Publications by authors named "Rima Arnaout"

The PRIME 2.0 checklist is an updated, domain-specific framework designed to standardize the development, evaluation, and reporting of artificial intelligence (AI) applications in cardiovascular imaging. This update specifically responds to rapid advances from traditional machine learning to deep learning, large language models, and multimodal generative AI.

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In the universal quest to optimize machine-learning classifiers, three factors-model architecture, dataset size, and class balance-have been shown to influence test-time performance but do not fully account for it. Previously, evidence was presented for an additional factor that can be referred to as dataset quality, but it was unclear whether this was actually a joint property of the dataset and the model architecture, or an intrinsic property of the dataset itself. If quality is truly dataset-intrinsic and independent of model architecture, dataset size, and class balance, then the same datasets should perform better (or worse) regardless of these other factors.

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Although genetic variant effects often interact nonadditively, strategies to uncover epistasis remain in their infancy. Here we develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy, using deep learning-derived left ventricular mass estimates from 29,661 UK Biobank cardiac magnetic resonance images. We report epistatic variants near CCDC141, IGF1R, TTN and TNKS, identifying loci deemed insignificant in genome-wide association studies.

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Segmentation and measurement of cardiac chambers from ultrasound is critical, but laborious and poorly reproducible. Neural networks can assist, but supervised approaches require the same problematic manual annotations. We build a pipeline for self-supervised segmentation combining computer vision, clinical knowledge, and deep learning.

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Artificial intelligence is poised to transform cardio-oncology by enabling personalized care for patients with cancer, who are at a heightened risk of cardiovascular disease due to both the disease and its treatments. The rising prevalence of cancer and the availability of multiple new therapeutic options has resulted in improved survival among patients with cancer and has expanded the scope of cardio-oncology to not only short-term but also long-term cardiovascular risks resulting from both cancer and its treatments. However, there is considerable heterogeneity in cardiovascular risk, driven by the nature of the malignancy as well as each individual's unique characteristics.

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Big data can revolutionize research and quality improvement for cardiac ultrasound. Text reports are a critical part of such analyses. Cardiac ultrasound reports include structured and free text and vary across institutions, hampering attempts to mine text for useful insights.

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In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly.

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Generative models hold great potential, but only if one can trust the evaluation of the data they generate. We show that many commonly used quality scores for comparing two-dimensional distributions of synthetic vs. ground-truth data give better results than they should, a phenomenon we call the "grade inflation problem.

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Article Synopsis
  • Machine-learning datasets are usually assessed by their size and class balance, but diversity measures that consider element frequencies and similarities are potentially more informative.
  • A new Python package has been developed to easily calculate these diversity measures for large datasets, filling a gap in the tools available for Python users compared to R and Julia.
  • The package can compute frequency-sensitive measures from Hill's D-number framework and other similarity measures, and it also compares datasets, with examples demonstrating its use in fields like immunomics, metagenomics, and medical imaging.
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Article Synopsis
  • - The text discusses the challenges of detecting complex genetic interactions (epistasis) that influence human traits, pointing out that traditional regression methods struggle with high-order interactions in large genomic datasets due to computational limitations and inadequacies in modeling biological interactions properly.
  • - It introduces the epiTree pipeline, built on a framework called Predictability, Computability, Stability (PCS), which utilizes tree-based models to identify higher-order interactions in genomic data by selecting relevant variants based on tissue-specific gene expression and employing iterative random forests.
  • - The efficacy of the epiTree pipeline is validated through two case studies from the UK Biobank, demonstrating its ability to reveal both known and novel genetic interactions in predicting traits like red hair and multiple sclerosis, thus potentially
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Article Synopsis
  • * The review covers various imaging methods like echocardiography, MRI, and 3D modeling, and emphasizes the role of artificial intelligence in enhancing these technologies.
  • * There is a need for further studies to assess the clinical effectiveness and cost-benefit of these imaging techniques, along with a focus on education and training for better implementation in clinical settings.
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Article Synopsis
  • The study challenges the common assumption that genetic variations affect traits in an additive manner by exploring non-additive interactions, specifically in the context of cardiac hypertrophy.
  • Researchers used advanced techniques, including low-signal signed iterative random forests and deep learning, to analyze cardiac MRI data from over 29,000 participants in the UK Biobank, revealing complex genetic interactions that traditional methods might overlook.
  • The findings highlight a sophisticated gene regulatory network, showing that certain genetic variants interact in intricate ways to influence cardiac structure, pointing to the importance of epistasis in understanding genetic contributions to heart diseases.
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Although genetic variant effects often interact non-additively, strategies to uncover epistasis remain in their infancy. Here, we develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy, using deep learning-derived left ventricular mass estimates from 29,661 UK Biobank cardiac MRIs. We report epistatic variants near , , , and , identifying loci deemed insignificant in genome-wide association studies.

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The evolution of the electronic health record, combined with advances in data curation and analytic technologies, increasingly enables data sharing and harmonization. Advances in the analysis of health-related and health-proxy information have already accelerated research discoveries and improved patient care. This American Heart Association policy statement discusses how broad data sharing can be an enabling driver of progress by providing data to develop, test, and benchmark innovative methods, scalable insights, and potential new paradigms for data storage and workflow.

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Article Synopsis
  • The transcript discusses the importance of multidisciplinary collaboration in echocardiography and how machine learning can enhance this collaboration.* -
  • It highlights advancements in foundation models, which are powerful machine learning frameworks that could improve diagnostic accuracy and efficiency in echocardiography.* -
  • The lecture also addresses the current limitations of these models while emphasizing their potential for future developments in the field.*
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Article Synopsis
  • AI has the potential to transform cardiovascular imaging, but it's not yet widely used in clinics despite ongoing research efforts.
  • A workshop led by the National Heart, Lung, and Blood Institute aimed to address the challenges and opportunities for implementing AI in this field through collaboration across various disciplines.
  • The paper outlines key findings from the workshop, emphasizing the need for institutional support to enhance research, validation, and implementation of AI in cardiovascular imaging.
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  • Deep learning (DL) is increasingly used in biomedical imaging, but the scarcity of labeled data from expert annotators makes training models difficult, leading to a need for instance selection to improve model performance.
  • The authors introduce ENRICH, a method designed to prioritize medical images based on the diversity they contribute to the training dataset, addressing the unique challenges posed by medical data.
  • ENRICH significantly enhances classification and segmentation results by using fewer images compared to random selection, while also helping to identify errors in medical imaging datasets efficiently.
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  • Domain-specific data augmentation can improve neural network training for medical imaging, but it hasn't been widely utilized yet.
  • This study specifically tested a cut-paste strategy on fetal ultrasound datasets (FETAL-125 and OB-125) and found that it produced valid training data and comparable model performance to traditional methods.
  • The research emphasizes the importance of designing bespoke data augmentations and offers open-source code to support this process for future medical imaging tasks.
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