AIMC Topic: Phenotype

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Genetic variant effect prediction by supervised nonnegative matrix tri-factorization.

Molecular omics Oct 11, 2021
Discriminating between deleterious and neutral mutations among numerous non-synonymous single nucleotide variants (nsSNVs) that may be observed through whole exome sequencing (WES) is considered a great challenge. In this regard, many machine learnin...
Algorithms Phenotype Proteins Amino Acid Sequence Machine Learning
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Investigation of a dysmorphic facial phenotype in patients with Gaucher disease types 2 and 3.

Molecular genetics and metabolism Oct 5, 2021
Gaucher disease (GD) is a rare lysosomal storage disorder that is divided into three subtypes based on presentation of neurological manifestations. Distinguishing between the types has important implications for treatment and counseling. Yet, patient...
Humans Artificial Intelligence Software Musculoskeletal Abnormalities Adolescent Young Adult Phenotype Cohort Studies Adult Female Child, Preschool Male Child Infant, Newborn Infant ROC Curve Gaucher Disease Facial Recognition
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Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes.

BMC bioinformatics Oct 4, 2021
BACKGROUND: Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popul...
Computer Simulation Genome-Wide Association Study Epistasis, Genetic Polymorphism, Single Nucleotide Algorithms Multifactor Dimensionality Reduction Models, Genetic Phenotype
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Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View Semantic Embedding With Self-Training.

IEEE transactions on medical imaging Sep 30, 2021
Zero-shot learning (ZSL) is one of the most promising avenues of annotation-efficient machine learning. In the era of deep learning, ZSL techniques have achieved unprecedented success. However, the developments of ZSL methods have taken place mostly ...
Machine Learning X-Rays Phenotype Radiography Semantics
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Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships.

Nature communications Sep 24, 2021
Inferring phenotypic outcomes from genomic features is both a promise and challenge for systems biology. Using gene expression data to predict phenotypic outcomes, and functionally validating the genes with predictive powers are two challenges we add...
Zea mays Nitrogen Genetic Variation Genomics Species Specificity Machine Learning Genotype Genome, Plant Phenotype Models, Genetic Gene Expression Regulation, Plant Transcriptome Evolution, Molecular Arabidopsis
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Analyses of child cardiometabolic phenotype following assisted reproductive technologies using a pragmatic trial emulation approach.

Nature communications Sep 23, 2021
Assisted reproductive technologies (ART) are increasingly used, however little is known about the long-term health of ART-conceived offspring. Weak selection of comparison groups and poorly characterized mechanisms impede current understanding. In a ...
Prospective Studies Calcium-Binding Proteins Female Skinfold Thickness Adult Body Weight Child DNA Methylation Body Height Humans Blood Pressure Cardiovascular System Machine Learning Singapore Reproductive Techniques, Assisted Phenotype
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Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data.

BMC bioinformatics Sep 22, 2021
BACKGROUND: With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts the development of precision medicine. Deep learning is a promising approach for phenotype predict...
Gene Ontology Neural Networks, Computer Phenotype Humans Neoplasms Gene Expression
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Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.

PLoS computational biology Sep 22, 2021
Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for micr...
Humans Neural Networks, Computer Algorithms Phenotype Inflammatory Bowel Diseases Deep Learning Host Microbial Interactions Prevotella Databases, Genetic Natural Language Processing Microbiota Proof of Concept Study Computational Biology Gastrointestinal Microbiome RNA, Ribosomal, 16S
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GenNet framework: interpretable deep learning for predicting phenotypes from genetic data.

Communications biology Sep 17, 2021
Applying deep learning in population genomics is challenging because of computational issues and lack of interpretable models. Here, we propose GenNet, a novel open-source deep learning framework for predicting phenotypes from genetic variants. In th...
Humans Neural Networks, Computer Phenotype Deep Learning
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Genetic dissection of complex traits using hierarchical biological knowledge.

PLoS computational biology Sep 17, 2021
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical bio...
Multifactorial Inheritance Benomyl Nucleotidyltransferases Gene Ontology Hydroxyurea Chromosome Mapping Metabolic Networks and Pathways Copper Mutation Polymorphism, Single Nucleotide Glucose Glycine Machine Learning Computational Biology Knowledge Bases Phenotype Systems Biology Neural Networks, Computer Saccharomyces cerevisiae Genome-Wide Association Study Models, Genetic
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