AIMC Topic: Phenotype

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Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities.

Briefings in bioinformatics Jul 20, 2023
Human Phenotype Ontology (HPO)-based approaches have gained popularity in recent times as a tool for genomic diagnostics of rare diseases. However, these approaches do not make full use of the available information on disease and patient phenotypes. ...
Humans Phenotype Biological Ontologies Rare Diseases Genomics Semantics
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ChatGPT for phenotypes extraction: one model to rule them all?

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference Jul 1, 2023
Information Extraction (IE) is a core task in Natural Language Processing (NLP) where the objective is to identify factual knowledge in textual documents (often unstructured), and feed downstream use cases with the resulting output. In genomic medici...
Humans Language Machine Learning Information Storage and Retrieval Phenotype Electronic Health Records
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AttOmics: attention-based architecture for diagnosis and prognosis from omics data.

Bioinformatics (Oxford, England) Jun 30, 2023
MOTIVATION: The increasing availability of high-throughput omics data allows for considering a new medicine centered on individual patients. Precision medicine relies on exploiting these high-throughput data with machine-learning models, especially t...
Phenotype Neural Networks, Computer Precision Medicine Machine Learning
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COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data.

Bioinformatics (Oxford, England) Jun 30, 2023
MOTIVATION: The size of available omics datasets is steadily increasing with technological advancement in recent years. While this increase in sample size can be used to improve the performance of relevant prediction tasks in healthcare, models that ...
Multiomics Neural Networks, Computer Software Algorithms Phenotype
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Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics.

Bioinformatics (Oxford, England) Jun 1, 2023
MOTIVATION: Developing new crop varieties with superior performance is highly important to ensure robust and sustainable global food security. The speed of variety development is limited by long field cycles and advanced generation selections in plan...
Phenomics Selection, Genetic Plant Breeding Genomics Genotype Triticum Edible Grain Phenotype Deep Learning
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Using machine learning to realize genetic site screening and genomic prediction of productive traits in pigs.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology Jun 1, 2023
Genomic prediction, which is based on solving linear mixed-model (LMM) equations, is the most popular method for predicting breeding values or phenotypic performance for economic traits in livestock. With the need to further improve the performance o...
Machine Learning Reproducibility of Results Animals Algorithms Phenotype Genomics Genome Swine
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End-to-end interpretable disease-gene association prediction.

Briefings in bioinformatics May 19, 2023
Identifying disease-gene associations is a fundamental and critical biomedical task towards understanding molecular mechanisms, the diagnosis and treatment of diseases. It is time-consuming and expensive to experimentally verify causal links between ...
Algorithms Neural Networks, Computer Phenotype
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Multimodal deep learning methods enhance genomic prediction of wheat breeding.

G3 (Bethesda, Md.) May 2, 2023
While several statistical machine learning methods have been developed and studied for assessing the genomic prediction (GP) accuracy of unobserved phenotypes in plant breeding research, few methods have linked genomics and phenomics (imaging). Deep ...
Deep Learning Genotype Triticum Genomics Models, Genetic Phenotype Plant Breeding
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Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets.

Bioinformatics (Oxford, England) Apr 3, 2023
MOTIVATION: Human traits are typically represented in both the biomedical literature and large population studies as descriptive text strings. Whilst a number of ontologies exist, none of these perfectly represent the entire human phenome and exposom...
Natural Language Processing Biological Ontologies Humans Language Semantics Phenotype
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POPDx: an automated framework for patient phenotyping across 392 246 individuals in the UK Biobank study.

Journal of the American Medical Informatics Association : JAMIA Jan 18, 2023
OBJECTIVE: For the UK Biobank, standardized phenotype codes are associated with patients who have been hospitalized but are missing for many patients who have been treated exclusively in an outpatient setting. We describe a method for phenotype recog...
United Kingdom Phenotype Machine Learning Rare Diseases Biological Specimen Banks
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