Dispersed differential hunger games search for high dimensional gene data feature selection

Population characteristic exploitation-based multi-orientation multi-objective gene selection for microarray data classification

Gene selection is a process of selecting discriminative genes from microarray data that helps to diagnose and classify cancer samples effectively. Swarm intelligence evolution-based gene selection algorithms can never circumvent the problem that the population is prone to local optima in the process of gene selection. To tackle this challenge, previous research has focused primarily on two aspects: mitigating premature convergence to local optima and escaping from local optima. In contrast to these strategies, this paper introduces a novel perspective by adopting reverse thinking, where the issue of local optima is seen as an opportunity rather than an obstacle. Building on this foundation, we propose MOMOGS-PCE, a novel gene selection approach that effectively exploits the advantageous characteristics of populations trapped in local optima to uncover global optimal solutions. Specifically, MOMOGS-PCE employs a novel population initialization strategy, which involves the initialization of multiple populations that explore diverse orientations to foster distinct population characteristics. The subsequent step involved the utilization of an enhanced NSGA-II algorithm to amplify the advantageous characteristics exhibited by the population. Finally, a novel exchange strategy is proposed to facilitate the transfer of characteristics between populations that have reached near maturity in evolution, thereby promoting further population evolution and enhancing the search for more optimal gene subsets. The experimental results demonstrated that MOMOGS-PCE exhibited significant advantages in comprehensive indicators compared with six competitive multi-objective gene selection algorithms. It is confirmed that the "reverse-thinking" approach not only avoids local optima but also leverages it to uncover superior gene subsets for cancer diagnosis.

Variable selection for nonlinear dimensionality reduction of biological datasets through bootstrapping of correlation networks

Identifying the most relevant variables or features in massive datasets for dimensionality reduction can lead to improved and more informative display, faster computation times, and more explainable models of complex systems. Despite significant advances and available algorithms, this task generally remains challenging, especially in unsupervised settings. In this work, we propose a method that constructs correlation networks using all intervening variables and then selects the most informative ones based on network bootstrapping. The method can be applied in both supervised and unsupervised scenarios. We demonstrate its functionality by applying Uniform Manifold Approximation and Projection for dimensionality reduction to several high-dimensional biological datasets, derived from 4D live imaging recordings of hundreds of morpho-kinetic variables, describing the dynamics of thousands of individual leukocytes at sites of prominent inflammation. We compare our method with other standard ones in the field, such as Principal Component Analysis and Elastic Net, showing that it outperforms them. The proposed method can be employed in a wide range of applications, encompassing data analysis and machine learning.

A new population initialization of metaheuristic algorithms based on hybrid fuzzy rough set for high-dimensional gene data feature selection

In the realm of modern medicine and biology, vast amounts of genetic data with high complexity are available. However, dealing with such high-dimensional data poses challenges due to increased processing complexity and size. Identifying critical genes to reduce data dimensionality is essential. The filter-wrapper hybrid method is a commonly used approach in feature selection. Most of these methods employ filters such as MRMR and ReliefF, but the performance of these simple filters is limited. Rough set methods, on the other hand, are a type of filter method that outperforms traditional filters. Simultaneously, many studies have pointed out the crucial importance of good initialization strategies for the performance of the metaheuristic algorithm (a type of wrapper-based method). Combining these two points, this paper proposes a novel filter-wrapper hybrid method for high-dimensional feature selection. To be specific, we utilize the variant of bWOA (binary Whale Optimization Algorithm) based on Hybrid Fuzzy Rough Set to perform attribute reduction, and the reduced attributes are used as prior knowledge to initialize the population. We then employ metaheuristics for further feature selection based on this initialized population. We conducted experiments using five different algorithms on 14 UCI datasets. The experiment results show that after applying the initialization method proposed in this article, the performance of five enhanced algorithms, has shown significant improvement. Particularly, the improved bMFO using our initialization method: fuzzy_bMFO outperformed six currently advanced algorithms, indicating that our initialization method for metaheuristic algorithms is suitable for high-dimensional feature selection tasks.