Do little interactions get lost in dark random forests?
- Marvin N. Wright^{1},
- Andreas Ziegler^{1, 2, 3} and
- Inke R. König^{1}Email author
https://doi.org/10.1186/s12859-016-0995-8
© Wright et al. 2016
Received: 12 January 2016
Accepted: 21 March 2016
Published: 31 March 2016
Abstract
Background
Random forests have often been claimed to uncover interaction effects. However, if and how interaction effects can be differentiated from marginal effects remains unclear. In extensive simulation studies, we investigate whether random forest variable importance measures capture or detect gene-gene interactions. With capturing interactions, we define the ability to identify a variable that acts through an interaction with another one, while detection is the ability to identify an interaction effect as such.
Results
Of the single importance measures, the Gini importance captured interaction effects in most of the simulated scenarios, however, they were masked by marginal effects in other variables. With the permutation importance, the proportion of captured interactions was lower in all cases. Pairwise importance measures performed about equal, with a slight advantage for the joint variable importance method. However, the overall fraction of detected interactions was low. In almost all scenarios the detection fraction in a model with only marginal effects was larger than in a model with an interaction effect only.
Conclusions
Random forests are generally capable of capturing gene-gene interactions, but current variable importance measures are unable to detect them as interactions. In most of the cases, interactions are masked by marginal effects and interactions cannot be differentiated from marginal effects. Consequently, caution is warranted when claiming that random forests uncover interactions.
Keywords
Random forests Trees Variable importance Gene-gene interactions EpistasisBackground
To investigate how random forests deal with interaction effects, we are interested in two aspects. For the first, we consider an example reported in the studies by Droździk et al. [10] and Zschiedrich et al. [11] on a polymorphism in the MDR1 gene as a susceptibility factor for Parkinson’s disease. Only a very small marginal genetic effect was shown, but there was a significant interaction between the variant and pesticide exposure on disease risk. Hence, it is of interest whether this genetic variant would nonetheless be identified as a predictor in random forests. If a variable is identified by the random forest that contributes to the classification with an interaction effect, this interaction effect is captured by the model. The second aspect is whether random forests are able to identify the interaction effect per se and the predictor variables interacting with each other. We will use the term detect for this in the following. Many authors argue that random forests capture interactions [1–5], while others even state that they identify, uncover or detect them [6–8]. However, empirical studies are rare.
It has been shown that variable importance measures are, in principle, suitable to capture interactions [12, 13]. However, current methods seem to fail in high dimensional data [14], and the effect of various different interaction models on importance measures has not been investigated. To detect interactions, the standard variable importance measures of random forests, Gini and permutation importance, are by design not suitable. Therefore, different methods specifically designed to detect effects of pairs of variables in random forests were proposed [15–17]. These methods measure a joint variable importance to rank variable pairs by their interaction effects. The efficacy of these approaches has only been investigated in small simulations and without considering marginal effects or different interaction scenarios.
In an extensive simulation study, we therefore investigate whether random forests variable importance measures capture or detect interactions effects. In the first part, the Gini and permutation variable importance measures are used to capture interaction effects between single nucleotide polymorphisms (SNPs). Since these methods cannot detect interaction effects, we consider only the pairwise importance measures in the second part, in which we focus on the detection of interacting SNPs. In our simulation, we consider various interaction models, vary effect sizes, minor allele frequencies (MAF) and the number of SNPs randomly selected as splitting candidates (mtry). Even though SNPs are used as predictive variables, all results naturally generalize to other kinds of categorical data.
Methods
Random forests
Detailed descriptions of random forests are available in the original [18] and more recent literature [19, 20]. In brief, random forests are ensembles of decision trees. Depending on the outcome, trees can be classification or regression trees (CARTs) [21], survival trees [22] or probability estimation trees (PETs) [23], among others. For random forests, a number of trees are grown that differ because of two components. First, each tree is based on a prespecified number of bootstrap samples or subsamples of individuals. Second, only a random subset of the variables is considered as splitting candidates at each split in the trees. To classify a subject in the random forest, the results of the single trees are aggregated in an appropriate way, depending on the type of random forest. A great advantage of random forests is that the bootstrapping or subsampling for each tree yields subsets of observations, termed out-of-bag (OOB) observations, which are not included in the tree growing process. These are used to estimate the prediction performance or variable importance. There are two specifically important parameters to random forests: The number mtry of randomly selected splitting candidates is usually kept fixed for all splits. In most implementations, the default value for mtry is \(\sqrt {p}\), where p is the number of variables in the dataset. However, for datasets with a large number of variables, a larger value is required to capture more relevant variables [3]. Typically, mtry is tuned, e.g. by comparing the prediction performance of several values using cross validation. Another important parameter of random forests is the size of single trees. This size is usually controlled by stopping the tree growth if a minimal terminal node size is reached. For regression and survival outcomes, the terminal node size is usually tuned together with the mtry value, while for classification the trees are grown to purity.
Gini importance
The standard splitting rule in random forests for classification outcomes is to maximize the decrease of impurity that is introduced by a split. For this, the impurity is typically measured by the Gini index [21]. Since a large Gini index suggests a large decrease of impurity, a split with large Gini index can be considered to be important for classification. Thus, the Gini importance for a variable x _{ i } in a tree can be computed by summing the Gini index values of all nodes in which a split on x _{ i } has been conducted. The average of all tree importance values for x _{ i } is then termed Gini importance of the random forest for x _{ i }. In our simulation studies, the R package ranger [24] was used to compute the Gini importance.
Permutation importance
The basic idea of the permutation variable importance approach [18] is to consider a variable important if it has a positive effect on the prediction performance. To evaluate this, a tree is grown in the first step, and the prediction accuracy in the OOB observations is calculated. In the second step, any association between the variable of interest x _{ i } and the outcome is broken by permuting the values of all individuals for x _{ i }, and the prediction accuracy is computed again. The difference between the two accuracy values is the permutation importance for x _{ i } from a single tree. The average of all tree importance values in a random forest then gives the random forest permutation importance of this variable. The procedure is repeated for all variables of interest. The package ranger [24] was used in our analyses.
Pairwise permutation importance (PPI)
To measure the permutation importance for a pair of variables, a modification of the permutation importance was proposed [15]. Instead of permuting a single variable, two variables x _{ i } and x _{ j } are permuted simultaneously. As for the standard permutation importance, the difference in prediction accuracy with and without permutation is computed and used as importance value for the respective pair of variables. This procedure is repeated for all variable pairs of interest. Here, usually, only a subset of the variable pairs is selected to reduce runtime. Although the concept could easily be extended to higher orders of interaction, this would lead to high computational costs. Originally, the approach was implemented in FORTRAN 77 [15]. For easier usage and higher computational speed, we included the PPI measure in the R package ranger [24] (see Additional file 1 for a version including this measure).
Joint importance by maximal subtrees (JMST)
The joint importance by maximal subtrees measure ([17], JMST) is based on maximal subtrees introduced by Ishwaran et al. [16]. For this, any subtree of the original tree is called an x _{ i }-subtree if the root node is split by x _{ i }. A subtree is a maximal subtree if it is not a subtree of a larger x _{ i }-subtree. It can now be assumed that variables with subtrees closer to the root node have a larger impact on the prediction and are therefore more important than others. The distance of the maximal subtree to the root node is termed the minimal depth of a variable and gives the importance value. For interactions, second-order maximal (x _{ j }, x _{ i })-subtrees are used that are defined as the maximal x _{ j }-subtree within a maximal x _{ i }-subtree. Here, the minimal depth is the distance of the maximal (x _{ j }, x _{ i })-subtree to the root of the maximal x _{ i }-subtree. For the simulation studies, the find.interaction function of the R package randomForestSRC [25] was used with the option maxsubtree. A matrix with normalized minimal depths for all pairs of variables of interest is returned. Since we are interested in two-way interactions, we used the average of the minimal depths of (x _{ j }, x _{ i }) and (x _{ i }, x _{ j })-subtrees to compute the joint importance of x _{ i } and x _{ j }.
Joint variable importance (JVIMP)
For the joint variable importance measure ([16], JVIMP), maximal subtrees are utilized again. As in permutation importance, the association between a variable x _{ i } and the outcome is broken by randomization. However, instead of permuting the variable, a so-called noise-up procedure is employed: Each observation is dropped down the tree until a maximal x _{ i }-subtree is reached. From then on, all further splits are replaced by random child node assignments. This is repeated for all trees. The importance of variable x _{ i } is now measured by the difference between the OOB prediction accuracy of the noised-up forest and the original forest. For pairs of variables x _{ i } and x _{ j }, the random assignments start as soon as a maximal subtree of x _{ i } or x _{ j } is reached. The importance of the interaction effect of x _{ i } and x _{ j } is computed by the difference of the sum of both single importance values (additive effect) and the joint importance value (pairwise effect). The find.interaction function of randomForestSRC [25] was used with the option vimp.
Genetic interaction models
Simulation studies
Logit model generation
Interaction model | SNP1 | SNP2 | SNP1 x SNP2 |
---|---|---|---|
Interaction only | 0 | 0 | β _{ I } |
Modifier SNP | 0 | β _{ I } | β _{ I } |
No interaction | β _{ I } | β _{ I } | 0 |
Redundant | β _{ I } | β _{ I } | −β _{ I } |
Synergistic | β _{ I } | β _{ I } | β _{ I } |
Simulation parameters
Parameter | Description | Values |
---|---|---|
β _{ M } | Effect of marginal-only SNPs | 0.4, 0.8 |
β _{ I } | Interaction effect (see Table 1) | 0.4, 0.8 |
M A F _{ M } | Minor allele frequencies for marginal-only SNPs | 0.2, 0.4 |
M A F _{ I } | Minor allele frequencies for interacting SNPs | 0.2, 0.4 |
mtry | Number of SNPs randomly selected as splitting candidates | 10, 50 |
Penetrance table for model Interaction only, β _{ I }=0.4, M A F _{ I }=0.4. A _{1} and B _{1} represent the major alleles and A _{2} and B _{2} the minor alleles
SNP 1 | ||||
---|---|---|---|---|
A _{1} A _{1} | A _{1} A _{2} | A _{2} A _{2} | ||
B _{1} B _{1} | 0.35 | 0.35 | 0.35 | |
SNP 2 | B _{1} B _{2} | 0.35 | 0.44 | 0.54 |
B _{2} B _{2} | 0.35 | 0.54 | 0.72 |
To study the influence of the fixed parameters, we further simulated datasets where the number of marginal-only SNPs was reduced to 2 and datasets where the number of noise SNPs was increased to 2493. In both cases, the effects were fixed to β _{ M }=β _{ I }=0.4 and the MAF to M A F _{ M }=M A F _{ I }=0.2. To investigate the impact of linkage disequilibrium (LD), we simulated LD structures based on data from phase 3 of the 1000 genomes project [27]. A random region on chromosome 22 was chosen, and 1000 SNPs without missing data and a MAF between 0.05 and 0.2 were selected. The mean pairwise LD between these SNPs was D ^{′}=0.69 (SD 0.35) and the correlation r ^{2}=0.14 (SD 0.23). For each simulated dataset, 100 SNPs were randomly selected out of these region, and new data with LD structure was simulated using HapSim [28]. Effects of β _{ M }=β _{ I }=0 and all combinations of β _{ M }=(0.4,0.8) and β _{ I }=(0.4,0.8) were simulated.
On each dataset, random forests with 500 trees each were grown with a varying number of SNPs randomly selected as splitting candidates (mtry value), chosen from (10,50). To investigate the capture of interacting SNPs, two measures of importance for single variables were computed in the first part, the Gini importance and the permutation importance. Second, to investigate the detection of interactions, we computed the pairwise importance measures PPI [15], JMST [17] and JVIMP [16]. In total, 800 simulation scenarios were analyzed, and for each scenario, we ran 100 replications. Using every importance measure, the variables were ranked, and the ranks of the true interaction SNPs or, in case of the pairwise measures, their combination were saved. Inspired by Lunetta et al. [12] and McKinney et al. [29], the proportion of replicates in which both true interaction SNPs were among the top k ranks is plotted for k=2,…,10 for the single variable importance measures. A high value for k=2 means that the interacting SNPs are ranked before all other SNPs and the interaction is captured by the random forest. High values for k=3,…,10 indicate that the interaction is still captured, but masked by marginal effects or noise.
For the pairwise measures, we plot the proportion of replicates in which the combination of the true interacting SNPs was among the top k ranks for k=1,…,10. To make the analyses computationally feasible, combinations containing noise SNPs were excluded from the ranking. Here, a high value for a small k indicates a high proportion of detection of the true interaction, with the exception of the No interaction model, where the interaction effect is 0 and any detection would be a false positive result. To compare the ranking of the interacting SNPs with the marginal-only SNPs the proportion of replicates, in which the single variable importance measures ranked the 5 marginal-only SNPs among the top k ranks is shown for k=5,…,15. For the pairwise importance measures, the proportion of replicates, in which all 10 combinations of marginal-only SNPs are among the top k pairs, is shown for k=10,…,20. Replication code for all simulation studies is included in Additional file 3.
Results
Capturing interaction effects by single variable importance measures
Detecting interaction effects by pairwise variable importance measures
Discussion
In our extensive simulation studies, we found that random forests are capable of capturing SNP-SNP interactions, i.e. of including them in the model. Of the single variable importance measures, the Gini importance ranks the interacting SNPs higher than the permutation importance. The single importance measures are unable to detect interactions, and this by design. They can thus not differentiate between marginal and interaction effects. But since, in most cases, the interacting SNPs are ranked higher than noise SNPs even if no marginal effects are present, we conclude that the interaction effects are thereby captured in random forests. In general, the ranking depends heavily on the MAF, with more frequent SNPs being ranked higher.
The results of the pairwise importance measures suggest that they are unable to detect interactions in the presence of marginal effects. With all measures, marginal effects were detected as interaction effects, and true interactions were not found if other SNPs with strong marginal effects were present. Again, SNPs were ranked higher if the MAF was increased. All methods ranked the interacting SNPs higher in the model without interaction, compared with the model with interaction only, suggesting that interaction effects cannot be differentiated from marginal effect. Of the compared methods, JVIMP [16] achieved the best results, since detection was highest for the model with interaction only and lowest for the model without interaction in most of the simulation scenarios.
To study SNP-SNP interactions with random forest, we used 5 interaction models in a simplified setting. We simulated rather strong effects and large MAF values. Our results show that the pairwise importance measures are unable to detect interactions in this setting. In simulations with an increased number of noise SNPs, the single importance measures performed worse and the pairwise measures about equal. If LD was considered, only very strong effects were detected at all and again marginal effects were detected as interactions.
Despite the difficulty of the pairwise variable importance measures to detect interactions, our data suggest that interaction effects are generally captured by random forests. One approach to improve the detection rate might be to use random forests to perform a variable selection first and applying another method to identify interactions subsequently [30, 31]. However, interaction effects might again be masked by marginal effects in that approach. A related idea is to uncover marginal effects in a first step and project the remaining effects on a space orthogonal to the marginal effects, to detect interactions in a second step [32, 33]. On a different route, the detection of interactions might be facilitated by developing new pairwise importance measures based on standard random forests [34]. However, it is argued that in the case of many predictor variables, it is unlikely that interacting variables are selected simultaneously in a given tree [9]. Second, for combinations of variables, the attributable risk [35] can be small, in particular for variants with small MAF. This means that only a small proportion of cases is attributable to the interaction, and even for large effect sizes these interactions are difficult to detect. Finally, it can be argued that random forests are by design unable to split on interactions [36]. As shown in Fig. 1 a, if interacting variables have no marginal effect at all, no first split is possible and the interaction cannot be captured. To solve this, the tree growing process in the random forest itself could be modified to better incorporate interactions. A promising, yet computationally intensive new approach are reinforcement learning trees [37], which employ reinforcement learning in each node, to additionally incorporate future splits down in the tree. Several other approaches have been proposed [38], but these are based on single trees only, limiting their usage to low dimensional settings. With fast random forest implementations now available for large sample sizes [39] and high dimensional data [24] these or new methods could be integrated into the random forest framework.
Conclusions
We conclude that random forests are generally capable of capturing SNP-SNP interactions, but current variable importance measures are unable to detect them. The Gini importance performs better than the permutation importance in identifying SNPs involved in an interaction. However, both methods are not designed to uncover interactions as such, and consequently, in most of the cases, the interactions are masked by other SNPs with marginal effects. None of the pairwise importance measures is able to reliably detect interactions. Marginal effects are detected as interaction effects and here, too, other SNPs with marginal effects hinder the detection of interactions. As a result one should be cautious when claiming that random forests uncover interaction effects.
Availability of data and materials
The software and simulation code supporting the conclusions of this article are included within the article and its additional files.
Declarations
Acknowledgements
This work was supported in part by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant 01ZX1313A-2014), the German Centre for Cardiovascular Research (DZHK; Deutsches Zentrum für Herz-Kreislauf-Forschung) and the European Union FP7 project BiomarCaRE (HEALTH-F2-2011-278913).
Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Authors’ Affiliations
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