کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
5790174 1553966 2014 15 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Machine learning methods and predictive ability metrics for genome-wide prediction of complex traits
ترجمه فارسی عنوان
روش های یادگیری ماشین و معیارهای توان پیش بینی برای پیش بینی ژنوم ویژگی های پیچیده
کلمات کلیدی
پرورش حیوانات، اعتبار سنجی متقابل، پیش بینی گسترده ژنوم، فراگیری ماشین، غیر پارامتریک، دقت پیش بینی،
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک علوم دامی و جانورشناسی
چکیده انگلیسی


- We review non-parametric and machine learning methods for genome-wide prediction.
- We review metrics for assessing predictive ability in genomic prediction.
- Support vector machines and random forests seem preferred for classification problems.
- Reproducing Kernel Hilbert Spaces and boosting may suit better regression problems.
- Predictive mean squared error is the main but not only metric for model comparison.

Genome-wide prediction of complex traits has become increasingly important in animal and plant breeding, and is receiving increasing attention in human genetics. Most common approaches are whole-genome regression models where phenotypes are regressed on thousands of markers concurrently, applying different prior distributions to marker effects. While use of shrinkage or regularization in SNP regression models has delivered improvements in predictive ability in genome-based evaluations, serious over-fitting problems may be encountered as the ratio between markers and available phenotypes continues increasing. Machine learning is an alternative approach for prediction and classification, capable of dealing with the dimensionality problem in a computationally flexible manner. In this article we provide an overview of non-parametric and machine learning methods used in genome wide prediction, discuss their similarities as well as their relationship to some well-known parametric approaches. Although the most suitable method is usually case dependent, we suggest the use of support vector machines and random forests for classification problems, whereas Reproducing Kernel Hilbert Spaces regression and boosting may suit better regression problems, with the former having the more consistently higher predictive ability. Neural Networks may suffer from over-fitting and may be too computationally demanded when the number of neurons is large.We further discuss on the metrics used to evaluate predictive ability in model comparison under cross-validation from a genomic selection point of view. We suggest use of predictive mean squared error as a main but not only metric for model comparison. Visual tools may greatly assist on the choice of the most accurate model.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Livestock Science - Volume 166, August 2014, Pages 217-231
نویسندگان
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