A tutorial on open-source large language models for behavioral science.

Large language models (LLMs) have the potential to revolutionize behavioral science by accelerating and improving the research cycle, from conceptualization to data analysis. Unlike closed-source solutions, open-source frameworks for LLMs can enable transparency, reproducibility, and adherence to data protection standards, which gives them a crucial advantage for use in behavioral science. To help researchers harness the promise of LLMs, this tutorial offers a primer on the open-source Hugging Face ecosystem and demonstrates several applications that advance conceptual and empirical work in behavioral science, including feature extraction, fine-tuning of models for prediction, and generation of behavioral responses.

Noninvasive assessment of organ-specific and shared pathways in multi-organ fibrosis using T1 mapping.

Fibrotic diseases affect multiple organs and are associated with morbidity and mortality. To examine organ-specific and shared biologic mechanisms that underlie fibrosis in different organs, we developed machine learning models to quantify T1 time, a marker of interstitial fibrosis, in the liver, pancreas, heart and kidney among 43,881 UK Biobank participants who underwent magnetic resonance imaging. In phenome-wide association analyses, we demonstrate the association of increased organ-specific T1 time, reflecting increased interstitial fibrosis, with prevalent diseases across multiple organ systems.

Training pathologists to assess stromal tumour-infiltrating lymphocytes in breast cancer synergises efforts in clinical care and scientific research.

A growing body of research supports stromal tumour-infiltrating lymphocyte (TIL) density in breast cancer to be a robust prognostic and predicive biomarker. The gold standard for stromal TIL density quantitation in breast cancer is pathologist visual assessment using haematoxylin and eosin-stained slides. Artificial intelligence/machine-learning algorithms are in development to automate the stromal TIL scoring process, and must be validated against a reference standard such as pathologist visual assessment.

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task.

Framework for Research in Equitable Synthetic Control Arms.

Randomized Clinical Trials (RCTs) measure an intervention's efficacy, but they may not be generalizable to a desired target population if the RCT is not equitable. Thus, representativeness of RCTs has become a national priority. Synthetic Controls (SCs) that incorporate observational data into RCTs have shown great potential to produce more efficient studies, but their equity is rarely considered.

Identifying Game-Based Digital Biomarkers of Cognitive Risk for Adolescent Substance Misuse: Protocol for a Proof-of-Concept Study.

Background: Adolescents at risk for substance misuse are rarely identified early due to existing barriers to screening that include the lack of time and privacy in clinic settings. Games can be used for screening and thus mitigate these barriers. Performance in a game is influenced by cognitive processes such as working memory and inhibitory control.

Patient Engagement in a Multimodal Digital Phenotyping Study of Opioid Use Disorder.

Background: Multiple digital data sources can capture moment-to-moment information to advance a robust understanding of opioid use disorder (OUD) behavior, ultimately creating a digital phenotype for each patient. This information can lead to individualized interventions to improve treatment for OUD.

Objective: The aim is to examine patient engagement with multiple digital phenotyping methods among patients receiving buprenorphine medication for OUD.

Genetics of myocardial interstitial fibrosis in the human heart and association with disease.

Myocardial interstitial fibrosis is associated with cardiovascular disease and adverse prognosis. Here, to investigate the biological pathways that underlie fibrosis in the human heart, we developed a machine learning model to measure native myocardial T1 time, a marker of myocardial fibrosis, in 41,505 UK Biobank participants who underwent cardiac magnetic resonance imaging. Greater T1 time was associated with diabetes mellitus, renal disease, aortic stenosis, cardiomyopathy, heart failure, atrial fibrillation, conduction disease and rheumatoid arthritis.

Informing clinical assessment by contextualizing post-hoc explanations of risk prediction models in type-2 diabetes.

Medical experts may use Artificial Intelligence (AI) systems with greater trust if these are supported by 'contextual explanations' that let the practitioner connect system inferences to their context of use. However, their importance in improving model usage and understanding has not been extensively studied. Hence, we consider a comorbidity risk prediction scenario and focus on contexts regarding the patients' clinical state, AI predictions about their risk of complications, and algorithmic explanations supporting the predictions.

Refining the Definition of Stage 1 Type 1 Diabetes: An Ontology-Driven Analysis of the Heterogeneity of Multiple Islet Autoimmunity.

Objective: To estimate the risk of progression to stage 3 type 1 diabetes based on varying definitions of multiple islet autoantibody positivity (mIA).

Research Design And Methods: Type 1 Diabetes Intelligence (T1DI) is a combined prospective data set of children from Finland, Germany, Sweden, and the U.S.

Islet autoantibody screening in at-risk adolescents to predict type 1 diabetes until young adulthood: a prospective cohort study.

Background: Screening for islet autoantibodies in children and adolescents identifies individuals who will later develop type 1 diabetes, allowing patient and family education to prevent diabetic ketoacidosis at onset and to enable consideration of preventive therapies. We aimed to assess whether islet autoantibody screening is effective for predicting type 1 diabetes in adolescents aged 10-18 years with an increased risk of developing type 1 diabetes.

Methods: Data were harmonised from prospective studies from Finland (the Diabetes Prediction and Prevention study), Germany (the BABYDIAB study), and the USA (Diabetes Autoimmunity Study in the Young and the Diabetes Evaluation in Washington study).

BMI-adjusted adipose tissue volumes exhibit depot-specific and divergent associations with cardiometabolic diseases.

For any given body mass index (BMI), individuals vary substantially in fat distribution, and this variation may have important implications for cardiometabolic risk. Here, we study disease associations with BMI-independent variation in visceral (VAT), abdominal subcutaneous (ASAT), and gluteofemoral (GFAT) fat depots in 40,032 individuals of the UK Biobank with body MRI. We apply deep learning models based on two-dimensional body MRI projections to enable near-perfect estimation of fat depot volumes (R in heldout dataset = 0.

Clinical Implementation of Combined Monogenic and Polygenic Risk Disclosure for Coronary Artery Disease.

Background: State-of-the-art genetic risk interpretation for a common complex disease such as coronary artery disease (CAD) requires assessment for both monogenic variants-such as those related to familial hypercholesterolemia-as well as the cumulative impact of many common variants, as quantified by a polygenic score.

Objectives: The objective of the study was to describe a combined monogenic and polygenic CAD risk assessment program and examine its impact on patient understanding and changes to clinical management.

Methods: Study participants attended an initial visit in a preventive genomics clinic and a disclosure visit to discuss results and recommendations, primarily via telemedicine.

Islet Autoantibody Levels Differentiate Progression Trajectories in Individuals With Presymptomatic Type 1 Diabetes.

In our previous data-driven analysis of evolving patterns of islet autoantibodies (IAb) against insulin (IAA), GAD (GADA), and islet antigen 2 (IA-2A), we discovered three trajectories, characterized according to multiple IAb (TR1), IAA (TR2), or GADA (TR3) as the first appearing autoantibodies. Here we examined the evolution of IAb levels within these trajectories in 2,145 IAb-positive participants followed from early life and compared those who progressed to type 1 diabetes (n = 643) with those remaining undiagnosed (n = 1,502). With use of thresholds determined by 5-year diabetes risk, four levels were defined for each IAb and overlaid onto each visit.

Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data.

The clinical presentation of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease, varies widely across patients, making it challenging to determine if potential therapeutics slow progression. We sought to determine whether there were common patterns of disease progression that could aid in the design and analysis of clinical trials. We developed an approach based on a mixture of Gaussian processes to identify clusters of patients sharing similar disease progression patterns, modeling their average trajectories and the variability in each cluster.

Silhouette images enable estimation of body fat distribution and associated cardiometabolic risk.

Inter-individual variation in fat distribution is increasingly recognized as clinically important but is not routinely assessed in clinical practice, in part because medical imaging has not been practical to deploy at scale for this task. Here, we report a deep learning model trained on an individual's body shape outline-or "silhouette" -that enables accurate estimation of specific fat depots of interest, including visceral (VAT), abdominal subcutaneous (ASAT), and gluteofemoral (GFAT) adipose tissue volumes, and VAT/ASAT ratio. Two-dimensional coronal and sagittal silhouettes are constructed from whole-body magnetic resonance images in 40,032 participants of the UK Biobank and used as inputs for a convolutional neural network to predict each of these quantities.

Prediction performance and fairness heterogeneity in cardiovascular risk models.

Prediction models are commonly used to estimate risk for cardiovascular diseases, to inform diagnosis and management. However, performance may vary substantially across relevant subgroups of the population. Here we investigated heterogeneity of accuracy and fairness metrics across a variety of subgroups for risk prediction of two common diseases: atrial fibrillation (AF) and atherosclerotic cardiovascular disease (ASCVD).

Cardiac Arrest in Young Adults With Ischemic Heart Disease in the United States, 2004-2018.

Cardiac arrest (CA) among young adults (<45 y) with ischemic heart disease (IHD) remained understudied. We evaluated the trends in clinical profile, in-hospital mortality, and health care resource utilization in CA-related hospitalizations among young adults with IHD. National Inpatient Sample (2004-2018) was used to identify adults aged 18-45 years.

Inherited basis of visceral, abdominal subcutaneous and gluteofemoral fat depots.

For any given level of overall adiposity, individuals vary considerably in fat distribution. The inherited basis of fat distribution in the general population is not fully understood. Here, we study up to 38,965 UK Biobank participants with MRI-derived visceral (VAT), abdominal subcutaneous (ASAT), and gluteofemoral (GFAT) adipose tissue volumes.

Human-centered explainability for life sciences, healthcare, and medical informatics.

Rapid advances in artificial intelligence (AI) and availability of biological, medical, and healthcare data have enabled the development of a wide variety of models. Significant success has been achieved in a wide range of fields, such as genomics, protein folding, disease diagnosis, imaging, and clinical tasks. Although widely used, the inherent opacity of deep AI models has brought criticism from the research field and little adoption in clinical practice.

The Feasibility and Utility of Harnessing Digital Health to Understand Clinical Trajectories in Medication Treatment for Opioid Use Disorder: D-TECT Study Design and Methodological Considerations.

Introduction: Across the U.S., the prevalence of opioid use disorder (OUD) and the rates of opioid overdoses have risen precipitously in recent years.