Keywords
Feature selection, algorithms, R package, computational efficiency
Feature selection, algorithms, R package, computational efficiency
We are grateful to the reviewers for their time to read the paper and the comments they raised. We have addressed all comments raised by the reviewers and proof read it and made some additional changes. We hope the paper is easier to read right now.
See the authors' detailed response to the review by Thodoris Kypraios
See the authors' detailed response to the review by Huitong Qiu
Given a target (response or dependent) variable Y of n measurements and a set X of p features (predictor or independent variables) the problem of feature (or variable) selection (FS) is to identify the minimal set of features with the highest predictabilitya on the target variable (outcome) of interest. The natural question that arises, is why should researchers and practitioners perform FS. The answer to this is for a variety of reasons1, such as: a) many features may be expensive (and/or unnecessary) to measure, especially in the clinical and medical domains; b) FS may result in more accurate models (of higher predictability) by removing noise while treating the curse-of-dimensionality; c) the final produced parsimonious models are computationally cheaper and often easier to understand and interpret; d) future experiments can benefit from prior feature selection tasks and provide more insight into the problem of interest, its characteristics and structure. e) FS is indissolubly connected with causal inference that tries to identify the system’s causal mechanism that generated the data.
R contains thousands of packages, but only a small portion of them are dedicated to the task of FS, yet offering limited or narrow capabilities. For example, some packages accept few or specific types of target variables (e.g. binary and multi-class only). This leaves many types of target variables, e.g. percentages, left censored, positive valued, matched case-control data, etc., untreated. The availability of regression models for some types of data is rather small. Count data is such an example, for which Poisson regression is the only model considered in nearly all R packages. Most algorithms including statistical tests offer limited statistical tests, e.g. likelihood ratio test only. Almost all available FS algorithms are devised for large sample sized data, thus they cannot be used in many biological settings where the number of observations rarely (or never in some cases) exceeds 100, but the number of features is in the order of tens of thousands. Finally, some packages are designed for high volume datab only.
In this paper we present MXMc 2; an R package that overcomes the above shortcomings. It contains many FS algorithmsd, which can handle numerous and diverse types of target variables, while offering a pool of regression models to choose from and feed the FS algorithms. There is a plethora of statistical tests (likelihood-ratio, Wald, permutation based) and information criteria (BIC and eBIC) to plug into the FS algorithms. MXM offers algorithms that work with small and large sample sized data, algorithms that have been customized for high volume data, and an algorithm that returns multiple sets of statistically equivalent features are some of the key characteristics of MXM.
Over the next sections, a brief qualitative comparison of MXM with other packages available on CRAN and Bioconductor is presented, its (dis)advantages are discussed, its FS algorithms and related functions are mentioned. Finally a demonstration takes place, applying some FS algorithms available in MXM on real high dimensional data.
When searching for FS packages on CRAN and Bioconductor repositories using the keywords "feature selection", "variable selection", "selection", "screening" and "LASSO"e, we detected 184 R packages until the 7th of May 2018f. Table 1 shows the frequency of the target variable types those packages acceptg, while Figure 1 shows the frequency of R packages whose FS algorithms can treat at least k types of target variables, for k = 1, 2, . . . , 8, of those presented in Table 1. Table 2 presents the frequency of pairwise types of target variables offered in R packages and Table 3 contains information on packages allowing for less frequent regression models. Most packages offer FS algorithms that are oriented towards specific types of target variables, methodology and regression models, offering at most 3–4 options. Out of these 184 packages, 65 (35.32%) offer LASSO type FS algorithms, while 19 (10.32%) address the problem of FS from the Bayesian perspective. Only 2 (1.08%) R packages treat the case of FS with multiple datasetsh while only 4 (2.17%) packages are devised for high volume data.
Table 4 summarizes the types of target variables treated by MXM’ FS algorithms along with the appropriate regression models that can be employed. The list is not exhaustive, as in some cases the type of the predictor variables (continuous or categorical) affects the decision of using a regression model or a test (Pearson and Spearman for continuous and G2 test of independence for categorical). With percentages for example, MXM offers numerous regression models to plug into its FS algorithms: beta regression, quasi binomial regression or any linear regression model (robust or not) after transforming the percentages using the logistic transformation. For repeated measurements (correlated data), there are two options offered, the GeneralisedGeneralised Linear Mixed Models (GLMM) and Generalised Estimating Equations (GEE) which can also be used with various types of target variables, not mentioned here. We emphasize that MXM is the only package that covers all types of response variables mentioned on Table 1, many types of which are not available in any other FS package, such as left censored data for example. MXM also covers 3 out 4 cases that appear on Table 3.
Most of the currently available FS algorithms in the MXM package have been developed by the creators and authors of the package (see the last column of Table 5). The Incremental Association Markov Blanket (IAMB) algorithm was suggested by 3. The algorithm first performs the classical Forward Selection Regression (FSR) and then performs a variant of the classical Backward Selection Regression (BSR). Instead of removing the least significant feature detected at each step, it removes all non significant features. The Max Min Parents and Children (MMPC) algorithm also developed4, is designed for small sample sized data and also performs a variant of FSR. At every step, when searching for the next best feature it does not use all currently selected features, but subsets of them and the non significant features are removed from further consideration. The Max Min Markov Blanket (MMMB) algorithm proposed by 4 picks the features MMPC selected and applies MMPC using each of them as target variable. The Statistically Equivalent Signatures (SES) algorithm suggested by 2 builds upon MMPC in order to identify statistically equivalent features; features that carry the same information with a selected feature. The Forward Backward with Early Dropping (FBED) algorithm is the most recently suggested FS algorithm by 5 (two authors of the MXM R package) and improves the computational cost of FSR by removing the non significant features at every step. In the end all the removed features can be tested again multiple times. Finally BSR is applied to remove possibly falsely selected features. Finally, the generalised Orthogonal Matching Pursuit (gOMP)6 is a generalisation of OMP (Orthogonal Matching Pursuit)7–9. OMP applies a residual based FSR with continuous target variables only. We have generalised it to accept numerous types of target variables, such as binary, nominal, ordinal, counts, multivariate, time-to-event, left censored, proportions, etc, while for each of them the user can choose their regression model to employ.
Algorithm | Cases | ||||||
---|---|---|---|---|---|---|---|
n small & p small | n small & p big | n big & p small | n big & p big | High volume data | Multiple solutions | Authors development | |
BSR | ✓ | ||||||
FBED | ✓ | ✓ | ✓ | ✓ | |||
FSR | ✓ | ||||||
gOMP | ✓ | ✓ | ✓ | ✓ | |||
IAMB | ✓ | ✓ | |||||
MMMB | ✓ | ✓ | ✓ | ✓ | |||
MMPC | ✓ | ✓ | ✓ | ✓ | |||
SES | ✓ | ✓ | ✓ | ✓ | ✓ |
These algorithms have been tested and compared with other state-of-the-art algorithms under different scenarios and types of data. IAMB3 was on par with or outperforming competing machine learning algorithms, when both the target variable and features are categorical. MMPC and MMMB algorithms4 were tested in the context of Bayesian Network learning showing great success with MMPC shown to achieve excellent false positive rates10. MMPC formed the basis of Max Min Hill Climbing (MMHC)11, a prototypical algorithm for learning the structure of a Bayesian network which outperformed all other Bayesian network learning algorithms with categorical data. For time-to-event and nominal categorical target variable, MMPC12, and 13 respectively, outperformed or was on par with LASSO and other FS algorithms. SES2 was contrasted against LASSO with continuous, binary and survival target variables, resulting in similar conclusions as before. With temporal and time-course data, SES14 outperformed the LASSO algorithm15 both in predictive performance and computational efficiency. FBED5 was compared to LASSO for the task of binary classification with sparse data exhibiting performance similar to that of LASSO. As for gOMP, our experiments have showed very promising results, achieving similar or better performance, while enjoying higher computational efficiency than LASSO6.
The main advantage of MXM is that all FS algorithms accept numerous and diverse types of target variables. MMPC, SES and FBED treat all types of target variables presented in Table 4, while gOMP handles fewer typesi.
MXM is the only R package that offers many different regression models to be employed by the FS algorithms, even for the same type of response variable, such as Poisson, quasi Poisson, negative binomial and zero inflated Poisson regression for count data. For repeated measurements, the user has the option of using GLMM or the GEE methodology (the latter with more options in the correlation structure) and for time-to-event data, Cox, Weibull and exponential regression models are the available options.
A range of statistical tests and methodologies to select the features is offered. Instead of the usual log-likelihood ratio test, the user has the option to use the Wald test or produce a p-value based on permutations. The latter is useful and advised when the sample size is small, emphasizing the need for use of MMPC and SES, both of which are designed for small sample sized datasets. FBED on the other hand, appart from the log-likelihood ratio test offers the possibility of using information criteria, such as BIC16 and eBIC17.
No p-values correction (e.g. Benjamini and Hochberg18,) is applied. Specifically MMPC (and SES essentially) has been proved to control the False Discovery Rate19. However, we allow for permutation-based p-values when performing MMPC and SES. FBED addresses this issue either by removing the non-significant variables or by using information criteria such as the extended BIC17. Borboudakis and Tsamardinos5 have conducted experiments showing that FBED reduces the percentage of falsely selected features. gOMP on the other hand relies on correlations and does not select the candidate feature using p-values.
Statistically Equivalent Signatures (SES)2,20 builds upon the ideas of MMPC and returns multiple (statistically equivalent) sets of predictor variables, making it one of the few FS algorithms suggested in the literature, and available in CRAN, with this trait21. demonstrated that multiple, equivalent prognostic signatures for breast cancer can be extracted just by analyzing the same dataset with a different partition in training and test sets, showing the existence of several genes which are practically interchangeable in terms of predictive power. SES along with MMPC are two among the few algorithms, available on CRAN , that can be used to perform FS with multiple datasets in a meta-analytic way, following22. MXM contains FS algorithms for small sample sized data (MMPC, MMMB, and SES)j and for large sample sized data (FBED, gOMP). FBED and gOMP have been adopted for high volume data, going beyond the limits of R. The importance of these customizations can be appreciated by the fact that nowadays large scale datasets are more frequent than before. Since classical FS algorithms cannot handle such data, modifications must be made, in an algorithm level, in a memory efficient manner, in a computer architecture level, and/or in any other way. MXM is using the efficient memory handling R package bigmemory23.
Finally, many utility functions are available, such as constructing a model from the object an algorithm returned, construct a regression model, long verbose output with useful information, etc. Using hash objects, the computational cost of MMPC and SES is significantly reduced. Further, communication between the input and outputs of the algorithms is possible. The univariate associations computed by MMPC can be supplied to SES and FBED, and vice versa, and save computational time.
Not all MXM’s FS algorithms and all regression models used are computationally efficient. The (algorithmic) order of complexity of the FS algortihms is comparable to state-of-art FS algorithms, but the nature of the other algorithms is such that many regression models must be fit increasing the computational burden. In addition, R itself does not allow for further speed improvement. For example, MMPC can be slow for many regression models, such as negative binomial or ordinal regression for which we rely on implementations in other R packages. gOMP, on the other hand, is the most efficient algorithm available in MXMk gOMP superseded the LASSO implementation in the package glmnet24 in both time and performance., because it is residual based and few regression models are fit. With clustered/longitudinal data, SES (and MMPC) were shown to scale to tens of thousands and be dramatically faster than LASSO14. Computational efficiency is also programming language-dependent. Most of the algorithms are currently written in R and we are constantly working towards transferring them to C++ so as to decrease the computational cost significantly.
It is impossible to cover all cases of target variables; we have no algorithms for time series, and do not treat multi-state time-to-event target variables for example, yet we regularly search for R packages that treat other types of target variables and link them to MXMl. All algorithms are limited to linear or generalised linear relationships, and we plan to address this issue in the future. The gOMP algorithm does not accept all types of target variables and works only with continuous predictor variables. This is a limitation of the algorithm, but we plan to address this in the future as well.
Cross-validation functions currently exist only for MMPC, SES and gOMP, but performance metrics are not available for all target variables. When the target variable is binary AUC, accuracy or the F score can be utilised, when the target takes continuous values, the mean squared error, the mean absolute error or the proportion of variance explained can be used, whereas with survival target variables the concordance index can be computed. Left censored data, is an example of target variable whose predictive performance estimation is not offered. A last drawback is that currently MXM does not offer graphical visualization of the algorithms and of the final produced models.
In terms of sample size, FBED and gOMP are generally advised for large-sample-sized datasets, whereas MMPC and SES are designed mainly for small-sample-sized datasetsm. In the case of a large sample size and few features, FSR or BSR are also suggested. In terms of number of features, gOMP is the only algorithm that scales up when the number of features is in the order of the hundreds of thousands. gOMP is also suitable for high volume data that contain a high number of features, really large sample sizes or both. FBED has been customized to handle high volume data as well, but with large sample sizes and only a few thousand features. If the user is interested in discovering more than one set of features, SES is suitable for returning multiple solutions, which are statistically equivalent. With multiple datasetsn, both MMPC and SES are currently the only two algorithms that can handle some cases (both the target variable and the set of features are continuous). As for the availability of the target variable, MMPC, SES and FBED handle all types of target variables available in MXM, listed in Table 4, while gOMP accepts fewer types of target variables. Regarding the type of features, gOMP currently works with continuous features only, whereas all other algorithms accept both continuous and categorical features. All this information is presented in Table 5.
MXM is an R package that makes use of (depends or imports) other packages that offer regression models or utility functions.
bigmemory: for large volume data.
doParallel: for parallel computations.
coxme: for frailty models.
geepack: for GEE models.
lme4: for mixed models.
MASS: for negative binomial regression, ordinal regression and robust (MM type) regression.
nnet: for multinomial regression.
ordinal: for ordinal regression.
quantreg: for quantile regression.
stats (built-in package): for generalised linear models.
survival: for survival regression and Tobit regression.
Rfast: for computational efficiency.
MXM contains functions for returning the selected features for a range of hyper-parameters for each algorithm. For example, mmpc.path runs MMPC for multiple combinations of threshold and maxk, and gomp.path runs gOMP for a range of stopping values. The exception is with FBED, for which the user can give a vector of values of K in fbed.reg instead of a single value. Unfortunately, the path of significance levels cannot be determined at a single runo.
MMPC and SES have been implemented in such a way that the user has the option to store the results (p-values and test statistic values) from a single run in a hash object. In subsequent runs, with different hyper-parameters this can lead to significant amounts of computational savings because it avoids performing tests that have been already been performed. These two algorithms give the user an extra advantage. They can search for the subset of feature(s) that rendered one more specific feature(s) independent of the target variable by using the function certificate.of.exclusion.
FBED, SES and MMPC are three algorithms that share common grounds. The list with the results of the univariate associations (test statistic and logged p-value) can be calculated from either algorithm and be passed onto any of them. When one is interested in running many algorithms, this can reduce the computational cost significantly. Note also that the univariate associations in MMPC and SES can be calculated in parallel, with multi-core machines. More FS related functions can be found in MXM’s reference manual and vignettes section available on CRAN.
MXM is distributed as part of the CRAN R package repository and is compatible with Mac OS X, Windows, Solaris and Linux operating systems. Once the package is installed and loaded
> install.packages("MXM")
> library(MXM)
it is ready to be used without internet connection. The system requirements are documented on MXM’s webpage on CRAN.
We will now demonstrate some FS algorithms available in MXM, using real datasets. Specifically we will show the relevant commands and describe part of their output. With user-friendliness taken into consideration, extra attention has been put in keeping the functions within the MXM package as consistent as the nature of the algorithms allows for, in terms of syntax, required input objects and parameter arguments. Table 6 contains a list of the current FS algorithms, but we will demonstrate some of them here. In all cases, the arguments "target", "dataset" and "test" refer to the target variable, set of features and type of regression model to be used.
We will use a variety of target variables and in some examples, we will show the results produced with different regression models. Nearly all datasets (except for the first one) contain tens of thousands of features. The difference is with the target variable or interest. For example, when trying to select features for a time-to-event target variable survival regression should be employed, with continuous target variable, linear regression can be employed, whereas for counts, negative binomial or quasi Poisson regression could be employed by the FS algorithm. Under no circumstances should the following examples be considered experimental or for the purpose of comparison. They are only for the purpose of algorithms’ demonstration, to give examples of different types of target variables and to show how the algorithms work. All computations took place in a desktop computer with Intel Core i5-4690K CPU @3.50GHz and 32 GB RAM.
The first dataset we used concerns breast cancer, with 295 women selected from the fresh-frozen–tissue bank of the Netherlands Cancer Institute25. The dataset contains 70 features and the target variable is time to event, with 63 censored valuesp. We need this information, to be passed as a numerical variable indicating the status (0 = censored, 1 = not censored), for example (1, 1, 0, 1, 1, 1, . . . ). We will make use of the R package survival26 for running the appropriate models (Cox and Weibull regression) and show the FBED algorithm with the default arguments. Part of the output is presented below. Information on the selected features, their test statistic and their associated logarithmically transformed p-valueq, along with some information on the number of regression models fitted is displayed.
> target <- survival::Surv(y, status)
> MXM::fbed.reg(target = target, dataset = dataset, test = "censIndCR")
$res
sel stat pval
1 28 8.183389 -5.466128
2 6 5.527486 -3.978164
$info
Number of vars Number of tests
K=0 2 73
The first column of $res denotes the selected features, i.e. the 28th and the 6th feature were selected. The second and third columns refer to the feature(s)’s associated test statistic and p-value. The $info informs the user on the value of K used, the number of selected features and the number of tests (or regression models) performed.
The above output was produced using Cox regression. If we used Weibull regression instead (test = "testIndWR"), the output would be slightly different. Only one feature (the 28th) was selected, and FBED performed 75 tests (based upon 75 fitted regression models).
> MXM::fbed.reg(target = target, dataset = dataset, test = "censIndWR")
$res
sel stat pval
Vars 28 8.489623 -5.634692
$info
Number of vars Number of tests
K=0 1 75
The second dataset we used again concerns breast cancer27 and contains 285 samples over 17,187 gene expressions (features). Since the target variable is binary, logistic regression was employed by gOMP.
> MXM::gomp(target = target, dataset = dataset, test = "testIndLogistic")
The element res presented below is one of the elements of the returned output. The first column shows the selected variables in order of inclusion and the second column is the deviance of each regression model. The first line refers to the regression model with 0 predictor variables (constant term only).
$res
Selected Vars Deviance
[1,] 0 332.55696
[2,] 4509 156.33519
[3,] 17606 131.04428
[4,] 3856 113.78382
[5,] 10101 95.76704
[6,] 16759 80.25748
[7,] 6466 67.78120
[8,] 11524 54.54652
[9,] 9794 44.17957
[10,] 4728 36.52319
[11,] 3620 20.48441
[12,] 13127 5.583645e-10
The next dataset we will use is NCBI Gene Expression Omnibus accession number GSE910528, which contains 22,283 features about skeletal muscles from 12 normal, healthy glucose-tolerant individuals exposed to acute physiological hyperinsulinemia, measured at 3 distinct time points. Following14, we will also use SES and not FBED because the sample size is small. The grouping variable that identifies the subject along with the time points is necessary in our case. If the data were clustered data, i.e. families, where no time is involved, the argument "reps" would not be provided. The user has the option to use GLMM29 or GEE30. The output of SES (and of MMPC) is long and verbose, and thus we present the first 10 set of equivalent signatures. The first row is the set of selected features, and every other row is an equivalent set. In this example, the last four columns are the same and only the first changes. This means, that the feature 2683 has 9 statistically equivalent features, (2, 7, 10, ...).
> MXM::SES.temporal(target = target, reps = reps, group = group,
dataset = dataset, test = "testIndGLMMReg")
@signatures[1:10,]
Var1 Var2 Var3 Var4 Var5
[1,] 2683 6155 9414 13997 21258
[2,] 2 6155 9414 13997 21258
[3,] 7 6155 9414 13997 21258
[4,] 10 6155 9414 13997 21258
[5,] 18 6155 9414 13997 21258
[6,] 213 6155 9414 13997 21258
[7,] 393 6155 9414 13997 21258
[8,] 699 6155 9414 13997 21258
[9,] 836 6155 9414 13997 21258
[10,] 1117 6155 9414 13997 21258
The next dataset we consider is from Human cerebral organoids recapitulate gene expression programs of fetal neocortex development31. The data are pre-processed RNA-seq, thus continuous data, with 729 samples and 58, 037 features. We selected the first feature as the target variable and all the rest were considered to be the features. In this case we used FBED and gOMP, employing the Pearson correlation coefficient because all measurements are continuous.
FBED performed 123, 173 tests and selected 63 features.
> MXM::fbed.reg(target = target, dataset = dataset, test = "testIndFisher")
$info
Number of vars Number of tests
K=0 63 123173
gOMP on the other hand was more parsimonious, selecting only 8 features. At this point we must highlight the fact that the selection of a feature was based on the adjusted R2 value. If the increase in the adjusted R2 due to the candidate feature was more than 0.01 or (1/%), the feature was selected.
> MXM::gomp(target = target, dataset = dataset, test = "testIndFisher",
method = "ar2", tol = 0.01)
$res
Vars adjusted R2
[1,] 0 0.0000000
[2,] 11394 0.3056431
[3,] 4143 0.4493530
[4,] 49524 0.4744709
[5,] 8 0.4936872
[6,] 29308 0.5096887
[7,] 8619 0.5287238
[8,] 3194 0.5411237
[9,] 5958 0.5513510
The final example is on discrete valued target variable (count data) for which Poisson and quasi-Poisson regression models will be employed by the gOMP algorithm. The dataset with GEO accession number GSE4777432 contains RNA-seq data with 256 samples and 43,919 features. We selected the first feature to be the target variable and all the rest are the features.
We ran gOMP using Poisson (test="testIndPois") and quasi Poisson (test="testIndQPois") regression models, but we changed the stopping value to tol=12. Due to over-dispersion (variance > mean), quasi Poisson is more appropriater than Poisson regression that assumes that the mean and the variance are equal. When Poisson was used, 107 features were selected; since the wrong model was used, many false positive features were included, while with the quasi Poisson regression only 10 features were selected.
> MXM::gomp(target = target, dataset = dataset, test = "testIndQPois",
tol = 12)
$res
Selected Vars Deviance
[1,] 0 3821661.14
[2,] 6391 145967.17
[3,] 12844 129639.56
[4,] 26883 113706.51
[5,] 32680 108387.15
[6,] 29370 102407.46
[7,] 4274 96817.48
[8,] 43570 91373.77
[9,] 43294 86125.30
[10,] 31848 81659.51
[11,] 38299 77295.71
The case of ordinal target variable (i.e. very low, low, high, very high) has been treated previously33 for unrevealing interesting features measuring the user perceived quality of experience with YouTube video streaming applications and the Quality of Service (target variable) of the underlying network under different network conditions.
More recently34, applied MMPC in order to identify the features that provide novel information about steady-state plasma glucose (SSPG, a measure of peripheral insulin resistance) and are thus most useful for prediction35. used gOMP and identified the viscoelastic properties of the arterial tree as an important contributor to the circulating bubble production after a dive. Finally36, applied SES and gOMP were applied in the field of fisheries for identifying the genetic SNP loci that are associated with certain phenotypes of the gilthead seabream (Sparus aurata). Measurements from multiple cultured seabream families were taken, and since the data were correlated and GLMM was applied. The study led to a catalogue of genetic markers that set the ground for understanding growth and other traits of interest in Gilthead seabream, in order to maximize the aquaculture yield.
We presented the R package MXM and some of its feature selection algorithms. We discussed its advantages and disadvantages and compared it, at a high level, with other competing R packages. We then demonstrated, using real high-dimensional data with a diversity of types of target variables, four FS algorithms, including different regression models in some cases.
The package is constantly being updated with new functions and improvements being added and algorithms being transferred to C++ to decrease the computational cost. Computational efficiency was mentioned as one of MXM’ disadvantage which we are trying to address. However, computational efficiency is one aspect, and flexibility another. Towards flexibility we plan to add of more regression models, more functionalities, options and graphical visualizations.
The first dataset we used (survival target variable) is available from Computational Cancer Biology.
The second dataset we used (unmatched case control target variable) is available from GEO.
The third dataset we used (longitudinal data) is available from GEO.
The fourth dataset we used (continuous target variable) is available from GEO.
The fifth dataset we used (count data) is available from GEO.
MXM is available from: https://cran.r-project.org/web/packages/MXM/index.html.
Source code is available from: https://github.com/mensxmachina/MXM-R-Package
Archived source code at time of publication: https://doi.org/10.5281/zenodo.345801337
License: GPL-2.
We would like to acknowledge Stefanos Fafalios, Zacharias Papadovasilakis, Christina Chatzipantsiou, Kleio-Maria Verrou, and Manos Papadakis for their constructive feedback.
aPredictive performance metrics include AUC, accuracy, mean squared error, mean absolute error, concordance index, F score, proportion of variance explained, etc.
bIn statistics and in the R packages the term "big data" is used to refer to such data. In the computer science terminology, big data are of much higher volume and require specific technology. For this reason we chose to use the term "high volume" instead of "big data".
dMXM is mainly FS oriented, but it offers (Bayesian) network learning algorithms (for causal inference) as well. In fact, many feature selection algorithms offered in MXM are Bayesian network inspired.
fWe highlight the fact that especially on hrefhttps://cran.r-project.org/CRAN, packages are uploaded at a super-linear rate. Bioconductor is more strict with the addition of new packages. The phenomenon of abandoned or not maintained packages for a long time is not at all unusual. Such an example is "biospear", removed from CRAN (archived) in the 30th of April 2018. On the other hand we manualy added in our list a package that performs FS without mentioning it in its title.
gWe manually examined each package to identify the types of target variables it accepts and regression models it offers.
hInstead of having a target variable and a set of features, one can have two or more sets of target variables and features. The algorithm we have devised for this case uses simultaneously all target variables and sets of features
iFor this long list of available target variables and regression models, expanding Table 4, see Guide on performing FS with the R package MXM.
jThe Wald and log-likelihood ratio tests are asymptotic tests. In addition, the fitted regression models require large sample size. With small sample sizes, the fitted regression models must not contain many predictor variables in order not to estimate many parameters. To address these issues both MMPC and SES perform conditional independence tests using subsets of selected variables, thus reducing the number of estimated parameters.
kBased on our experiments6.
lCurrently, with little effort, one should be able to plug-in their own regression model into some of the algorithms. We plan to expand this possibility for all algorithms.
mTo the best of our knowledge there are not many FS algorithms dealing with small sample sized data.
nInstead of having one dataset only to analyze one might have multiple datasets from different sources. We do not combine all datasets into a larger one, neither perform FS for each dataset separately. Each step of the MMPC and SES algorithms is performed simultaneously to all datasets.
pCensoring occurs when partial information about some observations is available. It might be the case that some individuals will experience the event after completion of the study. Or when an individual is not part of the study for anymore, for a reason other than the occurrence of the event of interest. In a study about cancer, for example, some patients may die of another cause, e.g. another disease or car accident for example. The survival times of those patients has been recorded, but offer limited information.
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Competing Interests: No competing interests were disclosed.
Reviewer Expertise: statistical machine learning, feature selection, high dimensional data, graphical models, time series analysis, clinical trial design
Competing Interests: No competing interests were disclosed.
Is the rationale for developing the new software tool clearly explained?
Yes
Is the description of the software tool technically sound?
Yes
Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others?
Partly
Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool?
Partly
Are the conclusions about the tool and its performance adequately supported by the findings presented in the article?
Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: statistical machine learning, feature selection, high dimensional data, graphical models, time series analysis, clinical trial design
Is the rationale for developing the new software tool clearly explained?
Yes
Is the description of the software tool technically sound?
Yes
Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others?
Yes
Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool?
Partly
Are the conclusions about the tool and its performance adequately supported by the findings presented in the article?
Yes
Competing Interests: No competing interests were disclosed.
Alongside their report, reviewers assign a status to the article:
Invited Reviewers | ||
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Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list:
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