ENHANCE NMF-BASED RECOMMENDATION SYSTEMS WITH AUXILIARY INFORMATION IMPUTATION

This dissertation studies the factors that negatively impact the accuracy of the collaborative filtering recommendation systems based on nonnegative matrix factorization (NMF). The keystone in the recommendation system is the rating that expresses the user\u27s opinion about an item. One of the most significant issues in the recommendation systems is the lack of ratings. This issue is called cold-start issue, which appears clearly with New-Users who did not rate any item and New-Items, which did not receive any rating. The traditional recommendation systems assume that users are independent and identically distributed and ignore the connections among users whereas the recommendation actually is a social activity. This dissertation aims to enhance NMF-based recommendation systems by utilizing the imputation method and limiting the errors that are introduced in the system. External information such as trust network and item categories are incorporated into NMF-based recommendation systems through the imputation. The proposed approaches impute various subsets of the missing ratings. The subsets are defined based on the total number of the ratings of the user or item before the imputation, such as impute the missing ratings of New-Users, New-Items, or cold-start users or items that suffer from the lack of the ratings. In addition, several factors are analyzed that affect the prediction accuracy when the imputation method is utilized with NMF-based recommendation systems. These factors include the total number of the ratings of the user or item before the imputation, the total number of imputed ratings for each user and item, the average of imputed rating values, and the value of imputed rating values. In addition, several strategies are applied to select the subset of missing ratings for the imputation that lead to increasing the prediction accuracy and limiting the imputation error. Moreover, a comparison is conducted with some popular methods that are in common with the proposed method in utilizing the imputation to handle the lack of ratings, but they differ in the source of the imputed ratings. Experiments on different large-size datasets are conducted to examine the proposed approaches and analyze the effects of the imputation on accuracy. Users and items are divided into three groups based on the total number of the ratings before the imputation is applied and their recommendation accuracy is calculated. The results show that the imputation enhances the recommendation system by capacitating the system to recommend items to New-Users, introduce New-Items to users, and increase the accuracy of the cold-start users and items. However, the analyzed factors play important roles in the recommendation accuracy and limit the error that is introduced from the imputation

Improved genome-scale multitarget virtual screening via a novel collaborative filtering approach to cold-start problem

Conventional one-drug-one-gene approach has been of limited success in modern drug discovery. Polypharmacology, which focuses on searching for multi-targeted drugs to perturb disease-causing networks instead of designing selective ligands to target individual proteins, has emerged as a new drug discovery paradigm. Although many methods for single-target virtual screening have been developed to improve the efficiency of drug discovery, few of these algorithms are designed for polypharmacology. Here, we present a novel theoretical framework and a corresponding algorithm for genome-scale multitarget virtual screening based on the one-class collaborative filtering technique. Our method overcomes the sparseness of the protein-chemical interaction data by means of interaction matrix weighting and dual regularization from both chemicals and proteins. While the statistical foundation behind our method is general enough to encompass genome-wide drug off-target prediction, the program is specifically tailored to find protein targets for new chemicals with little to no available interaction data. We extensively evaluate our method using a number of the most widely accepted gene-specific and cross-gene family benchmarks and demonstrate that our method outperforms other state-of-the-art algorithms for predicting the interaction of new chemicals with multiple proteins. Thus, the proposed algorithm may provide a powerful tool for multi-target drug design