Dataset Information

Technical note: an R package for fitting sparse neural networks with application in animal breeding.

ABSTRACT: Neural networks (NNs) have emerged as a new tool for genomic selection (GS) in animal breeding. However, the properties of NN used in GS for the prediction of phenotypic outcomes are not well characterized due to the problem of over-parameterization of NN and difficulties in using whole-genome marker sets as high-dimensional NN input. In this note, we have developed an R package called snnR that finds an optimal sparse structure of a NN by minimizing the square error subject to a penalty on the L1-norm of the parameters (weights and biases), therefore solving the problem of over-parameterization in NN. We have also tested some models fitted in the snnR package to demonstrate their feasibility and effectiveness to be used in several cases as examples. In comparison of snnR to the R package brnn (the Bayesian regularized single layer NNs), with both using the entries of a genotype matrix or a genomic relationship matrix as inputs, snnR has greatly improved the computational efficiency and the prediction ability for the GS in animal breeding because snnR implements a sparse NN with many hidden layers.

SUBMITTER: Wang Y

PROVIDER: S-EPMC6140926 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Technical note: an R package for fitting sparse neural networks with application in animal breeding.

Wang Yangfan Y Mi Xue X Rosa Guilherme J M GJM Chen Zhihui Z Lin Ping P Wang Shi S Bao Zhenmin Z

Journal of animal science 20180501 5

Neural networks (NNs) have emerged as a new tool for genomic selection (GS) in animal breeding. However, the properties of NN used in GS for the prediction of phenotypic outcomes are not well characterized due to the problem of over-parameterization of NN and difficulties in using whole-genome marker sets as high-dimensional NN input. In this note, we have developed an R package called snnR that finds an optimal sparse structure of a NN by minimizing the square error subject to a penalty on the ...[more]

PMID: 29529218

Similar Datasets

Project description:PurposeRadiation dose delivered to targets located near the upper abdomen or thorax are significantly affected by respiratory motion, necessitating large margins, limiting dose escalation. Surrogate motion management devices, such as the Real-time Position Management (RPM™) system (Varian Medical Systems, Palo Alto, CA), are commonly used to improve normal tissue sparing. Alternative to current solutions, we have developed and evaluated the feasibility of a real-time position management system that leverages the motion data from the onboard hardware of Apple iOS devices to provide patients with visual coaching with the potential to improve the reproducibility of breathing as well as improve patient compliance and reduce treatment delivery time.Methods and materialsThe iOS application, coined the Instant Respiratory Feedback (IRF) system, was developed in Swift (Apple Inc., Cupertino, CA) using the Core-Motion library and implemented on an Apple iPhone® devices. Operation requires an iPhone®, a three-dimensional printed arm, and a radiolucent projector screen system for feedback. Direct comparison between IRF, which leverages sensor fusion data from the iPhone®, and RPM™, an optical-based system, was performed on multiple respiratory motion phantoms and volunteers. The IRF system and RPM™ camera tracking marker were placed on the same location allowing for simultaneous data acquisition. The IRF surrogate measurement of displacement was compared to the signal trace acquired using RPM™ with univariate linear regressions and Bland-Altman analysis.ResultsPeriodic motion shows excellent agreement between both systems, and subject motion shows good agreement during regular and irregular breathing motion. Comparison of IRF and RPM™ show very similar signal traces that were significantly related across all phantoms, including those motion with different amplitude and frequency, and subjects' waveforms (all r > 0.9, P < 0.0001). We demonstrate the feasibility of performing four-dimensional cone beam computed tomography using IRF which provided similar image quality as RPM™ when reconstructing dynamic motion phantom images.ConclusionsFeasibility of an iOS application to provide real-time respiratory motion is demonstrated. This system generated comparable signal traces to a commercially available system and offers an alternative method to monitor respiratory motion.

Dataset Information

Technical note: an R package for fitting sparse neural networks with application in animal breeding.

Publications

Technical note: an R package for fitting sparse neural networks with application in animal breeding.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets