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The epistasis is prevalent in the SNP interactions. Some of the existing methods are focused on constructing models for two SNPs. Other methods only find the SNPs in consideration of one-objective function. In this paper, we present a unified fast framework integrating adaptive ant colony optimization algorithm with multiobjective functions for detecting SNP epistasis in GWAS datasets. We compared our method with other existing methods using synthetic datasets and applied the proposed method to Late-Onset Alzheimer's Disease dataset. Our experimental results show that the proposed method outperforms other methods in epistasis detection, and the result of real dataset contributes to the research of mechanism underlying the disease.

Underlying a cancer phenotype is a specific gene regulatory network that represents the complex regulatory relationships between genes. However, it remains a challenge to find cancer-related gene regulatory network because of insufficient sample sizes and complex regulatory mechanisms in which gene is influenced by not only other genes but also other biological factors. With the development of high-throughput technologies and the unprecedented wealth of multi-omics data give us a new opportunity to design machine learning method to investigate underlying gene regulatory network. In this paper, we propose an approach, which use biweight midcorrelation to measure the correlation between factors and make use of nonconvex penalty based sparse regression for gene regulatory network inference (BMNPGRN). BMNCGRN incorporates multi-omics data (including DNA methylation and copy number variation) and their interactions in gene regulatory network model. The experimental results on synthetic datasets show that BMNPGRN outperforms popular and state-of-the-art methods (including DCGRN, ARACNE and CLR) under false positive control. Furthermore, we applied BMNPGRN on breast cancer (BRCA) data from The Cancer Genome Atlas database and provided gene regulatory network.

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