Machine learning applications in genetics and genomics pdf

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machine learning applications in genetics and genomics pdf

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Machine learning , a subfield of computer science involving the development of algorithms that learn how to make predictions based on data , has a number of emerging applications in the field of bioinformatics. Bioinformatics deals with computational and mathematical approaches for understanding and processing biological data [1]. Prior to the emergence of machine learning algorithms, bioinformatics algorithms had to be explicitly programmed by hand which, for problems such as protein structure prediction , proves extremely difficult. This multi-layered approach to learning patterns in the input data allows such systems to make quite complex predictions when trained on large datasets. In recent years, the size and number of available biological datasets have skyrocketed, enabling bioinformatics researchers to make use of these machine learning systems.
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Published 28.12.2018

James Zou: "Deep learning for genomics: Introduction and examples"

Machine learning in genetics and genomics

Genomic malformations are believed to be the driving factors of many diseases. Therefore, understanding the intrinsic mechanisms underlying the genome and informing clinical practices have become two important missions of large-scale genomic research. Recently, high-throughput molecular data have provided abundant information about the whole genome, and have popularized computational tools in genomics. However, traditional machine learning methodologies often suffer from strong limitations when dealing with high-throughput genomic data, because the latter are usually very high dimensional, highly heterogeneous, and can show complicated nonlinear effects. In this thesis, we present five new algorithms or models to address these challenges, each of which is applied to a specific genomic problem. Project 1 focuses on model selection in cancer diagnosis. Project 2 focuses on model selection in gene correlation analysis.

Metrics details. Machine learning has demonstrated potential in analyzing large, complex biological data. In practice, however, biological information is required in addition to machine learning for successful application. In the not so distant past, data generation was the bottleneck, now it is data mining, or extracting useful biological insights from large, complicated datasets. In the past decade, technological advances in data generation have advanced studies of complex biological phenomena.

In the past decade, precision genomics based medicine has emerged to provide tailored and effective healthcare for patients depending upon their genetic features. Genome Wide Association Studies have also identified population based risk genetic variants for common and complex diseases. In order to meet the full promise of precision medicine, research is attempting to leverage our increasing genomic understanding and further develop personalized medical healthcare through ever more accurate disease risk prediction models. Polygenic risk scoring and machine learning are two primary approaches for disease risk prediction. Despite recent improvements, the results of polygenic risk scoring remain limited due to the approaches that are currently used. By contrast, machine learning algorithms have increased predictive abilities for complex disease risk. This increase in predictive abilities results from the ability of machine learning algorithms to handle multi-dimensional data.

The field of machine learning promises to enable computers to assist humans in making sense of large, complex data sets. In this review, we outline some of the main applications of machine learning to genetic and genomic data.
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Identifying disease genes from a vast amount of genetic data is one of the most challenging tasks in the post-genomic era. Also, complex diseases present highly heterogeneous genotype, which difficult biological marker identification. Machine learning methods are widely used to identify these markers, but their performance is highly dependent upon the size and quality of available data. In this study, we demonstrated that machine learning classifiers trained on gene functional similarities, using Gene Ontology GO , can improve the identification of genes involved in complex diseases. For this purpose, we developed a supervised machine learning methodology to predict complex disease genes. A quantitative measure of gene functional similarities was obtained by employing different semantic similarity measures.


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    Machine learning applications have also been exten- sively used to assign analysis of genetic and genomic data sets. REVIEWS. NATURE.

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