Random KNN feature selection  a fast and stable alternative to Random Forests
 Shengqiao Li^{1, 2}Email author,
 E James Harner^{1} and
 Donald A Adjeroh^{3}Email author
https://doi.org/10.1186/1471210512450
© Li et al; licensee BioMed Central Ltd. 2011
Received: 31 January 2011
Accepted: 18 November 2011
Published: 18 November 2011
Abstract
Background
Successfully modeling highdimensional data involving thousands of variables is challenging. This is especially true for gene expression profiling experiments, given the large number of genes involved and the small number of samples available. Random Forests (RF) is a popular and widely used approach to feature selection for such "small n, large p problems." However, Random Forests suffers from instability, especially in the presence of noisy and/or unbalanced inputs.
Results
We present RKNNFS, an innovative feature selection procedure for "small n, large p problems." RKNNFS is based on Random KNN (RKNN), a novel generalization of traditional nearestneighbor modeling. RKNN consists of an ensemble of base knearest neighbor models, each constructed from a random subset of the input variables. To rank the importance of the variables, we define a criterion on the RKNN framework, using the notion of support. A twostage backward model selection method is then developed based on this criterion. Empirical results on microarray data sets with thousands of variables and relatively few samples show that RKNNFS is an effective feature selection approach for highdimensional data. RKNN is similar to Random Forests in terms of classification accuracy without feature selection. However, RKNN provides much better classification accuracy than RF when each method incorporates a featureselection step. Our results show that RKNN is significantly more stable and more robust than Random Forests for feature selection when the input data are noisy and/or unbalanced. Further, RKNNFS is much faster than the Random Forests feature selection method (RFFS), especially for large scale problems, involving thousands of variables and multiple classes.
Conclusions
Given the superiority of Random KNN in classification performance when compared with Random Forests, RKNNFS's simplicity and ease of implementation, and its superiority in speed and stability, we propose RKNNFS as a faster and more stable alternative to Random Forests in classification problems involving feature selection for highdimensional datasets.
Keywords
Background
Selection of a subset of important features (variables) is crucial for modeling high dimensional data in bioinformatics. For example, microarray gene expression data may include p ≥ 10, 000 genes. But the sample size, n, is much smaller, often less than 100. A model cannot be built directly since the model complexity is larger than the sample size. Technically, linear discriminant analysis can only fit a linear model up to n parameters. Such a model would provide a perfect fit, but it has no predictive power. This "small n, large p problem" has attracted a lot of research attention, aimed at removing nonessential or noisy features from the data, and thus determining a relatively small number of features which can mostly explain the observed data and the related biological processes.
Though much work has been done, feature selection still remains an active research area. The significant interest is attributed to its many benefits. As enumerated in [1], these include (i) reducing the complexity of computation for prediction; (ii) removing information redundancy (cost savings); (iii) avoiding the issue of overfitting; and (iv) easing interpretation. In general, the generalization error becomes lower as fewer features are included, and the higher the number of samples per feature, the better. This is sometimes referred to as the Occam's razor principle [2]. Here we give a brief summary on feature selection. For a recent review, see [3]. Basically, feature selection techniques can be grouped into three classes: Class I: Internal variable selection. This class mainly consists of Decision Trees (DT) [4], in which a variable is selected and split at each node by maximizing the purity of its descendant nodes. The variable selection process is done in the tree building process. The decision tree has the advantage of being easy to interpret, but it suffers from the instability of its hierarchical structures. Errors from ancestors pass to multiple descendant nodes and thus have an inflated effect. Even worse, a minor change in the root may change the tree structure significantly. An improved method based on decision trees is Random Forests [5], which grows a collection of trees by bootstrapping the samples and using a random selection of the variables. This approach decreases the prediction variance of a single tree. However, Random Forests may not remove certain variables, as they may appear in multiple trees. But Random Forests also provides a variable ranking mechanism that can be used to select important variables.
Class II: Variable filtering. This class encompasses a variety of filters that are principally used for the classification problem. A specific type of model may not be invoked in the filtering process. A filter is a statistic defined on a random variable over multiple populations. With the choice of a threshold, some variables can be removed. Such filters include tstatistics, Fstatistics, KullbackLeibler divergence, Fisher's discriminant ratio, mutual information [6], informationtheoretic networks [7], maximum entropy [8], maximum information compression index [9], relief [10, 11], correlationbased filters [12, 13], relevance and redundancy analysis [14], etc.
Class III: Wrapped methods. These techniques wrap a model into a search algorithm [15, 16]. This class includes foreward/backword, stepwise selection using a defined criterion, for instance, partial Fstatistics, Aikaike's Information Criterion (AIC) [17], Bayesian Information Criterion (BIC) [18], etc. In [19], sequential projection pursuit (SPP) was combined with partial least square (PLS) analysis for variable selection. Wrapped feature selection based on Random Forests has also been studied [20, 21]. There are two measures of importance for the variables with Random Forests, namely, mean decrease accuracy (MDA) and mean decrease Gini (MDG). Both measures are, however, biased [22]. One study shows that MDG is more robust than MDA [23]; however another study shows the contrary [24]. Our experiments show that both methods give very similar results. In this paper we present results only for MDA. The software package varSelRF in R developed in [21] will be used in this paper for comparisons. We call this method RFFS or RF when there is no confusion. Given the hierarchical structure of the trees in the forest, stability is still a problem.
The advantage of the filter approaches is that they are simple to compute and very fast. They are good for prescreening, rather than building the final model. Conversely, wrapped methods are suitable for building the final model, but are generally slower.
Recently, Random KNN (RKNN) which is specially designed for classification in high dimensional datasets was introduced in [25]. RKNN is a generalization of the knearest neighbor (KNN) algorithm [26–28]. Therefore, RKNN enjoys the many advantages of KNN. In particular, KNN is a nonparametric classification method. It does not assume any parametric form for the distribution of measured random variables. Due to the flexibility of the nonparametric model, it is usually a good classifier for many situations in which the joint distribution is unknown, or hard to model parametrically. This is especially the case for high dimensional datasets. Another important advantage of KNN is that missing values can be easily imputed [29, 30]. Troyanskaya et al. [30] also showed that KNN is generally more robust and more sensitive compared with other popular classifiers. In [25] it was shown that RKNN leads to a significant performance improvement in terms of both computational complexity and classification accuracy. In this paper, we present a novel feature selection method, RKNNFS, using the new classification and regression method, RKNN. Our empirical comparison with the Random Forests approach shows that RKNNFS is a promising approach to feature selection for high dimensional data.
Methods
Random KNN
The idea of Random KNN is motivated by the technique of Random Forests, and is similar in spirit to the method of random subspace selection used for Decision Forests [31]. Both Random Forests and Decision Forests [31] use decision trees as the base classifiers. Compared with the two, Random KNN uses KNN as base classifiers, with no hierarchical structure involved. Compared with decision trees, KNN is simple to implement and is stable [32]. Thus, Random KNN can be stabilized with a small number of base KNN's and hence only a small number of important variables will be needed. This implies that the final model with Random KNN will be simpler than that with Random Forests or Decision Forests. Specifically, a collection of r different KNN classifiers will be generated. Each one takes a random subset of the input variables. Since KNN is stable, bootstrapping is not necessary for KNN. Each KNN classifier classifies a test point by its majority, or weighted majority class, of its k nearest neighbors. The final classification in each case is determined by majority voting of r KNN classifications. This can be viewed as a sort of voting by a Majority of a Majority.
More formally, let F = {f_{1}, f_{2},..., f_{ p }} be the p input features, and X be the n original input data vectors of length p, i.e., an n × p matrix. For a given integer m < p, denote F^{(m)}= {f_{j 1}, f_{j 2},..., f_{ jm }f_{ jl }∈ F, 1 ≤ l ≤ m} a random subset drawn from F with equiprobability.
Similarly, let X^{(m)}be the data vectors in the subspace defined by F^{(m)}, i.e., an n × m matrix. Then a KNN^{(m)}classifier is constructed by applying the basic KNN algorithm to the random collection of features in X^{(m)}. A collection of r such base classifiers is then combined to build the final Random KNN classifier.
Feature support  a ranking criterion
Computing feature supports using Random KNN bidirectional voting
/* Generate n KNN classifiers using m features and compute accuracy acc for each KNN */ 

/* Return support for each feature */ 
p ← number of features in the data set; 
m ← number of features for each KNN; 
r ← number of KNN classifiers; 
F_{ i }← feature list for i^{ th }KNN classifier; 
C ← build r KNNs using m feature for each; 
Perform query from base data sets using each KNN; 
Compare predicted values with observed values; 
Calculate accuracy, acc, for each base KNN; 
$F\leftarrow {\bigcup}_{i=1}^{r}{F}_{i}$; {F is the list of features that appeared in r KNN classifiers}; 
for each f ∈ F do 
C(f) ← list of KNN classifiers that used f; 
$support\left(f\right)\leftarrow \frac{1}{\leftC\left(f\right)\right}{\sum}_{knn\in C\left(f\right)}acc\left(knn\right);$ 
end for 
To compute feature supports, data are partitioned into base and query subsets. Two partition methods may be used: (1) dynamic partition: For each KNN, the cases are randomly partitioned. One half is the base subset and the other half is the query subset; (2) the data set is partitioned once, and for all KNN's, the same base subset and query subset are used. That is, all base subsets are the same and all query subsets are also the same. For diversity of KNN's, the dynamic partition is preferred.
RKNN feature selection algorithm
Twostage variable backward elimination procedure for Random KNN
Stage 1: Geometric Elimination 

q ← proportion of the number features to be dropped each time; 
p ← number of features in data; 
$ni\leftarrow \u230aln\left(4\u2215p\right)\u2215ln\left(1q\right)\u230b$; /* number of iterations, minimum dimension 4*/ 
initialize rknn _list[m]; /* stores feature supports for each Random KNN */ 
initialize acc[m]; /* stores accuracy for each Random KNN */ 
for i from 1 to ni do 
if i == 1 then 
rknn ← compute supports via Random KNN from all variables of data; 
else 
$p\leftarrow \u230ap\cdot \left(1q\right)\u230b;$ 
rknn ← compute supports via Random KNN from p top important variables of rknn; 
end if 
rknn list[i] ← rknn; 
acc[i] ← accuracy of rknn; 
end for 
$max=\underset{1\le k\le ni}{argmax}\left(acc\left[k\right]\right);$ 
pre _max = max  1; 
rknn ← knn _list[pre _max]; /* This Random KNN goes to stage 2 */ 
Stage 2: Linear Reduction 
d ← number features to be dropped each time; 
p ← number of variables of rknn; 
$ni\leftarrow \u230a\left(p4\right)\u2215d\u230b$; /* number of iterations */ 
for i from 1 to ni do 
if i ≠ 1 then 
p ← p  d; 
end if 
rknn ← compute supports via Random KNN from p top important variables of rknn; 
acc[i] ← accuracy of rknn; 
rknn_list[i] ←rknn; 
end for 
$best\leftarrow \underset{1\le k\le ni}{argmax}\left(acc\left[k\right]\right);$ 
best _rknn ← rknn _list[best]; /* This gives final random KNN model */ 
return best _rknn; 
Time complexity
Time complexity for computing feature support
For each KNN, we have the typical time complexity as follows:

Data Partition: O(n);

Nearest Neighbor Searching: O(k 2^{ m }n log n);

Classification: O(kn);

Computing accuracy: O(n).
Adding the above 4 items together, we get a time needed for one KNN: O(k 2^{ m }n log n). For Random KNN, we have r KNN's; thus the total time for the above steps is O(rk 2^{ m }n log n). Since rm features are used in the Random KNN, the time for computing supports from these accuracies is O(rm). Thus the overall time is O(rk 2^{ m }n log n) + O(rm) = O(r(m + k 2^{ m }n log n)) = O(rk 2^{ m }n log n). Sorting these supports will take O(p log p). Since for most applications, log p < n log n, and p < rk 2^{ m }, the time complexity for computing and ranking feature supports still remains as O(rk 2^{ m }n log n).
Time complexity for feature selection
In stageone, the number of features decreases geometrically with proportion q. For simplicity, let us take m to be the squareroot of p and keep r fixed. Thus the sum of the component 2^{ m }is ${2}^{\sqrt{p}}+{2}^{\sqrt{pq}}+{2}^{\sqrt{p{q}^{2}}}+{2}^{\sqrt{p{q}^{3}}}+{2}^{\sqrt{p{q}^{4}}}+....$ The first term is dominant, since q is a fraction. Thus the time complexity will be in $O\left(rk{2}^{\sqrt{p}}nlogn\right)$.
In stagetwo, each time a fixed number of features is removed. In the extreme case, only one feature is removed per iteration, the total time will be $O\left(rk{2}^{{p}_{1}+1}nlogn\right)$, where p_{1} is the number of features at the start of stagetwo, and usually p_{1} < p^{1/2}. So on average, we have time in $O\left(rk{2}^{{p}_{1}+1}nlogn\right)=O\left(rk{2}^{\sqrt{p}}nlogn\right)$.
Therefore, the total time for the entire algorithm will be in $O\left(rk{2}^{\sqrt{p}}nlogn\right)$, the same as that for using Random KNN for classification, at $m=\sqrt{p}$ Basically, in theory, feature selection does not degrade the complexity of Random KNN. With m = log p, we obtain time complexity in O(rkpn log n). This is significant, as it means that with appropriate choice of m, we can essentially turn the exponential time complexity of feature selection to linear time, with respect to p, the number of variables.
Parameter setting
Results and discussion
Microarray datasets
Microarray gene expression datasets, Group I
Dataset  Sample Size, n  No. of Genes, p  No. of classes, c  p/n  p* c/n 

Ramaswamy  308  15009  26  49  1267 
Staunton  60  5726  9  95  859 
Nutt  50  10367  4  207  829 
Su  174  12533  11  72  792 
NCI60  61  5244  8  86  688 
Brain  42  5597  5  133  666 
Armstrong  72  11225  3  156  468 
Pomeroy  90  5920  5  66  329 
Bhattacharjee  203  12600  5  62  310 
Adenocarcinoma  76  9868  2  130  260 
Golub  72  5327  3  74  222 
Singh  102  10509  2  103  206 
Microarray gene expression datasets, Group II
Dataset  Sample Size, n  No. of Genes, p  No. of classes, c  p/n  p* c/n 

Lymphoma  62  4026  3  65  195 
Leukemia  38  3051  2  80  161 
Breast.3.Classes  95  4869  3  51  154 
SRBCT  63  2308  4  37  147 
Shipp  77  5469  2  71  142 
Breast.2.Classes  77  4869  2  63  126 
Prostate  102  6033  2  59  118 
Khan  83  2308  4  28  111 
Colon  62  2000  2  32  65 
Classwise sample sizes are from 2 to 139 (i.e., some datasets are unbalanced). The ratio of the number of genes, p, to the sample size, n, reflects the difficulty of a dataset and is listed in the table. The number of classes c, has a similar effect on the classification problem. Thus collectively, the quantity (p/n) * c is included in the tables as another measure of complexity of the classification problem for each dataset. Based on this, we divided the datasets into two groups  Group I  those with relatively high values for (p/n) * c (corresponding to relatively more complex classification problems), and Group II  those with relatively low values (corresponding to the datasets that present relatively simpler classification problems). We have organized our results around this grouping scheme.
Evaluation methods
In this study, we compare Random KNN with Random Forests since they both are ensemble methods. The difference is the base classifier. We perform leaveoneout crossvalidation (LOOCV) to obtain classification accuracies. LOOCV provides unbiased estimators of generalization error for stable classifiers such as KNN [33]. With LOOCV, we can also evaluate the effect of a single sample, i.e., the stability of a classifier. When feature selection is involved, the LOOCV is "external." In external LOOCV, feature selection is done n times separately for each set of n  1 cases. The number of base classifiers for Random KNN and Random Forests is set to 2,000. The number of variables for each base classifier is set to the squareroot of the total number of variables of the input dataset. Both k = 1 (R1NN) and k = 3 (R3NN) for Random KNN are evaluated.
Performance comparison without feature selection
Random Forests and Random KNN are applied to the two groups of datasets using all genes available. The results (data not shown) indicate that Random Forests was nominally better than Random KNN on 11 datasets while Random KNN was nominally better than Random Forests on 9 datasets. They have a tie on one dataset. Using the pvalues from the McNemar test [34], Random Forests was no better than Random KNN on any of the datasets, while R1NN was significantly better than Random Forests on the NCI data and Random Forests was better than R3NN on two datasets. Using the average accuracies, no significant difference was observed in Group I (0.80 for RF, 0.81 for R1NN, 0.78 for R3NN), or in Group II (0.86 for RF, 0.84 for R1NN, 0.86 for R3NN). Therefore from the test on the 21 datasets, we may conclude that without feature selection, Random KNN is generally equivalent to Random Forests in classification performance.
Performance comparison with feature selection
Comparative performance with gene selection, Group I
Dataset  p* c/n  Mean Accuracy  Standard Deviation  Coefficient of Variation  

RF  R1NN  R3NN  RF  R1NN  R3NN  RF  R1NN  R3NN  
Ramaswamy  1267  0.577  0.726  0.704  0.019  0.013  0.013  3.231  1.775  1.796 
Staunton  859  0.561  0.692  0.663  0.042  0.026  0.031  7.485  3.802  4.669 
Nutt  829  0.671  0.903  0.834  0.051  0.030  0.031  7.619  3.268  3.674 
Su  792  0.862  0.901  0.888  0.016  0.015  0.014  1.884  1.624  1.567 
NCI  688  0.813  0.854  0.836  0.033  0.027  0.023  4.083  3.135  2.796 
Brain  666  0.969  0.958  0.940  0.025  0.013  0.018  2.574  1.323  1.875 
Armstrong  468  0.936  0.993  0.980  0.020  0.009  0.013  2.166  0.938  1.345 
Pomeroy  329  0.858  0.933  0.863  0.025  0.016  0.017  2.892  1.762  1.991 
Bhattacharjee  310  0.934  0.956  0.954  0.015  0.006  0.006  1.572  0.620  0.618 
Adenocarcinoma  260  0.942  0.939  0.859  0.018  0.017  0.032  1.948  1.808  3.675 
Golub  222  0.943  0.986  0.986  0.022  0.003  0.004  2.328  0.289  0.369 
Singh  206  0.889  0.952  0.931  0.024  0.014  0.018  2.718  1.427  1.920 
Average  0.830  0.899  0.870  0.026  0.016  0.018  3.375  1.814  2.191 
Comparative performance with gene selection, Group II
Dataset  p* c/n  Mean Accuracy  Standard Deviation  Coefficient of Variation  

RF  R1NN  R3NN  RF  R1NN  R3NN  RF  R1NN  R3NN  
Lymphoma  195  0.993  1.000  1.000  0.012  0.000  0.000  1.162  0.000  0.000 
Leukemia  161  1.000  0.999  0.999  0.000  0.006  0.004  0.000  0.596  0.427 
Breast.3.class  154  0.778  0.793  0.761  0.024  0.037  0.035  3.023  4.665  4.639 
SRBCT  147  0.982  0.998  0.996  0.010  0.005  0.007  0.967  0.470  0.684 
Shipp  142  0.865  0.997  0.991  0.033  0.008  0.011  3.757  0.800  1.077 
Breast.2.class  126  0.838  0.841  0.822  0.024  0.052  0.042  2.894  6.206  5.049 
Prostate  118  0.947  0.941  0.917  0.007  0.011  0.016  0.703  1.154  1.701 
Khan  111  0.985  0.994  0.994  0.006  0.006  0.008  0.643  0.608  0.809 
Colon  65  0.894  0.944  0.910  0.010  0.013  0.025  1.163  1.337  2.733 
Average  0.920  0.945  0.932  0.014  0.015  0.016  1.590  1.760  1.902 
Stability
Average gene set size and standard deviation, Group I
Dataset  p* c/n  Mean Feature Set Size  Standard Deviation  

RF  R1NN  R3NN  RF  R1NN  R3NN  
Ramaswamy  1267  907  336  275  666  34  52 
Staunton  859  185  74  60  112  12  11 
Nutt  829  146  49  49  85  6  4 
Su  792  858  225  216  421  9  26 
NCI  688  126  187  163  118  41  33 
Brain  666  18  137  120  13  42  42 
Armstrong  468  249  76  73  1011  16  12 
Pomeroy  329  69  89  82  70  15  13 
Bhattacharjee  310  33  148  146  29  15  10 
Adenocarcinoma  260  8  38  11  4  20  11 
Golub  222  12  27  21  8  5  5 
Singh  206  26  25  13  32  6  6 
Average  220  118  102  214  18  19 
Average gene set size and standard deviation, Group II
Dataset  p* c/n  Mean Feature Set Size  Standard Deviation  

RF  R1NN  R3NN  RF  R1NN  R3NN  
Lymphoma  195  75  114  103  30  49  44 
Leukemia  161  2  28  36  0  22  18 
Breast.3.Class  154  47  43  36  35  23  8 
SRBCT  147  49  65  64  50  8  9 
Shipp  142  13  46  48  23  9  6 
Breast.2.Class  126  32  23  15  29  16  10 
Prostate  118  16  32  15  10  10  11 
Khan  111  17  67  36  5  11  14 
Colon  65  21  37  36  18  5  5 
Average  30  51  43  22  17  14 
Time comparison
Execution time comparison, Group I
Dataset  p* c/n  Time (min)  Ratio  

RF  R1NN  R3NN  RF/R1NN  RF/R3NN  
Ramaswamy  1267  22335  4262  4324  5.2  5.2 
Staunton  859  3310  744  753  4.4  4.4 
Nutt  829  176  195  195  0.9  0.9 
Su  792  3592  1284  1279  2.8  2.8 
NCI  688  142  177  178  0.8  0.8 
Brain  666  92  124  125  0.7  0.7 
Armstrong  468  327  301  297  1.1  1.1 
Pomeroy  329  296  319  320  0.9  0.9 
Bhattacharjee  310  4544  1725  1733  2.6  2.6 
Adenocarcinoma  260  274  272  273  1.0  1.0 
Golub  222  160  224  224  0.7  0.7 
Singh  206  646  503  498  1.3  1.3 
Total  35894  10130  10199  3.54  3.52 
Execution time comparison, Group II
Dataset  p* c/n  Time (min)  Ratio  

RF  R1NN  R3NN  RF/R1NN  RF/R3NN  
Lymphoma  195  57  146  147  0.4  0.4 
Leukemia  161  18  74  74  0.3  0.2 
Breast.3.Class  154  310  332  334  0.9  0.9 
SRBCT  147  97  177  178  0.5  0.5 
Shipp  142  238  293  286  0.8  0.8 
Breast.2.Class  126  167  221  222  0.8  0.8 
Prostate  118  370  389  391  1.0  0.9 
Khan  111  745  452  451  1.6  1.7 
Colon  65  75  156  157  0.5  0.5 
Total  2077  2240  2240  0.93  0.93 
Conclusion
In this paper, we introduce RKNNFS, a new feature selection method for the analysis of highdimensional data, based on the novel Random KNN classifier. We performed an empirical study using the proposed RKNNFS on 21 microarray datasets, and compared its performance with the popular Random Forests approach. From our comparative experimental results, we make the following observations: (1) The RKNNFS method is competitive with the Random Forests feature selection method (and most times better) in classification performance; (2) Random Forests can be very unstable under some scenarios (e.g., noise in the input data, or unbalanced datasets), while the Random KNN approach shows much better stability, whether measured by stability in classification rate, or stability in size of selected gene set; (3) In terms of processing speed, Random KNN is much faster than Random Forests, especially on the most timeconsuming tasks with large p and multiple classes. The concept of KNN is easier to understand than the decision tree classifier in Random Forests and is easier to implement. We have focused our analysis and comparison on Random Forests, given its popularity, and documented superiority in classification accuracy over other stateoftheart methods [20, 21]. Other results on the performance of RF and its variants are reported in [35, 36]. In future work, we will perform a comprehensive comparison of the proposed RKNNFS with these other classification and feature selection schemes, perhaps using larger and more diverse datasets, or on applications different from microarray analysis.
In summary, the RKNNFS approach provides an effective solution to pattern analysis and modeling with highdimensional data. In this work, supported by empirical results, we suggest the use of Random KNN as a faster and more stable alternative to Random Forests. The proposed methods have applications whenever one is faced with the "small n, large p problem", a significant challenge in the analysis of high dimensional datasets, such as in microarrays.
Declarations
Acknowledgements
The authors are grateful to Michael Kashon for his thoughtful comments and discussion. The findings and conclusions in this report are those of the author(s) and do not necessarily represent the views of the National Institute for Occupational Safety and Health. This work was supported in part by a WVEPSCoR RCG grant.
Authors’ Affiliations
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