AIMC Topic: Phenotype

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Type 2 Diabetes Subtyping via Phenotype and Genotype Co-Learning.

Studies in health technology and informatics
Interpreting and subtyping type 2 diabetes (T2D) is challenging yet essential for achieving fine-grained pathophysiological insights and precise clinical stratification. Previous studies have primarily relied on a small number of pre-selected risk fa...

Constrained Tensor Factorization for Cancer Phenotyping and Mortality Prediction.

Studies in health technology and informatics
Electronic health records (EHR) enable machine learning methods like tensor factorization to extract computational phenotypes. Using Northwestern Medicine data (2000-2015), we analyzed breast, prostate, colorectal, and lung cancer cohorts to predict ...

PheCatcher: Leveraging LLM-Generated Synthetic Data for Automated Phenotype Definition Extraction from Biomedical Literature.

Studies in health technology and informatics
Phenotype definitions are crucial for the progression of precision and personalized medicine. Although phenotype knowledge bases such as PheKB and the OHDSI library are available, they rely heavily on manual input. This study introduces PheCatcher, a...

An Ensemble Approach Integrating Retrieval-Augmented Large Language Models and Boosting Algorithms for Enhanced Catatonia Phenotyping.

Studies in health technology and informatics
A critical first step in using large-scale data to study catatonia is the development of precise phenotyping algorithms that can identify instances of the condition. In this work, we present an ensemble approach that combines retrieval-augmented gene...

Integrating Large Language Models and Machine Learning for Enhanced Catatonia Phenotyping: A Study on Clinical Data from Electronic Health Records.

Studies in health technology and informatics
Catatonia, a complex syndrome with diagnostic challenges, was studied using a novel approach combining LightGBM and GPT-4 to enhance phenotyping from electronic health record (EHR) data. LightGBM, trained on structured data, achieved superior perform...

CT Biomarkers for Phenotypic Biological Aging: Emerging Concepts and Advantages.

Radiographics : a review publication of the Radiological Society of North America, Inc
Aging is a complex phenomenon reflecting the time-dependent accumulation of damage that results in progressive structural and functional decline, disease risk, and death. Chronological age (CA) is an imperfect measure of health but remains an importa...

Confidence-linked and uncertainty-based staged framework for phenotype validation using large language models.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVES: This study develops and validates the confidence-linked and uncertainty-based staged (CLUES) framework by integrating large language models (LLMs) with uncertainty quantification to assist manual chart review while ensuring reliability th...

A review of the journey of field crop phenotyping: From trait stamp collections and fancy robots to phenomics-informed crop performance predictions.

Journal of plant physiology
Crop phenotyping encompasses methodologies for measuring plant growth, architecture, and composition with high precision across scales, from organs to canopies. Field-based phenotyping is pivotal in bridging genomic data with crop performance, offeri...

Clinical phenotypes and risk of early hemodynamic deterioration in intermediate-high-risk patients with acute pulmonary embolism.

Thrombosis research
INTRODUCTION: Intermediate-high-risk pulmonary embolism (PE) patients face elevated risks of sudden clinical deterioration in early hours after symptoms onset. We performed a hierarchical cluster analysis among intermediate-high risk PE patients to i...

Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm.

Cancer research
UNLABELLED: Cancer drug resistance is multifactorial, driven by heritable (epi)genetic changes but also by phenotypic plasticity. In this study, we dissected the drivers of resistance by perturbing organoids derived from patients with colorectal canc...