Information Theoretic Multi-Target Feature Selection via Output Space Quantization

Feature selection for kernel methods in systems biology

The substantial development of high-throughput biotechnologies has rendered large-scale multi-omics datasets increasingly available. New challenges have emerged to process and integrate this large volume of information, often obtained from widely heterogeneous sources. Kernel methods have proven successful to handle the analysis of different types of datasets obtained on the same individuals. However, they usually suffer from a lack of interpretability since the original description of the individuals is lost due to the kernel embedding. We propose novel feature selection methods that are adapted to the kernel framework and go beyond the well-established work in supervised learning by addressing the more difficult tasks of unsupervised learning and kernel output learning. The method is expressed under the form of a non-convex optimization problem with a ℓ₁ penalty, which is solved with a proximal gradient descent approach. It is tested on several systems biology datasets and shows good performances in selecting relevant and less redundant features compared to existing alternatives. It also proved relevant for identifying important governmental measures best explaining the time series of Covid-19 reproducing number evolution during the first months of 2020. The proposed feature selection method is embedded in the R package mixKernel version 0.8, published on CRAN. Installation instructions are available at http://mixkernel.clementine.wf/.

A Multi-Objective Multi-Label Feature Selection Algorithm Based on Shapley Value

Multi-label learning is dedicated to learning functions so that each sample is labeled with a true label set. With the increase of data knowledge, the feature dimensionality is increasing. However, high-dimensional information may contain noisy data, making the process of multi-label learning difficult. Feature selection is a technical approach that can effectively reduce the data dimension. In the study of feature selection, the multi-objective optimization algorithm has shown an excellent global optimization performance. The Pareto relationship can handle contradictory objectives in the multi-objective problem well. Therefore, a Shapley value-fused feature selection algorithm for multi-label learning (SHAPFS-ML) is proposed. The method takes multi-label criteria as the optimization objectives and the proposed crossover and mutation operators based on Shapley value are conducive to identifying relevant, redundant and irrelevant features. The comparison of experimental results on real-world datasets reveals that SHAPFS-ML is an effective feature selection method for multi-label classification, which can reduce the classification algorithm’s computational complexity and improve the classification accuracy.

Multi-Label Feature Selection Based on High-Order Label Correlation Assumption

Multi-label data often involve features with high dimensionality and complicated label correlations, resulting in a great challenge for multi-label learning. Feature selection plays an important role in multi-label learning to address multi-label data. Exploring label correlations is crucial for multi-label feature selection. Previous information-theoretical-based methods employ the strategy of cumulative summation approximation to evaluate candidate features, which merely considers low-order label correlations. In fact, there exist high-order label correlations in label set, labels naturally cluster into several groups, similar labels intend to cluster into the same group, different labels belong to different groups. However, the strategy of cumulative summation approximation tends to select the features related to the groups containing more labels while ignoring the classification information of groups containing less labels. Therefore, many features related to similar labels are selected, which leads to poor classification performance. To this end, Max-Correlation term considering high-order label correlations is proposed. Additionally, we combine the Max-Correlation term with feature redundancy term to ensure that selected features are relevant to different label groups. Finally, a new method named Multi-label Feature Selection considering Max-Correlation (MCMFS) is proposed. Experimental results demonstrate the classification superiority of MCMFS in comparison to eight state-of-the-art multi-label feature selection methods.