G-ACP: a machine learning approach to the prediction of therapeutic peptides for gastric cancer

Abstract

Conventional Gastrointestinal (GI) cancer treatments are quite expensive and have major hazards. Nowadays, a different strategy places more emphasis on creating tiny biologically active peptides that do not cause severe poisoning. Anticancer peptides (ACPs) are found through experimental screening, which is time-dependent and frequently fraught with difficulties. Gastric ACPs are emerging as a promising GI cancer treatment in the current day. It is crucial to identify novel gastric ACPs to have an improved knowledge of their functioning processes and treatment of gastric cancer. As a result of the post-genomic era's massive production of peptide sequences, rapid and effective ACPs using a computational method are essential. Several adaptive statistical techniques for distinguishing ACPs and non-ACPs have recently been developed. A variety of adapted statistically significant methods have been developed to differentiate between ACPs and non-ACPs. Despite significant progress, there is no specific model for the prediction of gastric ACPs because the specific model will predict a particular type of peptide more accurately and quickly. To overcome this, an initiative is taken for the creation of a reliable framework for the accurate identification of gastric ACPs. The current technique in particular contains four possible features along with one hybrid feature encoding mechanisms which are the target-class motif previously indicated by Amino Acid Composition, Dipeptide Composition, Tripeptide Composition (TPC), Pseudo Amino Acid Composition (PAAC), and their Hybrid. Machine Learning algorithms make high-performance and accurate prediction tools. Moreover, highly variable and ideal deep feature selection is done using an ANOVA-based F score for feature pruning. Experiments on a range of algorithms are carried out to identify the optimal operating strategy due to the diverse nature of learning. Following analysis of the empirical results, Naïve Bayes with TPC and Hybrid feature space outperforms other methods with 0.99 accuracy score on the testing dataset. To find the model generalization an external validation is carried out. In external datasets, the Extra Trees with PAAC features outperforms with the accuracy of 0.94. The comparison study shows that our suggested model will predict gastric ACPs more accurately and will be useful in drug development and gastric cancer. The predictive model can be freely accessed at https://github.com/humeraazad10/G-ACP.git.

Keywords: Cancer; anticancer peptides; gastrointestinal cancer; machine learning; non-anticancer peptides.