15 research outputs found
rFerns: An Implementation of the Random Ferns Method for General-Purpose Machine Learning
In this paper I present an extended implementation of the Random ferns
algorithm contained in the R package rFerns. It differs from the original by
the ability of consuming categorical and numerical attributes instead of only
binary ones. Also, instead of using simple attribute subspace ensemble it
employs bagging and thus produce error approximation and variable importance
measure modelled after Random forest algorithm. I also present benchmarks'
results which show that although Random ferns' accuracy is mostly smaller than
achieved by Random forest, its speed and good quality of importance measure it
provides make rFerns a reasonable choice for a specific applications
Robustness of Random Forest-based gene selection methods
Gene selection is an important part of microarray data analysis because it
provides information that can lead to a better mechanistic understanding of an
investigated phenomenon. At the same time, gene selection is very difficult
because of the noisy nature of microarray data. As a consequence, gene
selection is often performed with machine learning methods. The Random Forest
method is particularly well suited for this purpose. In this work, four
state-of-the-art Random Forest-based feature selection methods were compared in
a gene selection context. The analysis focused on the stability of selection
because, although it is necessary for determining the significance of results,
it is often ignored in similar studies.
The comparison of post-selection accuracy in the validation of Random Forest
classifiers revealed that all investigated methods were equivalent in this
context. However, the methods substantially differed with respect to the number
of selected genes and the stability of selection. Of the analysed methods, the
Boruta algorithm predicted the most genes as potentially important.
The post-selection classifier error rate, which is a frequently used measure,
was found to be a potentially deceptive measure of gene selection quality. When
the number of consistently selected genes was considered, the Boruta algorithm
was clearly the best. Although it was also the most computationally intensive
method, the Boruta algorithm's computational demands could be reduced to levels
comparable to those of other algorithms by replacing the Random Forest
importance with a comparable measure from Random Ferns (a similar but
simplified classifier). Despite their design assumptions, the minimal optimal
selection methods, were found to select a high fraction of false positives
Feature Selection with the Boruta Package
This article describes a R package Boruta, implementing a novel feature selection algorithm for finding \emph{all relevant variables}. The algorithm is designed as a wrapper around a Random Forest classification algorithm. It iteratively removes the features which are proved by a statistical test to be less relevant than random probes. The Boruta package provides a convenient interface to the algorithm. The short description of the algorithm and examples of its application are presented.
Feature Selection with the Boruta Package
This article describes a R package Boruta, implementing a novel feature selection algorithm for finding emph{all relevant variables}. The algorithm is designed as a wrapper around a Random Forest classification algorithm. It iteratively removes the features which are proved by a statistical test to be less relevant than random probes. The Boruta package provides a convenient interface to the algorithm. The short description of the algorithm and examples of its application are presented
Inferring causal molecular networks: empirical assessment through a community-based effort
Inferring molecular networks is a central challenge in computational biology. However, it has remained unclear whether causal, rather than merely correlational, relationships can be effectively inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge that focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results constitute the most comprehensive assessment of causal network inference in a mammalian setting carried out to date and suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess the causal validity of inferred molecular networks
Inferring causal molecular networks: empirical assessment through a community-based effort
It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense