Nimbus ruby library.

Nimbus is a ruby gem implementing random forest algorithm for genomic selection contexts.
http://www.nimbusgem.org

Slides of the presentation from the EAAP 2011 conference in Stavanger, Norway.

Transcript

1. An opensource library to implement random forests in genomic contexts Oscar González-Recio Juanjo Bazán Selma Forni
2. The Problem
3. The Problem Massive amount of information from high troughput genotyping platforms.
4. The Problem Massive amount of information from high troughput genotyping platforms. Need to extract knowledge from large, noisy, redundant, missing and fuzzy data.
5. The Problem Massive amount of information from high troughput genotyping platforms. Massive amount of information consumes the attention of its recipients. We need to allocate that attention efciently. Need to extract knowledge from large, noisy, redundant, missing and fuzzy data.
6. Why Random Forest?
7. Why Random Forest? Using Machine Learning techniques we can extract hidden relationships that exist in these huge volumes of data and do not follow a particular parametric design.
8. Why Random Forest? Using Machine Learning techniques we can extract hidden relationships that exist in these huge volumes of data and do not follow a particular parametric design. Random Forest have desirable statistical properties.
9. Why Random Forest? Using Machine Learning techniques we can extract hidden relationships that exist in these huge volumes of data and do not follow a particular parametric design. Random Forest have desirable statistical properties. Random Forest scales well computationally.
10. Using Machine Learning techniques we can extract hidden relationships that exist in these huge volumes of data and do not follow a particular parametric design. Random Forest have desirable statistical properties. Random Forest scales well computationally. Random Forest performs extremely well in a variety of possible complex domains (Breiman, 2001; Gonzalez-Recio & Forni, 2011). Why Random Forest?
11. The Algorithm
12. Ensemble methods: - Combination of diferent methods (usually simple models). - They have very good predictive ability because use additivity of models performances. Based on Classifcation And Regression Trees (CART). Use Randomization and Bagging. Performs Feature Subset Selection. Convenient for classifcation problems. Fast computation. Simple interpretation of results for human minds. Previous work in genome-wide prediction (Gonzalez-Recio and Forni, 2011) The Algorithm
13. The Algorithm Perform bootstrap on data: Ψ* = (y, X) Build a CART ( fi (y, X) = ht (x) ) using only mtry proportion of SNPs in each node. Repeat M times to reduce residuals by a factor of M. Average estimates c0 = μ ; ci = 1/M
14. Let Ψ = (y, X) be a set of data, with y = vector of phenotypes (response variables) X = (x1, x2) = matrix of features y1 x11 x12 … … ... yi xi1 xi2 … … ... yn xn1 xn2 The Algorithm Classifcation and regression trees:
15. The Algorithm
16. Nimbus library
17. Nimbus library Written in Ruby www.ruby-lang.org Open source programming language Syntax focused on simplicity Natural to read and easy to write
18. Nimbus library How to install: > gem install nimbus Prerequisites: Ruby and Rubygems (default library manager) installed in the system
19. Nimbus library How to run: > nimbus Confguration: Via confg.yml fle
20. Nimbus library confg.yml fle:
21. Nimbus library Input fles: training testing
22. Nimbus library Features, use cases: Training of a prediction forest Training of a prediction forest Genomic Prediction of a testing sample Using a training set of individuals Nimbus creates a reutilizable forest Nimbus calculates SNP importances Generalization error are computed for every tree in the forest Using a custom/reused forest, specif i ed via conf i g.yml Using a new trained forest
23. Outputs Random Forest fle In standard YAML format
24. Outputs Predictions for the training sample
25. Outputs Predictions for the testing sample
26. Outputs SNP importances
27. More info: Nimbus website: Source code: Report bugs/request features: www.nimbusgem.org www.github.com/xuanxu/nimbus/issues www.github.com/xuanxu/nimbus
28. Thank you!
29. Questions?