Reliable prediction of pediatric obesity can offer a valuable resource to providers, helping them engage in timely preventive interventions before the disease is established. Many efforts have been made to develop ML-based predictive models of obesity, and some studies have reported high predictive performances. However, no commonly used clinical decision support tool based on existing ML models currently exists. This study presents a novel end-to-end pipeline specifically designed for pediatric obesity prediction, which supports the entire process of data extraction, inference, and communication via an API or a user interface. While focusing only on routinely recorded data in pediatric electronic health records (EHRs), our pipeline uses a diverse expert-curated list of medical concepts to predict the 1-3 years risk of developing obesity. Furthermore, by using the Fast Healthcare Interoperability Resources (FHIR) standard in our design procedure, we specifically target facilitating low-effort integration of our pipeline with different EHR systems. In our experiments, we report the effectiveness of the predictive model as well as its alignment with the feedback from various stakeholders, including ML scientists, providers, health IT personnel, health administration representatives, and patient group representatives.

While electronic health records (EHRs) are widely used across various applications in healthcare, most applications use the EHRs in their raw (tabular) format. Relying on raw or simple data pre-processing can greatly limit the performance or even applicability of downstream tasks using EHRs. To address this challenge, we present HealthGAT, a novel graph attention network framework that utilizes a hierarchical approach to generate embeddings from EHR, surpassing traditional graph-based methods. Our model iteratively refines the embeddings for medical codes, resulting in improved EHR data analysis. We also introduce customized EHR-centric auxiliary pre-training tasks to leverage the rich medical knowledge embedded within the data. This approach provides a comprehensive analysis of complex medical relationships and offers significant advancement over standard data representation techniques. HealthGAT has demonstrated its effectiveness in various healthcare scenarios through comprehensive evaluations against established methodologies. Specifically, our model shows outstanding performance in node classification and downstream tasks such as predicting readmissions and diagnosis classifications. Our code is available at https://github.com/healthylaife/HealthGAT

An increasing amount of research is being devoted to applying machine learning methods to electronic health record (EHR) data for various clinical purposes. This growing area of research has exposed the challenges of the accessibility of EHRs. MIMIC is a popular, public, and free EHR dataset in a raw format that has been used in numerous studies. The absence of standardized pre-processing steps can be, however, a significant barrier to the wider adoption of this rare resource. Additionally, this absence can reduce the reproducibility of the developed tools and limit the ability to compare the results among similar studies. In this work, we provide a greatly customizable pipeline to extract, clean, and pre-process the data available in the fourth version of the MIMIC dataset (MIMIC-IV). The pipeline also presents an end-to-end wizard-like package supporting predictive model creations and evaluations. The pipeline covers a range of clinical prediction tasks which can be broadly classified into four categories - readmission, length of stay, mortality, and phenotype prediction.

Multivariate time-series data are used in many classification and regression predictive tasks, and recurrent models have been widely used for such tasks. Most common recurrent models assume that time-series data elements are of equal length and the ordered observations are recorded at regular intervals. However, real-world time-series data have neither a similar length nor a same number of observations. They also have missing entries, which hinders the performance of predictive tasks. In this paper, we approach these issues by presenting a model for the combined task of imputing and predicting values for the irregularly observed and varying length time-series data with missing entries. Our proposed model (Bi-GAN) uses a bidirectional recurrent network in a generative adversarial setting. The generator is a bidirectional recurrent network that receives actual incomplete data and imputes the missing values. The discriminator attempts to discriminate between the actual and the imputed values in the output of the generator. Our model learns how to impute missing elements in-between (imputation) or outside of the input time steps (prediction), hence working as an effective any-time prediction tool for time-series data. Our method has three advantages to the state-of-the-art methods in the field: (a) single model can be used for both imputation and prediction tasks; (b) it can perform prediction task for time-series of varying length with missing data; (c) it does not require to know the observation and prediction time window during training which provides a flexible length of prediction window for both long-term and short-term predictions. We evaluate our model on two public datasets and on another large real-world electronic health records dataset to impute and predict body mass index (BMI) values in children and show its superior performance in both settings.