About: Using deep learning to associate human genes with age-related diseases

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Title	Using deep learning to associate human genes with age-related diseases
described by	https://demo.openlinksw.com/about/id/entity/https/www.cs.kent.ac.uk/people/staff/akj22/materials/CO644/export_kar_RDFN3.n3 https://demo.openlinksw.com/about/id/entity/https/raw.githubusercontent.com/annajordanous/CO644Files/main/export_kar_RDFN3.n3
Date	2019-12-17
Creator	Fabio Fabris A. Freitas Daniel Palmer Joao Pedro de Magalhaes Khalid M. Salama
status	peer reviewed published
Publisher	Oxford University Press
abstract	Motivation: One way to identify genes possibly associated with ageing is to build a classification model (from the machine learning field) capable of classifying genes as associated with multiple age-related diseases. To build this model, we use a pre-compiled list of human genes associated with age-related diseases and apply a novel Deep Neural Network (DNN) method to find associations between gene descriptors (e.g. Gene Ontology terms, protein–protein interaction data and biological pathway information) and age-related diseases. Results: The novelty of our new DNN method is its modular architecture, which has the capability of combining several sources of biological data to predict which ageing-related diseases a gene is associated with (if any). Our DNN method achieves better predictive performance than standard DNN approaches, a Gradient Boosted Tree classifier (a strong baseline method) and a Logistic Regression classifier. Given the DNN model produced by our method, we use two approaches to identify human genes that are not known to be associated with age-related diseases according to our dataset. First, we investigate genes that are close to other disease-associated genes in a complex multi-dimensional feature space learned by the DNN algorithm. Second, using the class label probabilities output by our DNN approach, we identify genes with a high probability of being associated with age-related diseases according to the model. We provide evidence of these putative associations retrieved from the DNN model with literature support. The source code and datasets can be found at: https://github.com/fabiofabris/Bioinfo2019.
Is Part Of	Bioinformatics https://kar.kent.ac.uk/id/repository
Subject	Q335 Artificial intelligence
list of authors	https://kar.kent.ac.uk/id/eprint/79932#authors
issue	7
volume	36
is topic of	https://www.cs.kent.ac.uk/people/staff/akj22/materials/CO644/export_kar_RDFN3.n3 https://raw.githubusercontent.com/annajordanous/CO644Files/main/export_kar_RDFN3.n3
is primary topic of	HTML Summary of #79932 Using deep learning to associate human genes with age-related diseases

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