CAAT-EHR: Cross-Attentional Autoregressive Transformer for Multimodal Electronic Health Record Embeddings

Electronic health records (EHRs) provide a comprehensive source of longitudinal patient data, encompassing structured modalities such as laboratory results, imaging data, and vital signs, and unstructured clinical notes. These datasets, after necessary preprocessing to clean and format the data for analysis, often remain in their raw EHR form, representing numerical or categorical values without further transformation into task-agnostic embeddings. While such raw EHR data enables predictive modeling, its reliance on manual feature engineering or downstream task-specific optimization limits its utility for general-purpose applications. Deep learning (DL) techniques, such as recurrent neural networks (RNNs) and Transformers, have facilitated predictive tasks like disease progression and diagnosis prediction. However, these methods often struggle to fully exploit the temporal and multimodal dependencies inherent in EHR data due to their reliance on pre-processed but untransformed raw EHR inputs. In this study, we introduce CAAT-EHR, a novel architecture designed to bridge this gap by generating robust, task-agnostic longitudinal embeddings from raw EHR data. CAAT-EHR leverages self- and cross-attention mechanisms in its encoder to integrate temporal and contextual relationships across multiple modalities, transforming the data into enriched embeddings that capture complex dependencies. An autoregressive decoder complements the encoder by predicting future time points data during pre-training, ensuring that the resulting embeddings maintain temporal consistency and alignment. CAAT-EHR eliminates the need for manual feature engineering and enables seamless transferability across diverse downstream tasks. Extensive evaluations on benchmark datasets, demonstrate the superiority of CAAT-EHR-generated embeddings over pre-processed raw EHR data and other baseline approaches.

A machine learning approach for Premature Coronary Artery Disease Diagnosis according to Different Ethnicities in Iran

Premature coronary artery disease (PCAD) refers to the early onset of the disease, usually before the age of 55 for men and 65 for women. Coronary Artery Disease (CAD) develops when coronary arteries, the major blood vessels supplying the heart with blood, oxygen, and nutrients, become clogged or diseased. This is often due to many risk factors, including lifestyle and cardiometabolic ones, but few studies were done on ethnicity as one of these risk factors, especially in PCAD. In this study, we tested the rank of ethnicity among the major risk factors of PCAD, including age, gender, body mass index (BMI), visceral obesity presented as waist circumference (WC), diabetes mellitus (DM), high blood pressure (HBP), high low-density lipoprotein cholesterol (LDL-C), and smoking in a large national sample of patients with PCAD from different ethnicities. All patients who met the age criteria underwent coronary angiography to confirm CAD diagnosis. The weight of ethnicity was compared to the other eight features using feature weighting algorithms in PCAD diagnosis. In addition, we conducted an experiment where we ran predictive models (classification algorithms) to predict PCAD. We compared the performance of these models under two conditions: we trained the classification algorithms, including or excluding ethnicity. This study analyzed various factors to determine their predictive power influencing PCAD prediction. Among these factors, gender and age were the most significant predictors, with ethnicity being the third most important. The results also showed that if ethnicity is used as one of the input risk factors for classification algorithms, it can improve their efficiency. Our results show that ethnicity ranks as an influential factor in predicting PCAD. Therefore, it needs to be addressed in the PCAD diagnostic and preventive measures.

Extracting Inter-Protein Interactions Via Multitasking Graph Structure Learning

Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently, most PPI prediction methods focus primarily on the study of protein sequences, neglecting the critical role of the internal structure of proteins. This paper proposes a novel PPI prediction method named MgslaPPI, which utilizes graph attention to mine protein structural information and enhances the expressive power of the protein encoder through multitask learning strategy. Specifically, we decompose the end-to-end PPI prediction process into two stages: amino acid residue reconstruction (A2RR) and protein interaction prediction (PIP). In the A2RR stage, we employ a graph attention-based residue reconstruction method to explore the internal relationships and features of proteins. In the PIP stage, in addition to the basic interaction prediction task, we introduce two auxiliary tasks, i.e., protein feature reconstruction (PFR) and masked interaction prediction (MIP). The PFR task aims to reconstruct the representation of proteins in the PIP stage, while the MIP task uses partially masked protein features for PPI prediction, with both working in concert to prompt MgslaPPI to capture more useful information. Experimental results demonstrate that MgslaPPI significantly outperforms existing state-of-the-art methods under various data partitioning schemes.

Evaluating Spoken Language as a Biomarker for Automated Screening of Cognitive Impairment

Timely and accurate assessment of cognitive impairment is a major unmet need in populations at risk. Alterations in speech and language can be early predictors of Alzheimer's disease and related dementias (ADRD) before clinical signs of neurodegeneration. Voice biomarkers offer a scalable and non-invasive solution for automated screening. However, the clinical applicability of machine learning (ML) remains limited by challenges in generalisability, interpretability, and access to patient data to train clinically applicable predictive models. Using DementiaBank recordings (N=291, 64% female), we evaluated ML techniques for ADRD screening and severity prediction from spoken language. We validated model generalisability with pilot data collected in-residence from older adults (N=22, 59% female). Risk stratification and linguistic feature importance analysis enhanced the interpretability and clinical utility of predictions. For ADRD classification, a Random Forest applied to lexical features achieved a mean sensitivity of 69.4% (95% confidence interval (CI) = 66.4-72.5) and specificity of 83.3% (78.0-88.7). On real-world pilot data, this model achieved a mean sensitivity of 70.0% (58.0-82.0) and specificity of 52.5% (39.3-65.7). For severity prediction using Mini-Mental State Examination (MMSE) scores, a Random Forest Regressor achieved a mean absolute MMSE error of 3.7 (3.7-3.8), with comparable performance of 3.3 (3.1-3.5) on pilot data. Linguistic features associated with higher ADRD risk included increased use of pronouns and adverbs, greater disfluency, reduced analytical thinking, lower lexical diversity and fewer words reflecting a psychological state of completion. Our interpretable predictive modelling offers a novel approach for in-home integration with conversational AI to monitor cognitive health and triage higher-risk individuals, enabling earlier detection and intervention.

An Explainable Disease Surveillance System for Early Prediction of Multiple Chronic Diseases

This study addresses a critical gap in the healthcare system by developing a clinically meaningful, practical, and explainable disease surveillance system for multiple chronic diseases, utilizing routine EHR data from multiple U.S. practices integrated with CureMD's EMR/EHR system. Unlike traditional systems--using AI models that rely on features from patients' labs--our approach focuses on routinely available data, such as medical history, vitals, diagnoses, and medications, to preemptively assess the risks of chronic diseases in the next year. We trained three distinct models for each chronic disease: prediction models that forecast the risk of a disease 3, 6, and 12 months before a potential diagnosis. We developed Random Forest models, which were internally validated using F1 scores and AUROC as performance metrics and further evaluated by a panel of expert physicians for clinical relevance based on inferences grounded in medical knowledge. Additionally, we discuss our implementation of integrating these models into a practical EMR system. Beyond using Shapley attributes and surrogate models for explainability, we also introduce a new rule-engineering framework to enhance the intrinsic explainability of Random Forests.

Memorize and Rank: Elevating Large Language Models for Clinical Diagnosis Prediction

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

Exploring the Feasibility of Deep Learning Models for Long-term Disease Prediction: A Case Study for Wheat Yellow Rust in England

Wheat yellow rust, caused by the fungus Puccinia striiformis, is a critical disease affecting wheat crops across Britain, leading to significant yield losses and economic consequences. Given the rapid environmental changes and the evolving virulence of pathogens, there is a growing need for innovative approaches to predict and manage such diseases over the long term. This study explores the feasibility of using deep learning models to predict outbreaks of wheat yellow rust in British fields, offering a proactive approach to disease management. We construct a yellow rust dataset with historial weather information and disease indicator acrossing multiple regions in England. We employ two poweful deep learning models, including fully connected neural networks and long short-term memory to develop predictive models capable of recognizing patterns and predicting future disease outbreaks.The models are trained and validated in a randomly sliced datasets. The performance of these models with different predictive time steps are evaluated based on their accuracy, precision, recall, and F1-score. Preliminary results indicate that deep learning models can effectively capture the complex interactions between multiple factors influencing disease dynamics, demonstrating a promising capacity to forecast wheat yellow rust with considerable accuracy. Specifically, the fully-connected neural network achieved 83.65% accuracy in a disease prediction task with 6 month predictive time step setup. These findings highlight the potential of deep learning to transform disease management strategies, enabling earlier and more precise interventions. Our study provides a methodological framework for employing deep learning in agricultural settings but also opens avenues for future research to enhance the robustness and applicability of predictive models in combating crop diseases globally.

Integrating Probabilistic Trees and Causal Networks for Clinical and Epidemiological Data

Healthcare decision-making requires not only accurate predictions but also insights into how factors influence patient outcomes. While traditional Machine Learning (ML) models excel at predicting outcomes, such as identifying high risk patients, they are limited in addressing what-if questions about interventions. This study introduces the Probabilistic Causal Fusion (PCF) framework, which integrates Causal Bayesian Networks (CBNs) and Probability Trees (PTrees) to extend beyond predictions. PCF leverages causal relationships from CBNs to structure PTrees, enabling both the quantification of factor impacts and simulation of hypothetical interventions. PCF was validated on three real-world healthcare datasets i.e. MIMIC-IV, Framingham Heart Study, and Diabetes, chosen for their clinically diverse variables. It demonstrated predictive performance comparable to traditional ML models while providing additional causal reasoning capabilities. To enhance interpretability, PCF incorporates sensitivity analysis and SHapley Additive exPlanations (SHAP). Sensitivity analysis quantifies the influence of causal parameters on outcomes such as Length of Stay (LOS), Coronary Heart Disease (CHD), and Diabetes, while SHAP highlights the importance of individual features in predictive modeling. By combining causal reasoning with predictive modeling, PCF bridges the gap between clinical intuition and data-driven insights. Its ability to uncover relationships between modifiable factors and simulate hypothetical scenarios provides clinicians with a clearer understanding of causal pathways. This approach supports more informed, evidence-based decision-making, offering a robust framework for addressing complex questions in diverse healthcare settings.

VidSole: A Multimodal Dataset for Joint Kinetics Quantification and Disease Detection with Deep Learning

Understanding internal joint loading is critical for diagnosing gait-related diseases such as knee osteoarthritis; however, current methods of measuring joint risk factors are time-consuming, expensive, and restricted to lab settings. In this paper, we enable the large-scale, cost-effective biomechanical analysis of joint loading via three key contributions: the development and deployment of novel instrumented insoles, the creation of a large multimodal biomechanics dataset (VidSole), and a baseline deep learning pipeline to predict internal joint loading factors. Our novel instrumented insole measures the tri-axial forces and moments across five high-pressure points under the foot. VidSole consists of the forces and moments measured by these insoles along with corresponding RGB video from two viewpoints, 3D body motion capture, and force plate data for over 2,600 trials of 52 diverse participants performing four fundamental activities of daily living (sit-to-stand, stand-to-sit, walking, and running). We feed the insole data and kinematic parameters extractable from video (i.e., pose, knee angle) into a deep learning pipeline consisting of an ensemble Gated Recurrent Unit (GRU) activity classifier followed by activity-specific Long Short Term Memory (LSTM) regression networks to estimate knee adduction moment (KAM), a biomechanical risk factor for knee osteoarthritis. The successful classification of activities at an accuracy of 99.02 percent and KAM estimation with mean absolute error (MAE) less than 0.5 percent*body weight*height, the current threshold for accurately detecting knee osteoarthritis with KAM, illustrates the usefulness of our dataset for future research and clinical settings.

Classification of Mild Cognitive Impairment Based on Dynamic Functional Connectivity Using Spatio-Temporal Transformer

Dynamic functional connectivity (dFC) using resting-state functional magnetic resonance imaging (rs-fMRI) is an advanced technique for capturing the dynamic changes of neural activities, and can be very useful in the studies of brain diseases such as Alzheimer's disease (AD). Yet, existing studies have not fully leveraged the sequential information embedded within dFC that can potentially provide valuable information when identifying brain conditions. In this paper, we propose a novel framework that jointly learns the embedding of both spatial and temporal information within dFC based on the transformer architecture. Specifically, we first construct dFC networks from rs-fMRI data through a sliding window strategy. Then, we simultaneously employ a temporal block and a spatial block to capture higher-order representations of dynamic spatio-temporal dependencies, via mapping them into an efficient fused feature representation. To further enhance the robustness of these feature representations by reducing the dependency on labeled data, we also introduce a contrastive learning strategy to manipulate different brain states. Experimental results on 345 subjects with 570 scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) demonstrate the superiority of our proposed method for MCI (Mild Cognitive Impairment, the prodromal stage of AD) prediction, highlighting its potential for early identification of AD.