Hybrid semantic recommender system for chemical compounds in large-scale datasets

The large, and increasing, number of chemical compounds poses challenges to the exploration of such datasets. In this work, we propose the usage of recommender systems to identify compounds of interest to scientific researchers. Our approach consists of a hybrid recommender model suitable for implicit feedback datasets and focused on retrieving a ranked list according to the relevance of the items. The model integrates collaborative-filtering algorithms for implicit feedback (Alternating Least Squares and Bayesian Personalized Ranking) and a new content-based algorithm, using the semantic similarity between the chemical compounds in the ChEBI ontology. The algorithms were assessed on an implicit dataset of chemical compounds, CheRM-20, with more than 16.000 items (chemical compounds). The hybrid model was able to improve the results of the collaborative-filtering algorithms, by more than ten percentage points in most of the assessed evaluation metrics.

Drug-Target Interaction Prediction Based on Adversarial Bayesian Personalized Ranking

The prediction of drug-target interaction (DTI) is a key step in drug repositioning. In recent years, many studies have tried to use matrix factorization to predict DTI, but they only use known DTIs and ignore the features of drug and target expression profiles, resulting in limited prediction performance. In this study, we propose a new DTI prediction model named AdvB-DTI. Within this model, the features of drug and target expression profiles are associated with Adversarial Bayesian Personalized Ranking through matrix factorization. Firstly, according to the known drug-target relationships, a set of ternary partial order relationships is generated. Next, these partial order relationships are used to train the latent factor matrix of drugs and targets using the Adversarial Bayesian Personalized Ranking method, and the matrix factorization is improved by the features of drug and target expression profiles. Finally, the scores of drug-target pairs are achieved by the inner product of latent factors, and the DTI prediction is performed based on the score ranking. The proposed model effectively takes advantage of the idea of learning to rank to overcome the problem of data sparsity, and perturbation factors are introduced to make the model more robust. Experimental results show that our model could achieve a better DTI prediction performance.

A Survey of Latent Factor Models for Recommender Systems and Personalization

<p>Recommender systems aim to personalize the experience of a user and are critical for businesses like retail portals, e-commerce websites, book sellers, streaming movie websites and so on. The earliest personalized algorithms use matrix factorization or matrix completion using algorithms like the singular value decomposition (SVD). There are other more advanced algorithms, like factorization machines, Bayesian personalized ranking (BPR), and a more recent Hebbian graph embeddings (HGE) algorithm. In this work, we implement BPR and HGE and compare our results with SVD, Non-negative matrix factorization (NMF) using the MovieLens dataset.</p>

A Survey of Latent Factor Models for Recommender Systems and Personalization

<p>Recommender systems aim to personalize the experience of a user and are critical for businesses like retail portals, e-commerce websites, book sellers, streaming movie websites and so on. The earliest personalized algorithms use matrix factorization or matrix completion using algorithms like the singular value decomposition (SVD). There are other more advanced algorithms, like factorization machines, Bayesian personalized ranking (BPR), and a more recent Hebbian graph embeddings (HGE) algorithm. In this work, we implement BPR and HGE and compare our results with SVD, Non-negative matrix factorization (NMF) using the MovieLens dataset.</p>