengdu, China · Med-X Center for Informatics, Sichuan University, Chengdu, China · Department of National Key Laboratory of Fundamental Science on Synthetic Vision, Sichuan University, Chengdu, China +4

Disentangled Representation Learning Representation Learning Clinical Outcome Prediction Multi-Task Learning Orthogonal Representation Learning Multimodal Fusion

May 5, 2026cs.LG

Enhance the after-discharge mortality rate prediction via learning from the medical notes

With the increase of the Electronic Health Records (EHR) data, more and more researchers are developing machine learning models to learn from the medical notes. These unstructured text data pose significant challenges on the learning process as the quality of data is low. These data are often messy, repetitive and redundant. We have shown these notes data to be informative by conducting the after-discharge mortality rate prediction task. The AUC-ROC for models using the medical note information is generally 0.1 higher than those without the medical notes. Furthermore, we propose the Deep Neural Network(DNN) model with 'pooling' mechanism to enhance the mortality prediction. Based on the experimental results, we demonstrate that the proposed model outperforms the traditional machine learning models like the tree-based models. The proposed method learns from the most informative medical notes and improves the prediction accuracy significantly. The AUC-ROC for the proposed model is 2% to 14% higher than the traditional ones in 15-days, 30-days, 60-days, 365-days after-discharge mortality prediction tasks. Moreover, we can discover some interesting knowledge through the traditional and proposed models. These knowledge are inspiring but also consistent with the previous findings. The models are able to reveal the relationships between the informative keywords and documents from the medical notes and the severity of the patients.

Zijiang Yang

University of Texas at Austin, Austin TX 78712, USA

Healthcare Clinical Outcome Prediction Electronic Health Records Mortality Prediction

May 4, 2026cs.LG

Forecasting Medium-Horizon Alzheimer's Disease Progression: Residual Gap-Aware Transformers for 24-Month CDR-SB Change from ADNI Clinical and Biomarker Histories

Medium-horizon Alzheimer's disease progression prediction is difficult because future clinical scores can remain tied to baseline severity, while biomarker histories are irregular and incompletely observed. We develop an anchor-based analysis of 24-month Clinical Dementia Rating Sum of Boxes (CDR-SB) change using harmonized Alzheimer's Disease Neuroimaging Initiative (ADNI) tables. Each labeled sample is anchored at a mild cognitive impairment visit, uses only clinical and biomarker history observed at or before that anchor, and defines the response as CDR-SB at the future visit closest to 24 months within an 18--30 month window minus anchor CDR-SB. The analytic cohort contains 2,600 labeled anchors from 858 participants and 7,276 longitudinal rows. We propose a residual gap-aware transformer that combines a mixed-effects statistical reference with transformer-based residual learning from pre-anchor clinical and biomarker histories. The model uses participant-level random intercepts in the mixed-effects reference, observation-level triplet tokenization for irregular histories, and a learned nonnegative time-gap penalty inside self-attention. We compare the proposed model with a Bayesian-information-criterion-selected linear mixed-effects baseline, GRU-D, and STraTS under repeated participant-level train--test splits. Across five participant-level random seeds, the proposed model achieves the best mean test performance across all reported metrics, reducing MSE by 13.1% and increasing prediction--observation correlation by 26.4% relative to the mixed-effects baseline. It also improves over both GRU-D and STraTS in mean error and correlation. These results show that statistical anchoring and gap-aware residual learning provide a useful structure for medium-horizon Alzheimer's disease progression prediction.

Ran Tong, Tong Wang, Lanruo Wang +1

Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080, United States · Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States · Naveen Jindal School of Management, University of Texas at Dallas, Richardson, TX 75080, United States +1

Irregular Time-Series Modeling Alzheimer's Disease Residual Learning Clinical Outcome Prediction Alzheimer's Disease Progression Prediction Time Series Transformers

May 3, 2026cs.CV

GeoSAE: Geometric Prior-Guided Layer-Wise Sparse Autoencoder Annotation of Brain MRI Foundation Models

Brain MRI foundation models learn rich representations of anatomy, but interpreting what clinical information they encode remains an open problem. Standard sparse autoencoders (SAEs) suffer from severe feature collapse in deep transformer layers, and in Alzheimer's disease (AD) research, aging confounds nearly every clinical variable, making naive annotation unreliable. We propose GeoSAE, a geometry-guided SAE framework that uses the foundation model's learned manifold structure to prevent feature collapse and annotates each surviving feature via age-deconfounded partial correlations. Applied to ~14k T1-weighted MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Australian Imaging biomarkers and Lifestyle (AIBL) datasets, GeoSAE identifies a compact, fully interpretable feature set that predicts mild cognitive impairment (MCI)-to-AD conversion (AUC 0.746) using only 2% of the embedding dimensions, while comorbidity-annotated features achieve only chance-level performance. The identified features replicate across cohorts without retraining (r=0.97) and localize to neuroanatomically distinct regions consistent with Braak staging. This shows that geometry-guided SAEs can extract interpretable, biomarkers from frozen brain MRI foundation models.

Favour Nerrise, Lucy Yin, Mohammad H. Abbasi +2

Stanford University · Stanford University, CA

Alzheimer's Disease Medical Imaging Foundation Models Clinical Outcome Prediction Geometric Representation Learning Sparse Autoencoders Alzheimer's Disease Classification+3

May 2, 2026cs.CL

ReMedi: Reasoner for Medical Clinical Prediction

Predicting future clinical outcomes from electronic health records (EHR) remains challenging due to the complexity and heterogeneity of patient data. LLMs have shown strong potential for such predictive tasks, yet existing approaches mainly focus on enhancing medical knowledge through distillation or RAG while relying on the model's internal ability to interpret contextual information. In this work, we present ReMedi (Reasoner for Medical Clinical Prediction), a framework for improving clinical outcome prediction from EHR. ReMedi generates rationale-answer pairs using a challenging sample regeneration mechanism for complex clinical questions, which leverages ground-truth answers as hints to enhance reasoning for further fine-tuning and preference tuning. ReMedi integrates ground-truth outcome guidance into the preference data construction loop, regenerating rationale-answer variants. By tuning on these rationale-answer pairs, the model improves its predictive performance. Experiments on multiple EHR prediction tasks demonstrate substantial gains of up to 19.9 percent over state-of-the-art baselines in terms of F1 score, underscoring ReMedi's effectiveness in real-world clinical prediction.

Yushi Cao, Yiming Chen, Hongchao Jiang +2

ASUS Intelligent Cloud Services (AICS), Singapore · NTU Artificial Intelligence Center of Research Excellence (NTU AI-CoRE), Taiwan · National University of Singapore, Singapore

Fine-Tuning Clinical Outcome Prediction Clinical Reasoning Electronic Health Records Medical LLMs

May 2, 2026cs.AI

NEURON: A Neuro-symbolic System for Grounded Clinical Explainability

Clinical AI adoption is hindered by the black-box/grey-box nature of high-performing models, which lack the ontological grounding and narrative transparency required for professional-level explainability. We present NEURON, a neuro-symbolic system designed to enhance both predictive reliability and clinical interpretability. NEURON integrates SNOMED CT ontology-informed structural representations with machine learning models to bridge the gap between raw data and medical nomenclature. To facilitate human-aligned interaction, the system utilizes a Retrieval-Augmented Generation (RAG) grounded LLM layer to synthesize SHAP feature attributions and patient-specific clinical notes into coherent, natural-language explanations. Validated on the MIMIC-IV dataset for Acute Heart Failure mortality prediction, NEURON improved the AUC from 0.74-0.77 to 0.84-0.88 and significantly outperformed raw SHAP visualizations in human-aligned metrics (0.85 vs. 0.50). Our results demonstrate that NEURON offers a robust, scalable engineering solution for deploying trustworthy, human-centered connected health applications.

Anuradha Chandrasekaran, Dimitrios Zikos, Mutlu Mete +3

University of North Texas, USA and Texas Tech University Health Sciences Center, USA · Texas Tech University Health Sciences Center, USA · University of North Texas, USA

Explainable Artificial Intelligence Clinical Outcome Prediction Neuro-Symbolic AI Mortality Prediction

May 1, 2026cs.LG

Disease Is a Spectral Perturbation

We propose a novel method of understanding disease transformation from a healthy baseline with biomarker-level explainability. By modeling the biomarker covariance matrices of healthy controls and disease states, the perturbation can be individually characterized to accomplish mechanistic explanations of disease trajectories, both at a molecular level and for individual patients. Given a cohort of n patients each measured on p biomarkers, we define the biomarker "Hamiltonian" H = X^T X / n \in R^{p \times p}, where X \in R^{n \times p} is the covariant biomarker matrix. The eigenvectors of H define a set of normal modes of biomarker coordination, and the eigenvalues quantify the energy carried by each mode. In the healthy state, the reference Hamiltonian H_0 governs this structure where disease perturbs H_0 by an additive operator ΔH, thus shifting eigenvalues and rotating eigenvectors in proportion to the severity of pathological disruption. We formalize this framework, derive the spectral change given a disease perturbation, and demonstrate that the projection of a newly diagnosed patient's cumulative biomarker covariance structure onto disease-discriminant eigenmodes constitutes an optimal prognostic statistic for greater precision in disease prognosis. This work serves as a veritable white paper with application across a panoply of disease frameworks from cancer to neurodegenerative disorders.

John D. Mayfield, Matthew S. Rosen

Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital · Department of Radiology, Harvard Medical School, Boston, MA 02129

Clinical Outcome Prediction Spectral Methods

May 1, 2026cs.LG

Temporal Data Requirement for Predicting Unplanned Hospital Readmissions

With the proliferation of Electronic Health Records (EHRs), a critical challenge in building predictive models is determining the optimal historical data time window to maximize accuracy. This study investigates the impact of various observation windows ranging from the day of surgery to three years prior on predicting 30-day readmission following hip and knee arthroplasties. The dataset encompasses both structured encounter records (over 4 million) and unstructured clinical notes (80,000) from 7,174 patients. To extract meaning from the clinical notes, we employed a suite of non neural (BOW, count BOW, TF IDF, LDA) and neural encoders (BERT, 1D CNN, BiLSTM, Average). We subsequently evaluated models utilizing clinical notes alone, structured data alone, and a combination of both modalities. Our results demonstrate that the optimal time window for unstructured clinical notes is significantly shorter than for structured data, maximum predictive performance was achieved using notes from just three to six months prior to surgery. In contrast, performance using structured data improved as the time window lengthened, but strictly plateaued after twelve months. These modality-specific temporal patterns remained consistent regardless of model complexity or encoder type. Ultimately, these findings challenge the general assumption that more historical data inherently yields better machine learning predictions, establishing targeted time-window guidelines for optimizing readmission prediction models.

Ramin Mohammadi, Vahab vahdat, Sarthak Jain +3

Northeastern University, Boston, MA, US · Partners Healthcare Connected Health Innovation, Boston, MA, USA · MGH Institute for Technology Assessment, Boston, MA, USA +2

Clinical Outcome Prediction Clinical Prediction Longitudinal EHR Modeling Clinical Risk Prediction

May 1, 2026cs.LG

Deep Kernel Learning for Stratifying Glaucoma Trajectories

Effectively stratifying patient risk in chronic diseases like glaucoma is a major clinical challenge. Clinicians need tools to identify patients at high risk of progression from sparse and irregularly-sampled electronic health records (EHRs). We propose a novel deep kernel learning (DKL) architecture that leverages a Gaussian Process (GP) backend. The GP's kernel is defined by a transformer-based feature extractor applied to clinical-BERT embeddings to model glaucoma patient trajectories from multimodal EHR data. Our method successfully identifies three clinically distinct patient subgroups. Crucially, the model learns to decouple disease progression from current severity, identifying a high-risk group with a worsening trajectory despite having better average visual acuity than a second, stably poor group. This reveals that the model learns to identify progression risk rather than just the current disease state. This ability to stratify patients based on their risk trajectory progression offers a powerful tool for clinical decision support, enabling targeted interventions for high-risk individuals and improving the management of glaucoma care.

Bruce Rushing, Angela Danquah, Alireza Namazi +2

Research Computing, University of Virginia · School of Data Science, University of Virginia · School of Medicine, University of Virginia

Clinical Outcome Prediction Kernel Methods Longitudinal EHR Modeling Clinical Risk Prediction Gaussian Process Regression

Apr 30, 2026cs.LG

Linking spatial biology and clinical histology via Haiku

Integrating molecular, morphological, and clinical data is essential for basic and translational biomedical research, yet systematic frameworks for jointly modeling these modalities remain limited. Here we present Haiku, a tri-modal contrastive learning model trained on multiplexed immunofluorescence (mIF). It comprises 26.7 million spatial proteomics patches from 3,218 tissue sections across 1,606 patients spanning 11 organ types, with matched hematoxylin and eosin (H&E) histology and clinical metadata aligned in a shared embedding space. Haiku enables three-way cross-modal retrieval, improves downstream classification and clinical prediction tasks over unimodal baselines, and supports zero-shot biomarker inference through fusion retrieval conditioned on clinical metadata-only text descriptions. Across tasks, Haiku outperforms competing approaches, achieving cross-modal retrieval (Recall@50 up to 0.611 versus near-zero baseline), survival prediction (C-index 0.737, +7.91% relative improvement), and zero-shot biomarker inference (mean Pearson correlation 0.718 across 52 biomarkers). Furthermore, we introduce a counterfactual prediction framework in which modifying only clinical metadata while fixing tissue morphology surfaces niche-specific molecular shifts associated with breast cancer stage progression and lung cancer survival outcomes. In a lung adenocarcinoma case study, the counterfactual analysis recovers niche-specific shifts characterized by increased CD8 and granzyme B, reduced PD-L1, and decreased Ki67, broadly consistent with patterns reported for favorable outcomes. We present these counterfactual results as exploratory, hypothesis-generating signals rather than mechanistic claims. These capabilities demonstrate that tri-modal alignment via Haiku enables integrative analysis of spatial biology, bridging molecular measurements with clinical context for biological exploration.

Yan Cui, Jacob S. Leiby, Wenhui Lei +6

Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA · Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA · Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA +1

Computational Pathology Healthcare Clinical Outcome Prediction Cross-Modal Retrieval Multimodal Contrastive Learning

Apr 30, 2026cs.LG

PROMISE-AD: Progression-aware Multi-horizon Survival Estimation for Alzheimer's Disease Progression and Dynamic Tracking

Individualized Alzheimer's disease (AD) progression prediction requires models that use irregular visits, account for censoring, avoid diagnostic leakage, and provide calibrated horizon risks. We propose PROgression-aware MultI-horizon Survival Estimation for Alzheimer's Disease (PROMISE-AD), a leakage-safe survival framework for predicting conversion from cognitively normal (CN) to mild cognitive impairment (MCI) and from MCI to AD dementia using ADNI/TADPOLE tabular histories. PROMISE-AD converts pre-index visits into tokens with standardized measurements, missingness masks, longitudinal changes, time-normalized slopes, visit timing, and non-diagnostic categorical attributes. A temporal Transformer fuses global, attention-pooled, and latest-visit representations to estimate a progression score and latent discrete-time mixture hazards. Training combines survival likelihood, horizon-specific focal risk loss, progression ranking, hazard smoothness, and mixture-balance regularization, followed by validation-set isotonic calibration for 1-, 2-, 3-, and 5-year risks. In held-out testing across three seeds, PROMISE-AD achieved an integrated Brier score (IBS) of 0.085

\pm

0.012, C-index of 0.808

\pm

0.015, and mean time-dependent AUC of 0.840

\pm

0.081 for CN-to-MCI conversion, yielding the lowest IBS among compared methods. For MCI-to-AD conversion, PROMISE-AD achieved the highest C-index (0.894

\pm

0.018) and near-ceiling 5-year discrimination (AUROC 0.997

\pm

0.003; AUPRC 0.999

\pm

0.001), although some baselines had lower IBS. Ablations and interpretability supported longitudinal change features, fused temporal representations, mixture hazards, cognitive and functional measures, APOE4 status, and recent conversion-proximal visits. These findings suggest that progression-aware survival modeling can provide interpretable multi-horizon AD conversion risk estimates.

Qing Lyu, Jeremy Hudson, Mohammad Kawas +3

Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510 USA · Department of Radiology Oncology, Wake Forest University School of Medicine, Winston-Salem, NC 27157 USA · Department of Applied Mathematics & Statistics and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794 USA

Alzheimer's Disease Survival Analysis Clinical Outcome Prediction Alzheimer's Disease Progression Prediction Clinical Risk Prediction

Apr 30, 2026cs.CL

Multi-Level Narrative Evaluation Outperforms Lexical Features for Mental Health

How people narrate their experiences offers a window into how the mind organizes them. Computational approaches to therapeutic writing have evolved from lexical counting to neural methods, yet remain fragmented: dictionary tools miss discourse structure, while embeddings conflate local coherence with global organization. No existing framework maps these techniques onto the hierarchical processes through which narratives are constructed. Here we introduce a three-level framework - micro-level lexical features, meso-level semantic embeddings, and macro-level LLM narrative evaluation - and show, across 830 Chinese therapeutic texts spanning depression, anxiety, and trauma, that macro-level evaluation substantially outperforms lexical and embedding features for mental health prediction. This challenges the field's emphasis on word-counting: formal structural features (Labov's story grammar, RST coherence, propositional composition) demonstrate that narrative organization per se carries predictive signal, while clinically-grounded narrative dimensions capture how psychological states are expressed through discourse. Semantic embeddings add minimal independent value but yield incremental gains in multi-level classification. By grounding computational levels in discourse processing theory, this framework identifies macro-structural organization as the primary locus of clinical signal and generates testable hypotheses for intervention design and longitudinal research.

Yuxi Ma, Jieming Cui, Muyang Li +6

Institute for Artificial Intelligence, Peking University · School of Psychological and Cognitive Sciences, Peking University · School of Intelligence Science and Technology, Peking University +3

Document Understanding Depression Detection Mental Health Clinical Outcome Prediction Clinical Prediction Clinical NLP

Apr 29, 2026cs.AI

Toward Personalized Digital Twins for Cognitive Decline Assessment: A Multimodal, Uncertainty-Aware Framework

Cognitive decline is highly heterogeneous across individuals, which complicates prognosis, trial design, and treatment planning. We present the Personalized Cognitive Decline Assessment Digital Twin (PCD-DT), a multimodal and uncertainty-aware framework for modeling patient-specific disease trajectories from sparse, noisy, and irregular longitudinal data. The framework combines three methodological components: (1) latent state-space models for individualized temporal dynamics, (2) multimodal fusion for clinical, biomarker, and imaging features, and (3) uncertainty-aware validation and adaptive updating for robust digital twin operation. We also outline how conditional generative models can support data augmentation and stress testing for underrepresented progression patterns. As a preliminary feasibility study, we analyze longitudinal TADPOLE trajectories and show clear separation between cognitively normal and Alzheimer's disease cohorts in ADAS13, ventricle volume, and hippocampal volume over five years. We further conduct a multimodal next-visit prediction ablation using an LSTM sequence model on 3{,}003 visit-pair sequences derived from TADPOLE, where the combined cognitive plus MRI configuration achieves the lowest standardized RMSE for both ADAS13 (0.4419) and ventricle volume (0.5842), outperforming a Last Observation Carried Forward baseline. A Bayesian tensor modeling component for high-dimensional imaging fusion is also discussed. These results support the feasibility of the proposed architecture while also highlighting the need for stronger uncertainty calibration and longer-horizon predictive evaluation. The PCD-DT framework provides a principled starting point for personalized in silico modeling in neurodegenerative disease. This work positions PCD-DT as a foundational step toward clinically deployable, uncertainty-aware digital twin systems.

Bulent Soykan, Gulsah Hancerliogullari Koksalmis, Hsin-Hsiung Huang +1

Department of Mechanical, Industrial & Manufac. Eng. The University of Toledo Toledo, OH, USA · Department of Industrial Eng. and Mngt. Systems University of Central Florida Orlando, FL, USA · Department of Statistics and Data Science University of Central Florida Orlando, FL, USA +1

Alzheimer's Disease Clinical Outcome Prediction Digital Twins Alzheimer's Disease Progression Prediction

Apr 29, 2026cs.AI

Evaluating TabPFN for Mild Cognitive Impairment to Alzheimer's Disease Conversion in Data Limited Settings

Accurate prediction of conversion from Mild Cognitive Impairment (MCI) to Alzheimers Diseases (AD) is essential for early intervention, however, developing reliable conversion predictive models is difficult to develop due to limited longitudinal data availability We evaluate TabPFN (Tabular Pre-Trained Foundation Network) against traditional machine learning methods for predicting 3 year MCI to AD conversion using the TADPOLE dataset derived from ADNI. Using multimodal biomarker features extracted from demographics, APOE4, MRI volumes, CSF markers, and PET imaging, we conducted an experimental comparison across varying training set sizes (N=50 to 1000) and models including XGBoost, Random Forest, LightGBM, and Logistic Regression. TabPFN achieved one the highest performance (AUC=0.892), outperforming LightGBM (AUC=0.860) and demonstrating advantages in low data settings. At N=50 training samples, TabPFN maintained strong AUC while the traditional machine learning models struggles at small training samples. These findings demonstrate that foundation models are promising for disease prediction in data limited scenarios, such as Alzheimers diseases.

Brad Ye, Bulent Soykan, Gulsah Hancerliogullari Koksalmis +2

Department of Medicine, University of Central Florida College of Medicine, Orlando, FL, USA · NIMBUS Lab, University of Central Florida · Department of Mechanical, Industrial & Manufacturing Eng., The University of Toledo, Toledo, OH, USA +3

Tabular Foundation Models Alzheimer's Disease Clinical Outcome Prediction Prior-Data Fitted Networks Alzheimer's Disease Classification Alzheimer's Disease Progression Prediction

Apr 28, 2026cs.LG

Observable Neural ODEs for Identifiable Causal Forecasting in Continuous Time

Causal inference in continuous-time sequential decision problems is challenged by hidden confounding and partially observed states. We show that, under explicit structural assumptions, observability of the latent state enables identification of dynamic treatment effects through a continuous-time conditional front-door adjustment, even in the presence of hidden confounding. We derive a general adjustment formula and show that it reduces to a tractable state-space formula when unobserved contemporaneous disturbances are temporally uncorrelated. This formula expresses potential-outcome distributions under alternative treatment trajectories through the measurement model, latent dynamics, and the filtering distribution over latent states. We propose Observable Neural ODEs (ObsNODEs), Neural ODE models in observable normal form that implement this tractable adjustment for causal forecasting. ObsNODEs learn continuous-time dynamics with states reconstructible from observations, enabling outcome prediction under alternative treatment paths. Experiments on synthetic, semi-synthetic, and real-world clinical data demonstrate strong performance over recent sequence models, including external validation.

Jennifer Wendland, Nicolas Freitag, Maik Kschischo

Department of Computer Science University of Koblenz 53424 Koblenz, Germany

Causal Effect Estimation Clinical Outcome Prediction Causal Identifiability Causal Inference Neural ODEs