AIMC Topic: Phenotype

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The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.

Nucleic acids research Jan 6, 2023
The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industr...
Mice Polymorphism, Single Nucleotide Animals Genome-Wide Association Study Knowledge Bases National Human Genome Research Institute (U.S.) United States DNA Copy Number Variations Humans Software Phenotype
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Accurately modeling biased random walks on weighted networks using node2vec.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: Accurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased...
Neural Networks, Computer Epistasis, Genetic Machine Learning Phenotype Gene Regulatory Networks
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Defining the extent of gene function using ROC curvature.

Bioinformatics (Oxford, England) Dec 13, 2022
MOTIVATION: Interactions between proteins help us understand how genes are functionally related and how they contribute to phenotypes. Experiments provide imperfect 'ground truth' information about a small subset of potential interactions in a specif...
Machine Learning Phenotype Genome Proteins Gene Ontology
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Panicle Ratio Network: streamlining rice panicle measurement by deep learning with ultra-high-definition aerial images in the field.

Journal of experimental botany Nov 2, 2022
The heading date and effective tiller percentage are important traits in rice, and they directly affect plant architecture and yield. Both traits are related to the ratio of the panicle number to the maximum tiller number, referred to as the panicle ...
Crops, Agricultural Phenotype Deep Learning Oryza
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Clinical utility of automatic phenotype annotation in unstructured clinical notes: intensive care unit use.

BMJ health & care informatics Nov 1, 2022
OBJECTIVE: Clinical notes contain information that has not been documented elsewhere, including responses to treatment and clinical findings, which are crucial for predicting key outcomes in patients in acute care. In this study, we propose the autom...
Critical Care Intensive Care Units Hospital Mortality Phenotype Humans Machine Learning
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Natural Language Processing of Computed Tomography Reports to Label Metastatic Phenotypes With Prognostic Significance in Patients With Colorectal Cancer.

JCO clinical cancer informatics Sep 1, 2022
PURPOSE: Natural language processing (NLP) applied to radiology reports can help identify clinically relevant M1 subcategories of patients with colorectal cancer (CRC). The primary purpose was to compare the overall survival (OS) of CRC according to ...
Natural Language Processing Tomography, X-Ray Computed Retrospective Studies Humans Tomography Colorectal Neoplasms Phenotype Prognosis
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transferGWAS: GWAS of images using deep transfer learning.

Bioinformatics (Oxford, England) Jul 11, 2022
MOTIVATION: Medical images can provide rich information about diseases and their biology. However, investigating their association with genetic variation requires non-standard methods. We propose transferGWAS, a novel approach to perform genome-wide ...
Genome Phenotype Machine Learning Neural Networks, Computer Genome-Wide Association Study
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How the History of Changing Environments Affects Traits of Evolvable Robot Populations.

Artificial life Jun 28, 2022
The environment is one of the key factors in the emergence of intelligent creatures, but it has received little attention within the Evolutionary Robotics literature. This article investigates the effects of changing environments on morphological and...
Biological Evolution Phenotype Robotics
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Analysis of Causal Relationships in Integrated Ontologies of Diseases, Phenotypes, and Radiological Diagnosis.

Studies in health technology and informatics Jun 6, 2022
Biomedical ontologies encode knowledge in a form that makes it computable. The current study used the integration of three large biomedical ontologies-the Disease Ontology (DO), Human Phenotype Ontology (HPO), and Radiology Gamuts Ontology (RGO)-to e...
Phenotype Causality Biological Ontologies Radiography Radiology
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GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression.

Bioinformatics (Oxford, England) Apr 28, 2022
MOTIVATION: Medical care is becoming more and more specific to patients' needs due to the increased availability of omics data. The application to these data of sophisticated machine learning models, in particular deep learning (DL), can improve the ...
Gene Expression Machine Learning Gene Ontology Phenotype Neural Networks, Computer
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