AIMC Topic: Models, Genetic

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LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks.

BMC bioinformatics Jul 20, 2020
BACKGROUND: Gene Regulatory Networks (GRNs) have been previously studied by using Boolean/multi-state logics. While the gene expression values are usually scaled into the range [0, 1], these GRN inference methods apply a threshold to discretize the d...
Models, Genetic Escherichia coli Fuzzy Logic Gene Regulatory Networks Computational Biology Genes, Regulator Algorithms Computer Simulation Gene Expression Profiling
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Cross-species regulatory sequence activity prediction.

PLoS computational biology Jul 20, 2020
Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, mod...
Machine Learning Software Algorithms Humans Neural Networks, Computer Genome, Human Species Specificity Quantitative Trait Loci Genetic Variation Genomics Gene Expression Regulation Models, Genetic Computational Biology Databases, Genetic Epigenomics Models, Statistical Sequence Analysis, DNA Animals Mutation Mice Hepatocytes
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Association study based on topological constraints of protein-protein interaction networks.

Scientific reports Jul 1, 2020
The non-random interaction pattern of a protein-protein interaction network (PIN) is biologically informative, but its potentials have not been fully utilized in omics studies. Here, we propose a network-permutation-based association study (NetPAS) m...
Computational Biology Models, Genetic Gene Ontology Algorithms Protein Interaction Maps Gene Regulatory Networks
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KAML: improving genomic prediction accuracy of complex traits using machine learning determined parameters.

Genome biology Jun 17, 2020
Advances in high-throughput sequencing technologies have reduced the cost of genotyping dramatically and led to genomic prediction being widely used in animal and plant breeding, and increasingly in human genetics. Inspired by the efficient computing...
Models, Genetic Models, Statistical Quantitative Trait, Heritable Animals Cattle Genomics Machine Learning Software Humans
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Prediction of miRNA targets by learning from interaction sequences.

PloS one May 5, 2020
MicroRNAs (miRNAs) are involved in a diverse variety of biological processes through regulating the expression of target genes in the post-transcriptional level. So, it is of great importance to discover the targets of miRNAs in biological research. ...
Sequence Analysis, RNA Models, Genetic Algorithms MicroRNAs Humans Gene Expression Regulation Computer Simulation Neural Networks, Computer Animals
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Photosynthetic protein classification using genome neighborhood-based machine learning feature.

Scientific reports Apr 28, 2020
Identification of novel photosynthetic proteins is important for understanding and improving photosynthetic efficiency. Synergistically, genome neighborhood can provide additional useful information to identify photosynthetic proteins. We, therefore,...
Photosynthesis Support Vector Machine Bacteria Bacterial Proteins Models, Genetic Genome, Bacterial
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Automatically Designing CNN Architectures Using the Genetic Algorithm for Image Classification.

IEEE transactions on cybernetics Apr 21, 2020
Convolutional neural networks (CNNs) have gained remarkable success on many image classification tasks in recent years. However, the performance of CNNs highly relies upon their architectures. For the most state-of-the-art CNNs, their architectures a...
Algorithms Deep Learning Image Processing, Computer-Assisted Neural Networks, Computer Models, Genetic
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gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning.

Scientific reports Apr 21, 2020
The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromoso...
Base Sequence Nucleotide Motifs Consensus Sequence Software Gammaproteobacteria Machine Learning Phylogeny Replication Origin Models, Genetic
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LEAP: Using machine learning to support variant classification in a clinical setting.

Human mutation Apr 1, 2020
Advances in genome sequencing have led to a tremendous increase in the discovery of novel missense variants, but evidence for determining clinical significance can be limited or conflicting. Here, we present Learning from Evidence to Assess Pathogeni...
Humans Logistic Models Models, Genetic Models, Statistical Area Under Curve Machine Learning Neoplasms Mutation, Missense ROC Curve Cardiovascular Diseases Genomics
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Optimization of culture conditions for differentiation of melon based on artificial neural network and genetic algorithm.

Scientific reports Feb 26, 2020
Artificial neural network is an efficient and accurate fitting method. It has the function of self-learning, which is particularly important for prediction, and it could take advantage of the computer's high-speed computing capabilities and find the ...
Cucurbitaceae Neural Networks, Computer Models, Genetic
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