An Autoencoder Framework With Attention Mechanism for Cross-Domain Recommendation

DeepTPpred: A Deep Learning Approach With Matrix Factorization for Predicting Therapeutic Peptides by Integrating Length Information

The abuse of traditional antibiotics has led to increased resistance of bacteria and viruses. Efficient therapeutic peptide prediction is critical for peptide drug discovery. However, most of the existing methods only make effective predictions for one class of therapeutic peptides. It is worth noting that currently no predictive method considers sequence length information as a distinct feature of therapeutic peptides. In this article, a novel deep learning approach with matrix factorization for predicting therapeutic peptides (DeepTPpred) by integrating length information are proposed. The matrix factorization layer can learn the potential features of the encoded sequence through the mechanism of first compression and then restoration. And the length features of the sequence of therapeutic peptides are embedded with encoded amino acid sequences. To automatically learn therapeutic peptide predictions, these latent features are input into the neural networks with self-attention mechanism. On eight therapeutic peptide datasets, DeepTPpred achieved excellent prediction results. Based on these datasets, we first integrated eight datasets to obtain a full therapeutic peptide integration dataset. Then, we obtained two functional integration datasets based on the functional similarity of the peptides. Finally, we also conduct experiments on the latest versions of the ACP and CPP datasets. Overall, the experimental results show that our work is effective for the identification of therapeutic peptides.

An Approach to Semantic-Aware Heterogeneous Network Embedding for Recommender Systems

Recent studies on heterogeneous information network (HIN) embedding-based recommendations have encountered challenges. These challenges are related to the data heterogeneity of the associated unstructured attribute or content (e.g., text-based summary/description) of users and items in the context of HIN. In order to address these challenges, in this article, we propose a novel approach of semantic-aware HIN embedding-based recommendation, called SemHE4Rec. In our proposed SemHE4Rec model, we define two embedding techniques for efficiently learning the representations of both users and items in the context of HIN. These rich-structural user and item representations are then used to facilitate the matrix factorization (MF) process. The first embedding technique is a traditional co-occurrence representation learning (CoRL) approach which aims to learn the co-occurrence of structural features of users and items. These structural features are represented for their interconnections in terms of meta-paths. In order to do that, we adopt the well-known meta-path-based random walk strategy and heterogeneous Skip-gram architecture. The second embedding approach is a semantic-aware representation learning (SRL) method. The SRL embedding technique is designed to focus on capturing the unstructured semantic relations between users and item content for the recommendation task. Finally, all the learned representations of users and items are then jointly combined and optimized while integrating with the extended MF for the recommendation task. Extensive experiments on real-world datasets demonstrate the effectiveness of the proposed SemHE4Rec in comparison with the recent state-of-the-art HIN embedding-based recommendation techniques, and reveal that the joint text-based and co-occurrence-based representation learning can help to improve the recommendation performance.

Representation Learning: Recommendation With Knowledge Graph via Triple-Autoencoder

The last decades have witnessed a vast amount of interest and research in feature representation learning from multiple disciplines, such as biology and bioinformatics. Among all the real-world application scenarios, feature extraction from knowledge graph (KG) for personalized recommendation has achieved substantial performance for addressing the problem of information overload. However, the rating matrix of recommendations is usually sparse, which may result in significant performance degradation. The crucial problem is how to extract and extend features from additional side information. To address these issues, we propose a novel feature representation learning method for the recommendation in this paper that extends item features with knowledge graph via triple-autoencoder. More specifically, the comment information between users and items is first encoded as sentiment classification. These features are then applied as the input to the autoencoder for generating the auxiliary information of items. Second, the item-based rating, the side information, and the generated comment representations are incorporated into the semi-autoencoder for reconstructed output. The low-dimensional representations of this extended information are learned with the semi-autoencoder. Finally, the reconstructed output generated by the semi-autoencoder is input into a third autoencoder. A serial connection between the semi-autoencoder and the autoencoder is designed here to learn more abstract and higher-level feature representations for personalized recommendation. Extensive experiments conducted on several real-world datasets validate the effectiveness of the proposed method compared to several state-of-the-art models.

Deep Learning-Based Context-Aware Recommender System Considering Contextual Features

A context-aware recommender system can make recommendations to users by considering contextual information such as time and place, not only the scores assigned to items by users. However, as a user preferences matrix is expanded in a multidimensional matrix, data sparsity is maximized. In this paper, we propose a deep learning-based context-aware recommender system that considers the contextual features. Based on existing deep learning models, we combine a neural network and autoencoder to extract characteristics and predict scores in the process of restoring input data. The newly proposed model is able to easily reflect various type of contextual information and predicts user preferences by considering the feature of user, item and context. The experimental results confirm that the proposed method is mostly superior to the existing method in all datasets. Also, for the dataset with data sparsity problem, it was confirmed that the performance of the proposed method is higher than that of existing methods. The proposed method has higher precision by 0.01–0.05 than other recommender systems in a dataset with many context dimensions. And it showed good performance with a high precision of 0.03 to 0.09 in a small dimensional dataset.