The stability of feature selection is defined as the robustness of the sets of selected features with respect to small variations in the data on which the feature selection is conducted. To quantify stability, several datasets from the same data generating process can be used. Alternatively, a single dataset can be split into parts by resampling. Either way, all datasets used for feature selection must contain exactly the same features. The feature selection method of interest is applied on all of the datasets and the sets of chosen features are recorded. The stability of the feature selection is assessed based on the sets of chosen features using stability measures.
stabilitySechidis(features, sim.mat, threshold = 0.9, impute.na = NULL)list (length >= 2)
Chosen features per dataset. Each element of the list contains the features for one dataset.
The features must be given by their names (character) or indices (integerish).
numeric matrix
Similarity matrix which contains the similarity structure of all features based on
all datasets. The similarity values must be in the range of [0, 1] where 0 indicates
very low similarity and 1 indicates very high similarity. If the list elements of
features are integerish vectors, then the feature numbering must correspond to the
ordering of sim.mat. If the list elements of features are character
vectors, then sim.mat must be named and the names of sim.mat must correspond
to the entries in features.
numeric(1)
Threshold for indicating which features are similar and which are not. Two features
are considered as similar, if and only if the corresponding entry of sim.mat is greater
than or equal to threshold.
numeric(1)
In some scenarios, the stability cannot be assessed based on all feature sets.
E.g. if some of the feature sets are empty, the respective pairwise comparisons yield NA as result.
With which value should these missing values be imputed? NULL means no imputation.
numeric(1) Stability value.
The stability measure is defined as
$$1 - \frac{\mathop{\mathrm{trace}}(CS)}{\mathop{\mathrm{trace}}(C \Sigma)}$$ with (\(p \times p\))-matrices
$$(S)_{ij} = \frac{m}{m-1}\left(\frac{h_{ij}}{m} - \frac{h_i}{m} \frac{h_j}{m}\right)$$ and
$$(\Sigma)_{ii} = \frac{q}{mp} \left(1 - \frac{q}{mp}\right),$$
$$(\Sigma)_{ij} = \frac{\frac{1}{m} \sum_{i=1}^{m} |V_i|^2 - \frac{q}{m}}{p^2 - p} - \frac{q^2}{m^2 p^2}, i \neq j.$$
The matrix \(C\) is created from matrix sim.mat by setting all values of sim.mat that are smaller
than threshold to 0. If you want to \(C\) to be equal to sim.mat, use threshold = 0.
This stability measure is not corrected for chance.
Unlike for the other stability measures in this R package, that are not corrected for chance,
for stabilitySechidis, no correction.for.chance can be applied.
This is because for stabilitySechidis, no finite upper bound is known at the moment,
see listStabilityMeasures.
For the definition of all stability measures in this package,
the following notation is used:
Let \(V_1, \ldots, V_m\) denote the sets of chosen features
for the \(m\) datasets, i.e. features has length \(m\) and
\(V_i\) is a set which contains the \(i\)-th entry of features.
Furthermore, let \(h_j\) denote the number of sets that contain feature
\(X_j\) so that \(h_j\) is the absolute frequency with which feature \(X_j\)
is chosen.
Analogously, let \(h_{ij}\) denote the number of sets that include both \(X_i\) and \(X_j\).
Also, let \(q = \sum_{j=1}^p h_j = \sum_{i=1}^m |V_i|\) and \(V = \bigcup_{i=1}^m V_i\).
Sechidis K, Papangelou K, Nogueira S, Weatherall J, Brown G (2020). “On the Stability of Feature Selection in the Presence of Feature Correlations.” In Machine Learning and Knowledge Discovery in Databases, 327--342. Springer International Publishing. doi:10.1007/978-3-030-46150-8_20 .
Bommert A (2020). Integration of Feature Selection Stability in Model Fitting. Ph.D. thesis, TU Dortmund University, Germany. doi:10.17877/DE290R-21906 .