regionalpcs improve discovery of DNA methylation associations with complex traits.

We have developed the regionalpcs method, an approach for summarizing gene-level methylation. regionalpcs addresses the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease. In contrast to averaging, regionalpcs uses principal components analysis to capture complex methylation patterns across gene regions.

Machine Learning Enabled Prediction of Biologically Relevant Gene Expression Using CT-Based Radiomic Features in Non-Small Cell Lung Cancer.

Background: Non-small-cell lung cancer (NSCLC) remains a global health challenge, driving morbidity and mortality. The emerging field of radiogenomics utilizes statistical methods to correlate radiographic tumor features with genomic characteristics from biopsy samples. Radiomic techniques automate the precise extraction of imaging features from tumor regions in radiographic scans, which are subjected to machine learning (ML) to predict genomic attributes.

Hospitalization prediction from the emergency department using computer vision AI with short patient video clips.

In this study, we investigate the performance of computer vision AI algorithms in predicting patient disposition from the emergency department (ED) using short video clips. Clinicians often use "eye-balling" or clinical gestalt to aid in triage, based on brief observations. We hypothesize that AI can similarly use patient appearance for disposition prediction.

Multicohort Analysis of Bronchial Epithelial Cell Expression in Healthy Subjects and Patients with Asthma Reveals Four Clinically Distinct Clusters.

Asthma is a heterogeneous disease with variable presentation and characteristics. There is a critical need to identify underlying molecular endotypes of asthma. We performed the largest transcriptomic analysis of 808 bronchial epithelial cell (BEC) samples across 11 independent cohorts, including 3 cohorts from the Severe Asthma Research Program (SARP).

Establishing best practices in large language model research: an application to repeat prompting.

Objectives: We aimed to demonstrate the importance of establishing best practices in large language model research, using repeat prompting as an illustrative example.

Materials And Methods: Using data from a prior study investigating potential model bias in peer review of medical abstracts, we compared methods that ignore correlation in model outputs from repeated prompting with a random effects method that accounts for this correlation.

Results: High correlation within groups was found when repeatedly prompting the model, with intraclass correlation coefficient of 0.

Session Introduction: AI and Machine Learning in Clinical Medicine: Generative and Interactive Systems at the Human-Machine Interface.

Artificial Intelligence (AI) technologies are increasingly capable of processing complex and multilayered datasets. Innovations in generative AI and deep learning have notably enhanced the extraction of insights from both unstructured texts, images, and structured data alike. These breakthroughs in AI technology have spurred a wave of research in the medical field, leading to the creation of a variety of tools aimed at improving clinical decision-making, patient monitoring, image analysis, and emergency response systems.

Current Developments from Silicon Valley - How Artificial Intelligence is Changing Gynecology and Obstetrics.

Artificial intelligence (AI) has become an omnipresent topic in the media. Lively discussions are being held on how AI could revolutionize the global healthcare landscape. The development of innovative AI models, including in the medical sector, is increasingly dominated by large high-tech companies.

The text2term tool to map free-text descriptions of biomedical terms to ontologies.

There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types-such as disease names, cell types, or chemicals-that are used in metadata associated with biomedical data. When metadata are not well-structured or precise, the associated data are harder to find and are often burdensome to reuse, analyze, or integrate with other datasets due to the upfront curation effort required to make the data usable-typically through retrospective standardization and cleaning of the (meta)data. With the goal of facilitating the task of standardizing metadata-either in bulk or in a one-by-one fashion, e.

Learning from the EHR to implement AI in healthcare.

The introduction of the electronic health record was heralded as a technology solution to improve care quality and efficiency, but these tools have contributed to increased administrative burden and burnout for clinicians. Today, artificial intelligence is receiving much of the same attention and promises as electronic health records. Can healthcare learn from the failures of electronic health records to maximize the potential of artificial intelligence?

Sequence modeling and design from molecular to genome scale with Evo.

The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism's function. We present Evo, a long-context genomic foundation model with a frontier architecture trained on millions of prokaryotic and phage genomes, and report scaling laws on DNA to complement observations in language and vision. Evo generalizes across DNA, RNA, and proteins, enabling zero-shot function prediction competitive with domain-specific language models and the generation of functional CRISPR-Cas and transposon systems, representing the first examples of protein-RNA and protein-DNA codesign with a language model.

Recommendations for Clinicians, Technologists, and Healthcare Organizations on the Use of Generative Artificial Intelligence in Medicine: A Position Statement from the Society of General Internal Medicine.

Generative artificial intelligence (generative AI) is a new technology with potentially broad applications across important domains of healthcare, but serious questions remain about how to balance the promise of generative AI against unintended consequences from adoption of these tools. In this position statement, we provide recommendations on behalf of the Society of General Internal Medicine on how clinicians, technologists, and healthcare organizations can approach the use of these tools. We focus on three major domains of medical practice where clinicians and technology experts believe generative AI will have substantial immediate and long-term impacts: clinical decision-making, health systems optimization, and the patient-physician relationship.

Large Language Model Influence on Diagnostic Reasoning: A Randomized Clinical Trial.

Importance: Large language models (LLMs) have shown promise in their performance on both multiple-choice and open-ended medical reasoning examinations, but it remains unknown whether the use of such tools improves physician diagnostic reasoning.

Objective: To assess the effect of an LLM on physicians' diagnostic reasoning compared with conventional resources.

Design, Setting, And Participants: A single-blind randomized clinical trial was conducted from November 29 to December 29, 2023.

Large language models outperform traditional natural language processing methods in extracting patient-reported outcomes in IBD.

Background And Aims: Patient-reported outcomes (PROs) are vital in assessing disease activity and treatment outcomes in inflammatory bowel disease (IBD). However, manual extraction of these PROs from the free-text of clinical notes is burdensome. We aimed to improve data curation from free-text information in the electronic health record, making it more available for research and quality improvement.

Towards Digital Quantification of Ploidy from Pan-Cancer Digital Pathology Slides using Deep Learning.

Abnormal DNA ploidy, found in numerous cancers, is increasingly being recognized as a contributor in driving chromosomal instability, genome evolution, and the heterogeneity that fuels cancer cell progression. Furthermore, it has been linked with poor prognosis of cancer patients. While next-generation sequencing can be used to approximate tumor ploidy, it has a high error rate for near-euploid states, a high cost and is time consuming, motivating alternative rapid quantification methods.

Exploring the CIEDE2000 thresholds for lightness, chroma, and hue differences in dentistry.

Objective: To evaluate the perceptibility and acceptability CIEDE2000 (K:K:K) thresholds for lightness, chroma and hue differences in dentistry.

Method: A Python-based program was developed to conduct a psychophysical experiment based on visual assessments of computer-simulated images of human teeth. The experiment was performed on a calibrated display.

Large Language Model Influence on Management Reasoning: A Randomized Controlled Trial.

Importance: Large language model (LLM) artificial intelligence (AI) systems have shown promise in diagnostic reasoning, but their utility in management reasoning with no clear right answers is unknown.

Objective: To determine whether LLM assistance improves physician performance on open-ended management reasoning tasks compared to conventional resources.

Design: Prospective, randomized controlled trial conducted from 30 November 2023 to 21 April 2024.

Vignette-based comparative analysis of ChatGPT and specialist treatment decisions for rheumatic patients: results of the Rheum2Guide study.

Background: The complex nature of rheumatic diseases poses considerable challenges for clinicians when developing individualized treatment plans. Large language models (LLMs) such as ChatGPT could enable treatment decision support.

Objective: To compare treatment plans generated by ChatGPT-3.

Disparities in air pollution attributable mortality in the US population by race/ethnicity and sociodemographic factors.

There are large differences in premature mortality in the USA by race/ethnicity, education, rurality and social vulnerability index groups. Using existing concentration-response functions, published particulate matter (PM) air pollution estimates, population estimates at the census tract level and county-level mortality data from the US National Vital Statistics System, we estimated the degree to which these mortality discrepancies can be attributed to differences in exposure and susceptibility to PM. We show that differences in PM-attributable mortality were consistently more pronounced by race/ethnicity than by education, rurality or social vulnerability index, with the Black American population having the highest proportion of deaths attributable to PM in all years from 1990 to 2016.

Perspectives on computational modeling of biological systems and the significance of the SysMod community.

Motivation: In recent years, applying computational modeling to systems biology has caused a substantial surge in both discovery and practical applications and a significant shift in our understanding of the complexity inherent in biological systems.

Results: In this perspective article, we briefly overview computational modeling in biology, highlighting recent advancements such as multi-scale modeling due to the omics revolution, single-cell technology, and integration of artificial intelligence and machine learning approaches. We also discuss the primary challenges faced: integration, standardization, model complexity, scalability, and interdisciplinary collaboration.