AIMC Topic: Genome

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DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions.

Bioinformatics (Oxford, England) Sep 2, 2022
MOTIVATION: Accurate annotation of different genomic signals and regions (GSRs) from DNA sequences is fundamentally important for understanding gene structure, regulation and function. Numerous efforts have been made to develop machine learning-based...
Animals Deep Learning Software Genomics Drosophila melanogaster Genome Cattle Mice
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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 Neural Networks, Computer Phenotype Genome-Wide Association Study Machine Learning
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AutoDC: an automatic machine learning framework for disease classification.

Bioinformatics (Oxford, England) Jun 27, 2022
MOTIVATION: The emergence of next-generation sequencing techniques opens up tremendous opportunities for researchers to uncover the basic mechanisms of disease at the molecular level. Recently, automatic machine learning (AutoML) frameworks have been...
Genome Algorithms Genomics Machine Learning Data Analysis
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A Practical Guide to Integrating Multimodal Machine Learning and Metabolic Modeling.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Complex, distributed, and dynamic sets of clinical biomedical data are collectively referred to as multimodal clinical data. In order to accommodate the volume and heterogeneity of such diverse data types and aid in their interpretation when they are...
Genome Systems Biology Data Mining Machine Learning Neoplasms Humans
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Genome-Enabled Prediction Methods Based on Machine Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Growth of artificial intelligence and machine learning (ML) methodology has been explosive in recent years. In this class of procedures, computers get knowledge from sets of experiences and provide forecasts or classification. In genome-wide based pr...
Artificial Intelligence Animals Bayes Theorem Genome Machine Learning Algorithms
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AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom.

Briefings in bioinformatics Nov 5, 2021
With advancements in genomics, there has been substantial reduction in the cost and time of genome sequencing and has resulted in lot of data in genome databases. Antimicrobial host defense proteins provide protection against invading microbes. But c...
Antimicrobial Peptides Web Browser Workflow Genome Computational Biology Databases, Genetic Animals Drug Discovery Algorithms ROC Curve Reproducibility of Results Genomics Artificial Intelligence Phylogeny Machine Learning
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Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes.

Bioinformatics (Oxford, England) Jul 19, 2021
SUMMARY: Population studies such as genome-wide association study have identified a variety of genomic variants associated with human diseases. To further understand potential mechanisms of disease variants, recent statistical methods associate funct...
Neural Networks, Computer Genome-Wide Association Study Genotype Genome Humans Genomics
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Heuristic hyperparameter optimization of deep learning models for genomic prediction.

G3 (Bethesda, Md.) Jul 14, 2021
There is a growing interest among quantitative geneticists and animal breeders in the use of deep learning (DL) for genomic prediction. However, the performance of DL is affected by hyperparameters that are typically manually set by users. These hype...
Cattle Genomics Swine Animals Genome Deep Learning Genotype Heuristics
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keras_dna: a wrapper for fast implementation of deep learning models in genomics.

Bioinformatics (Oxford, England) Jul 12, 2021
SUMMARY: Prediction of genomic annotations from DNA sequences using deep learning is today becoming a flourishing field with many applications. Nevertheless, there are still difficulties in handling data in order to conveniently build and train model...
Genome Genomics DNA Software Deep Learning
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Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning.

Briefings in bioinformatics May 20, 2021
MOTIVATION: The genome-wide discovery of microRNAs (miRNAs) involves identifying sequences having the highest chance of being a novel miRNA precursor (pre-miRNA), within all the possible sequences in a complete genome. The known pre-miRNAs are usuall...
MicroRNAs Arabidopsis Humans Animals RNA Precursors Genome Computational Biology Machine Learning
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