Positive Synergy Index
In the past decades, a few synergistic feature selection algorithms have been published, which includes Cooperative Index (CI) and K-Top Scoring Pair (k-TSP). These algorithms consider the synergistic behavior of features when they are included in a feature panel.
Although promising results have been shown for these algorithms, there is lack of a comprehensive and fair comparison with other feature selection algorithms across a large number of microarray datasets in terms of classification accuracy and computational complexity.
There is a need in evaluating their performance and reducing the complexity of such algorithms. We compared the performance of synergistic feature selection algorithms with 11 other commonly used algorithms based on 22 microarray gene expression binary class datasets. The evaluation confirms that synergistic algorithms such as CI and k-TSP will gradually increase the classification performance as more features are used in the classifiers.
Also, in order to cut down computational cost, we proposed a new feature selection ranking score called Positive Synergy Index (PSI). Testing results show that features selected using PSI as well as synergistic feature selection algorithms provide better performance compared to with all other methods, while PSI has a computational complexity significantly lower than that of other synergistic algorithms.
Bari, M. G., Salekin, S. and Zhang, J. (2016), A Robust and Efficient Feature Selection Algorithm for Microarray Data. Mol. Inf.. doi:10.1002/minf.201600099.
Early Response Index
Identifying disease correlated features early before large numbers of molecules are impacted by disease progression with significant abundance change is very advantageous to biologists for developing early disease diagnosis biomarkers. Disease correlated features have relatively low level of abundance change at early stages. Finding them using existing bioinformatic tools in high throughput data is a challenging task since the technology suffers from limited dynamic range and significant noise. Most existing biomarker discovery algorithms can only detect molecules with high abundance changes, frequently missing early disease diagnostic markers.
In this work, we present a new statistic called early response index (ERI) to prioritize disease correlated molecules as potential early biomarkers. Instead of classification accuracy, ERI measures the average classification accuracy improvement attainable by a feature when it is united with other counterparts for classification. ERI is more sensitive to abundance changes than other ranking statistics. We have shown that ERI significantly outperforms SAM and Localfdr in detecting early responding molecules in a proteomics study of a mouse model of multiple sclerosis.
Importantly, ERI was able to detect many disease relevant proteins before those algorithms detect them at a later time point. ERI method is more sensitive for significant feature detection during early stage of disease development. It potentially has a higher specificity for biomarker discovery, and can be used to identify critical time frame for disease intervention.
In PSI study, 22 microarray datasets collected from different types of cancers are used to evaluate various feature selection algorithms. The MAT version of datasets are provided in table 1
Also, Table 2 and Table 3 provide the dataset used for ERI study.
Table 1: PSI - Datssets
Table 2: ERI - EAE Datsset
|1||EAE dataset between day 0 and 5|
|2||EAE dataset between day 0 and 25|
|3||All other days of EAE dataset|
Table 3: ERI - Clinical Datssets
|Dataset||Genes||Sample class size||Download|