Sk Md Mosaddek Hossain

Vaibhav Sinha, Siladitya Dash, Nazma Naskar et al.

In this work, we study and analyze different feature selection algorithms that can be used to classify cancer subtypes in case of highly varying high-dimensional data. We apply three different feature selection methods on five different types of cancers having two separate omics each. We show that the existing feature selection methods are computationally expensive when applied individually. Instead, we apply these algorithms sequentially which helps in lowering the computational cost and improving the predictive performance. We further show that reducing the number of features using some dimension reduction techniques can improve the performance of machine learning models in some cases. We support our findings through comprehensive data analysis and visualization.

Sk Mazharul Islam, Sk Md Mosaddek Hossain, Sumanta Ray

In-silico prediction of repurposable drugs is an effective drug discovery strategy that supplements de-nevo drug discovery from scratch. Reduced development time, less cost and absence of severe side effects are significant advantages of using drug repositioning. Most recent and most advanced artificial intelligence (AI) approaches have boosted drug repurposing in terms of throughput and accuracy enormously. However, with the growing number of drugs, targets and their massive interactions produce imbalanced data which may not be suitable as input to the classification model directly. Here, we have proposed DTI-SNNFRA, a framework for predicting drug-target interaction (DTI), based on shared nearest neighbour (SNN) and fuzzy-rough approximation (FRA). It uses sampling techniques to collectively reduce the vast search space covering the available drugs, targets and millions of interactions between them. DTI-SNNFRA operates in two stages: first, it uses SNN followed by a partitioning clustering for sampling the search space. Next, it computes the degree of fuzzy-rough approximations and proper degree threshold selection for the negative samples' undersampling from all possible interaction pairs between drugs and targets obtained in the first stage. Finally, classification is performed using the positive and selected negative samples. We have evaluated the efficacy of DTI-SNNFRA using AUC (Area under ROC Curve), Geometric Mean, and F1 Score. The model performs exceptionally well with a high prediction score of 0.95 for ROC-AUC. The predicted drug-target interactions are validated through an existing drug-target database (Connectivity Map (Cmap)).