NGQA: A Nutritional Graph Question Answering Benchmark for Personalized Health-aware Nutritional Reasoning

Diet plays a critical role in human health, yet tailoring dietary reasoning to individual health conditions remains a major challenge. Nutrition Question Answering (QA) has emerged as a popular method for addressing this problem. However, current research faces two critical limitations. On one hand, the absence of datasets involving user-specific medical information severely limits \textit{personalization}. This challenge is further compounded by the wide variability in individual health needs. On the other hand, while large language models (LLMs), a popular solution for this task, demonstrate strong reasoning abilities, they struggle with the domain-specific complexities of personalized healthy dietary reasoning, and existing benchmarks fail to capture these challenges. To address these gaps, we introduce the Nutritional Graph Question Answering (NGQA) benchmark, the first graph question answering dataset designed for personalized nutritional health reasoning. NGQA leverages data from the National Health and Nutrition Examination Survey (NHANES) and the Food and Nutrient Database for Dietary Studies (FNDDS) to evaluate whether a food is healthy for a specific user, supported by explanations of the key contributing nutrients. The benchmark incorporates three question complexity settings and evaluates reasoning across three downstream tasks. Extensive experiments with LLM backbones and baseline models demonstrate that the NGQA benchmark effectively challenges existing models. In sum, NGQA addresses a critical real-world problem while advancing GraphQA research with a novel domain-specific benchmark.

Is Attention All You Need For Actigraphy? Foundation Models of Wearable Accelerometer Data for Mental Health Research

Wearable accelerometry (actigraphy) has provided valuable data for clinical insights since the 1970s and is increasingly important as wearable devices continue to become widespread. The effectiveness of actigraphy in research and clinical contexts is heavily dependent on the modeling architecture utilized. To address this, we developed the Pretrained Actigraphy Transformer (PAT)--the first pretrained and fully attention-based model designed specifically to handle actigraphy. PAT was pretrained on actigraphy from 29,307 participants in NHANES, enabling it to deliver state-of-the-art performance when fine-tuned across various actigraphy prediction tasks in the mental health domain, even in data-limited scenarios. For example, when trained to predict benzodiazepine usage using actigraphy from only 500 labeled participants, PAT achieved an 8.8 percentage-point AUC improvement over the best baseline. With fewer than 2 million parameters and built-in model explainability, PAT is robust yet easy to deploy in health research settings. GitHub: https://github.com/njacobsonlab/Pretrained-Actigraphy-Transformer/

Exploring Nutritional Impact on Alzheimer's Mortality: An Explainable AI Approach

This article uses machine learning (ML) and explainable artificial intelligence (XAI) techniques to investigate the relationship between nutritional status and mortality rates associated with Alzheimers disease (AD). The Third National Health and Nutrition Examination Survey (NHANES III) database is employed for analysis. The random forest model is selected as the base model for XAI analysis, and the Shapley Additive Explanations (SHAP) method is used to assess feature importance. The results highlight significant nutritional factors such as serum vitamin B12 and glycated hemoglobin. The study demonstrates the effectiveness of random forests in predicting AD mortality compared to other diseases. This research provides insights into the impact of nutrition on AD and contributes to a deeper understanding of disease progression.

Causality in the Can: Diet Coke's Impact on Fatness

Artificially sweetened beverages like Diet Coke are often considered healthier alternatives, but the debate over their impact on obesity persists. Previous research has predominantly relied on observational data or randomized controlled trials (RCTs), which may not accurately capture the causal relationship between Diet Coke consumption and obesity. This study uses causal inference methods, employing data from the National Health and Nutrition Examination Survey (NHANES) to examine this relationship across diverse demographics. Instead of relying on RCT data, we constructed a causal graph and applied the back-door criterion with its adjustment formula to estimate the RCT distributions. We then calculated the counterfactual quantity, the Probability of Necessity and Sufficiency (PNS), using both NHANES data and estimated RCT data. We propose that PNS is the essential metric for assessing the impact of Diet Coke on obesity. Our results indicate that between 20% to 50% of individuals, especially those with poor dietary habits, are more likely to gain weight from Diet Coke. Conversely, in groups like young females with healthier diets, only a small proportion experience weight gain due to Diet Coke. These findings highlight the influence of individual lifestyle and potential hormonal factors on the varied effects of Diet Coke, providing a new framework for understanding its nutritional impacts on health.

Deep Learning Framework with Uncertainty Quantification for Survey Data: Assessing and Predicting Diabetes Mellitus Risk in the American Population

Complex survey designs are commonly employed in many medical cohorts. In such scenarios, developing case-specific predictive risk score models that reflect the unique characteristics of the study design is essential. This approach is key to minimizing potential selective biases in results. The objectives of this paper are: (i) To propose a general predictive framework for regression and classification using neural network (NN) modeling, which incorporates survey weights into the estimation process; (ii) To introduce an uncertainty quantification algorithm for model prediction, tailored for data from complex survey designs; (iii) To apply this method in developing robust risk score models to assess the risk of Diabetes Mellitus in the US population, utilizing data from the NHANES 2011-2014 cohort. The theoretical properties of our estimators are designed to ensure minimal bias and the statistical consistency, thereby ensuring that our models yield reliable predictions and contribute novel scientific insights in diabetes research. While focused on diabetes, this NN predictive framework is adaptable to create clinical models for a diverse range of diseases and medical cohorts. The software and the data used in this paper is publicly available on GitHub.

NHANES-GCP: Leveraging the Google Cloud Platform and BigQuery ML for reproducible machine learning with data from the National Health and Nutrition Examination Survey

Summary: NHANES, the National Health and Nutrition Examination Survey, is a program of studies led by the Centers for Disease Control and Prevention (CDC) designed to assess the health and nutritional status of adults and children in the United States (U.S.). NHANES data is frequently used by biostatisticians and clinical scientists to study health trends across the U.S., but every analysis requires extensive data management and cleaning before use and this repetitive data engineering collectively costs valuable research time and decreases the reproducibility of analyses. Here, we introduce NHANES-GCP, a Cloud Development Kit for Terraform (CDKTF) Infrastructure-as-Code (IaC) and Data Build Tool (dbt) resources built on the Google Cloud Platform (GCP) that automates the data engineering and management aspects of working with NHANES data. With current GCP pricing, NHANES-GCP costs less than $2 to run and less than $15/yr of ongoing costs for hosting the NHANES data, all while providing researchers with clean data tables that can readily be integrated for large-scale analyses. We provide examples of leveraging BigQuery ML to carry out the process of selecting data, integrating data, training machine learning and statistical models, and generating results all from a single SQL-like query. NHANES-GCP is designed to enhance the reproducibility of analyses and create a well-engineered NHANES data resource for statistics, machine learning, and fine-tuning Large Language Models (LLMs). Availability and implementation" NHANES-GCP is available at https://github.com/In-Vivo-Group/NHANES-GCP

Information Fusion via Symbolic Regression: A Tutorial in the Context of Human Health

This tutorial paper provides a general overview of symbolic regression (SR) with specific focus on standards of interpretability. We posit that interpretable modeling, although its definition is still disputed in the literature, is a practical way to support the evaluation of successful information fusion. In order to convey the benefits of SR as a modeling technique, we demonstrate an application within the field of health and nutrition using publicly available National Health and Nutrition Examination Survey (NHANES) data from the Centers for Disease Control and Prevention (CDC), fusing together anthropometric markers into a simple mathematical expression to estimate body fat percentage. We discuss the advantages and challenges associated with SR modeling and provide qualitative and quantitative analyses of the learned models.

Predicting blood pressure under circumstances of missing data: An analysis of missing data patterns and imputation methods using NHANES

The World Health Organization defines cardio-vascular disease (CVD) as "a group of disorders of the heart and blood vessels," including coronary heart disease and stroke (WHO 21). CVD is affected by "intermediate risk factors" such as raised blood pressure, raised blood glucose, raised blood lipids, and obesity. These are predominantly influenced by lifestyle and behaviour, including physical inactivity, unhealthy diets, high intake of salt, and tobacco and alcohol use. However, genetics and social/environmental factors such as poverty, stress, and racism also play an important role. Researchers studying the behavioural and environmental factors associated with these "intermediate risk factors" need access to high quality and detailed information on diet and physical activity. However, missing data are a pervasive problem in clinical and public health research, affecting both randomized trials and observational studies. Reasons for missing data can vary substantially across studies because of loss to follow-up, missed study visits, refusal to answer survey questions, or an unrecorded measurement during an office visit. One method of handling missing values is to simply delete observations for which there is missingness (called Complete Case Analysis). This is rarely used as deleting the data point containing missing data (List wise deletion) results in a smaller number of samples and thus affects accuracy. Additional methods of handling missing data exists, such as summarizing the variables with its observed values (Available Case Analysis). Motivated by the pervasiveness of missing data in the NHANES dataset, we will conduct an analysis of imputation methods under different simulated patterns of missing data. We will then apply these imputation methods to create a complete dataset upon which we can use ordinary least squares to predict blood pressure from diet and physical activity.

VertXNet: An Ensemble Method for Vertebrae Segmentation and Identification of Spinal X-Ray

Reliable vertebrae annotations are key to perform analysis of spinal X-ray images. However, obtaining annotation of vertebrae from those images is usually carried out manually due to its complexity (i.e. small structures with varying shape), making it a costly and tedious process. To accelerate this process, we proposed an ensemble pipeline, VertXNet, that combines two state-of-the-art (SOTA) segmentation models (respectively U-Net and Mask R-CNN) to automatically segment and label vertebrae in X-ray spinal images. Moreover, VertXNet introduces a rule-based approach that allows to robustly infer vertebrae labels (by locating the 'reference' vertebrae which are easier to segment than others) for a given spinal X-ray image. We evaluated the proposed pipeline on three spinal X-ray datasets (two internal and one publicly available), and compared against vertebrae annotated by radiologists. Our experimental results have shown that the proposed pipeline outperformed two SOTA segmentation models on our test dataset (MEASURE 1) with a mean Dice of 0.90, vs. a mean Dice of 0.73 for Mask R-CNN and 0.72 for U-Net. To further evaluate the generalization ability of VertXNet, the pre-trained pipeline was directly tested on two additional datasets (PREVENT and NHANES II) and consistent performance was observed with a mean Dice of 0.89 and 0.88, respectively. Overall, VertXNet demonstrated significantly improved performance for vertebra segmentation and labeling for spinal X-ray imaging, and evaluation on both in-house clinical trial data and publicly available data further proved its generalization.

Modeling Non-deterministic Human Behaviors in Discrete Food Choices

We establish a non-deterministic model that predicts a user's food preferences from their demographic information. Our simulator is based on NHANES dataset and domain expert knowledge in the form of established behavioral studies. Our model can be used to generate an arbitrary amount of synthetic datapoints that are similar in distribution to the original dataset and align with behavioral science expectations. Such a simulator can be used in a variety of machine learning tasks and especially in applications requiring human behavior prediction.