GCFMCL: predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning.

Studies have shown that the mechanism of action of many drugs is related to miRNA. In-depth research on the relationship between miRNA and drugs can provide theoretical foundations and practical approaches for various areas, such as drug target discovery, drug repositioning and biomarker research. Traditional biological experiments to test miRNA-drug susceptibility are costly and time-consuming. Thus, sequence- or topology-based deep learning methods are recognized in this field for their efficiency and accuracy. However, these methods have limitations in dealing with sparse topologies and higher-order information of miRNA (drug) feature. In this work, we propose GCFMCL, a model for multi-view contrastive learning based on graph collaborative filtering. To the best of our knowledge, this is the first attempt that incorporates contrastive learning strategy into the graph collaborative filtering framework to predict the sensitivity relationships between miRNA and drug. The proposed multi-view contrastive learning method is divided into topological contrastive objective and feature contrastive objective: (1) For the homogeneous neighbors of the topological graph, we propose a novel topological contrastive learning method via constructing the contrastive target through the topological neighborhood information of nodes. (2) The proposed model obtains feature contrastive targets from high-order feature information according to the correlation of node features, and mines potential neighborhood relationships in the feature space. The proposed multi-view comparative learning effectively alleviates the impact of heterogeneous node noise and graph data sparsity in graph collaborative filtering, and significantly enhances the performance of the model. Our study employs a dataset derived from the NoncoRNA and ncDR databases, encompassing 2049 experimentally validated miRNA-drug sensitivity associations. Five-fold cross-validation shows that the Area Under the Curve (AUC), Area Under the Precision-Recall Curve (AUPR) and F1-score (F1) of GCFMCL reach 95.28%, 95.66% and 89.77%, which outperforms the state-of-the-art (SOTA) method by the margin of 2.73%, 3.42% and 4.96%, respectively. Our code and data can be accessed at https://github.com/kkkayle/GCFMCL.

Fusing graph transformer with multi-aggregate GCN for enhanced drug-disease associations prediction.

BACKGROUND: Identification of potential drug-disease associations is important for both the discovery of new indications for drugs and for the reduction of unknown adverse drug reactions. Exploring the potential links between drugs and diseases is crucial for advancing biomedical research and improving healthcare. While advanced computational techniques play a vital role in revealing the connections between drugs and diseases, current research still faces challenges in the process of mining potential relationships between drugs and diseases using heterogeneous network data. RESULTS: In this study, we propose a learning framework for fusing Graph Transformer Networks and multi-aggregate graph convolutional network to learn efficient heterogenous information graph representations for drug-disease association prediction, termed WMAGT. This method extensively harnesses the capabilities of a robust graph transformer, effectively modeling the local and global interactions of nodes by integrating a graph convolutional network and a graph transformer with self-attention mechanisms in its encoder. We first integrate drug-drug, drug-disease, and disease-disease networks to construct heterogeneous information graph. Multi-aggregate graph convolutional network and graph transformer are then used in conjunction with neural collaborative filtering module to integrate information from different domains into highly effective feature representation. CONCLUSIONS: Rigorous cross-validation, ablation studies examined the robustness and effectiveness of the proposed method. Experimental results demonstrate that WMAGT outperforms other state-of-the-art methods in accurate drug-disease association prediction, which is beneficial for drug repositioning and drug safety research.

Drug-target interactions prediction via deep collaborative filtering with multiembeddings.

Drug-target interactions (DTIs) prediction research presents important significance for promoting the development of modern medicine and pharmacology. Traditional biochemical experiments for DTIs prediction confront the challenges including long time period, high cost and high failure rate, and finally leading to a low-drug productivity. Chemogenomic-based computational methods can realize high-throughput prediction. In this study, we develop a deep collaborative filtering prediction model with multiembeddings, named DCFME (deep collaborative filtering prediction model with multiembeddings), which can jointly utilize multiple feature information from multiembeddings. Two different representation learning algorithms are first employed to extract heterogeneous network features. DCFME uses the generated low-dimensional dense vectors as input, and then simulates the drug-target relationship from the perspective of both couplings and heterogeneity. In addition, the model employs focal loss that concentrates the loss on sparse and hard samples in the training process. Comparative experiments with five baseline methods show that DCFME achieves more significant performance improvement on sparse datasets. Moreover, the model has better robustness and generalization capacity under several harder prediction scenarios.

A Personalized Collaborative Filtering Recommendation System Based on Bi-Graph Embedding and Causal Reasoning.

The integration of graph embedding technology and collaborative filtering algorithms has shown promise in enhancing the performance of recommendation systems. However, existing integrated recommendation algorithms often suffer from feature bias and lack effectiveness in personalized user recommendation. For instance, users' historical interactions with a certain class of items may inaccurately lead to recommendations of all items within that class, resulting in feature bias. Moreover, accommodating changes in user interests over time poses a significant challenge. This study introduces a novel recommendation model, RCKFM, which addresses these shortcomings by leveraging the CoFM model, TransR graph embedding model, backdoor tuning of causal inference, KL divergence, and the factorization machine model. RCKFM focuses on improving graph embedding technology, adjusting feature bias in embedding models, and achieving personalized recommendations. Specifically, it employs the TransR graph embedding model to handle various relationship types effectively, mitigates feature bias using causal inference techniques, and predicts changes in user interests through KL divergence, thereby enhancing the accuracy of personalized recommendations. Experimental evaluations conducted on publicly available datasets, including "MovieLens-1M" and "Douban dataset" from Kaggle, demonstrate the superior performance of the RCKFM model. The results indicate a significant improvement of between 3.17% and 6.81% in key indicators such as precision, recall, normalized discount cumulative gain, and hit rate in the top-10 recommendation tasks. These findings underscore the efficacy and potential impact of the proposed RCKFM model in advancing recommendation systems.

GATCF: Graph Attention Collaborative Filtering for Reliable Blockchain Services Selection in BaaS.

Blockchain technology is a decentralized ledger that allows the development of applications without the need for a trusted third party. As service-oriented computing continues to evolve, the concept of Blockchain as a Service (BaaS) has emerged, providing a simplified approach to building blockchain-based applications. The growing demand for blockchain services has resulted in numerous options with overlapping functionalities, making it difficult to select the most reliable ones for users. Choosing the best-trusted blockchain peers is a challenging task due to the sparsity of data caused by the multitude of available options. To address the aforementioned issues, we propose a novel collaborative filtering-based matrix completion model called Graph Attention Collaborative Filtering (GATCF), which leverages both graph attention and collaborative filtering techniques to recover the missing values in the data matrix effectively. By incorporating graph attention into the matrix completion process, GATCF can effectively capture the underlying dependencies and interactions between users or peers, and thus mitigate the data sparsity scenarios. We conduct extensive experiments on a large-scale dataset to assess our performance. Results show that our proposed method achieves higher recovery accuracy.

Bidirectional Trust-Enhanced Collaborative Filtering for Point-of-Interest Recommendation.

A personalized point-of-interest (POI) recommender system is of great significance to facilitate the daily life of users. However, it suffers from some challenges, such as trustworthiness and data sparsity problems. Existing models only consider the trust user influence and ignore the role of the trust location. Furthermore, they fail to refine the influence of context factors and fusion between the user preference and context models. To address the trustworthiness problem, we propose a novel bidirectional trust-enhanced collaborative filtering model, which investigates the trust filtering from the views of users and locations. To tackle the data sparsity problem, we introduce temporal factor into the trust filtering of users as well as geographical and textual content factors into the trust filtering of locations. To further alleviate the sparsity of user-POI rating matrices, we employ a weighted matrix factorization fused with the POI category factor to learn the user preference. To integrate the trust filtering models and the user preference model, we develop a fused framework with two kinds of integrating methods in relation to the different impacts of factors on the POIs that users have visited and the POIs that users have not visited. Finally, we conduct extensive experiments on Gowalla and Foursquare datasets to evaluate our proposed POI recommendation model, and the results show that our proposed model improves by 13.87% at precision@5 and 10.36% at recall@5 over the state-of-the-art model, which demonstrates that our proposed model outperforms the state-of-the-art method.

Hybrid Recommendation Network Model with a Synthesis of Social Matrix Factorization and Link Probability Functions.

Recommender systems are becoming an integral part of routine life, as they are extensively used in daily decision-making processes such as online shopping for products or services, job references, matchmaking for marriage purposes, and many others. However, these recommender systems are lacking in producing quality recommendations owing to sparsity issues. Keeping this in mind, the present study introduces a hybrid recommendation model for recommending music artists to users which is hierarchical Bayesian in nature, known as Relational Collaborative Topic Regression with Social Matrix Factorization (RCTR-SMF). This model makes use of a lot of auxiliary domain knowledge and provides seamless integration of Social Matrix Factorization and Link Probability Functions into Collaborative Topic Regression-based recommender systems to attain better prediction accuracy. Here, the main emphasis is on examining the effectiveness of unified information related to social networking and an item-relational network structure in addition to item content and user-item interactions to make predictions for user ratings. RCTR-SMF addresses the sparsity problem by utilizing additional domain knowledge, and it can address the cold-start problem in the case that there is hardly any rating information available. Furthermore, this article exhibits the proposed model performance on a large real-world social media dataset. The proposed model provides a recall of 57% and demonstrates its superiority over other state-of-the-art recommendation algorithms.

Drug Recommendation System for Diabetes Using a Collaborative Filtering and Clustering Approach: Development and Performance Evaluation.

BACKGROUND: Diabetes is a public health problem worldwide. Although diabetes is a chronic and incurable disease, measures and treatments can be taken to control it and keep the patient stable. Diabetes has been the subject of extensive research, ranging from disease prevention to the use of technologies for its diagnosis and control. Health institutions obtain information required for the diagnosis of diabetes through various tests, and appropriate treatment is provided according to the diagnosis. These institutions have databases with large volumes of information that can be analyzed and used in different applications such as pattern discovery and outcome prediction, which can help health personnel in making decisions about treatments or determining the appropriate prescriptions for diabetes management. OBJECTIVE: The aim of this study was to develop a drug recommendation system for patients with diabetes based on collaborative filtering and clustering techniques as a complement to the treatments given by the treating doctor. METHODS: The data set used contains information from patients with diabetes available in the University of California Irvine Machine Learning Repository. Data mining techniques were applied for processing and analysis of the data set. Unsupervised learning techniques were used for dimensionality reduction and patient clustering. Drug predictions were obtained with a user-based collaborative filtering approach, which enabled creating a patient profile that can be compared with the profiles of other patients with similar characteristics. Finally, recommendations were made considering the identified patient groups. The performance of the system was evaluated using metrics to assess the quality of the groups and the quality of the predictions and recommendations. RESULTS: Principal component analysis to reduce the dimensionality of the data showed that eight components best explained the variability of the data. We identified six groups of patients using the clustering algorithm, which were evenly distributed. These groups were identified based on the available information of patients with diabetes, and then the variation between groups was examined to predict a suitable medication for a target patient. The recommender system achieved good results in the quality of predictions with a mean squared error metric of 0.51 and accuracy in the quality of recommendations of 0.61, which is acceptable. CONCLUSIONS: This work presents a recommendation system that suggests medications according to drug information and the characteristics of patients with diabetes. Some aspects related to this disease were analyzed based on the data set used from patients with diabetes. The experimental results with clustering and prediction techniques were found to be acceptable for the recommendation process. This system can provide a novel perspective for health institutions that require technologies to support health care personnel in the management of diabetes treatment and control.

Knowledge-Aware Multispace Embedding Learning for Personalized Recommendation.

Recommender systems help users filter items they may be interested in from massive multimedia content to alleviate information overload. Collaborative filtering-based models perform recommendation relying on users' historical interactions, which meets great difficulty in modeling users' interests with extremely sparse interactions. Fortunately, the rich semantics hidden in items may be promising in helping to describing users' interests. In this work, we explore the semantic correlations between items on modeling users' interests and propose knowledge-aware multispace embedding learning (KMEL) for personalized recommendation. KMEL attempts to model users' interests across semantic structures to leverage valuable knowledge. High-order semantic collaborative signals are extracted in multiple independent semantic spaces and aggregated to describe users' interests in each specific semantic. The semantic embeddings are adaptively integrated with a target-aware attention mechanism to learn cross-space multisemantic embeddings for users and items, which are fed to the subsequent pairwise interaction layer for personalized recommendation. Experiments on real-world datasets demonstrate the effectiveness of the proposed KMEL model.

A Ranking Recommendation Algorithm Based on Dynamic User Preference.

In recent years, hybrid recommendation techniques based on feature fusion have gained extensive attention in the field of list ranking. Most of them fuse linear and nonlinear models to simultaneously learn the linear and nonlinear features of entities and jointly fit user-item interactions. These methods are based on implicit feedback, which can reduce the difficulty of data collection and the time of data preprocessing, but will lead to the lack of entity interaction depth information due to the lack of user satisfaction. This is equivalent to artificially reducing the entity interaction features, limiting the overall performance of the model. To address this problem, we propose a two-stage recommendation model named A-DNR, short for Attention-based Deep Neural Ranking. In the first stage, user short-term preferences are modeled through an attention mechanism network. Then the user short-term preferences and user long-term preferences are fused into dynamic user preferences. In the second stage, the high-order and low-order feature interactions are modeled by a matrix factorization (MF) model and a multi-layer perceptron (MLP) model, respectively. Then, the features are fused through a fully connected layer, and the vectors are mapped to scores. Finally, a ranking list is output through the scores. Experiments on three real-world datasets (Movielens100K, Movielens1M and Yahoo Movies) show that our proposed model achieves significant improvements compared to existing methods.

Neural Collaborative Filtering with Ontologies for Integrated Recommendation Systems.

Machine learning (ML) and especially deep learning (DL) with neural networks have demonstrated an amazing success in all sorts of AI problems, from computer vision to game playing, from natural language processing to speech and image recognition. In many ways, the approach of ML toward solving a class of problems is fundamentally different than the one followed in classical engineering, or with ontologies. While the latter rely on detailed domain knowledge and almost exhaustive search by means of static inference rules, ML adopts the view of collecting large datasets and processes this massive information through a generic learning algorithm that builds up tentative solutions. Combining the capabilities of ontology-based recommendation and ML-based techniques in a hybrid system is thus a natural and promising method to enhance semantic knowledge with statistical models. This merge could alleviate the burden of creating large, narrowly focused ontologies for complicated domains, by using probabilistic or generative models to enhance the predictions without attempting to provide a semantic support for them. In this paper, we present a novel hybrid recommendation system that blends a single architecture of classical knowledge-driven recommendations arising from a tailored ontology with recommendations generated by a data-driven approach, specifically with classifiers and a neural collaborative filtering. We show that bringing together these knowledge-driven and data-driven worlds provides some measurable improvement, enabling the transfer of semantic information to ML and, in the opposite direction, statistical knowledge to the ontology. Moreover, the novel proposed system enables the extraction of the reasoning recommendation results after updating the standard ontology with the new products and user behaviors, thus capturing the dynamic behavior of the environment of our interest.

A QoS Prediction Approach Based on Truncated Nuclear Norm Low-Rank Tensor Completion.

With the rise of mobile edge computing (MEC), mobile services with the same or similar functions are gradually increasing. Usually, Quality of Service (QoS) has become an indicator to measure high-quality services. In the real MEC service invocation environment, due to time and network instability factors, users' QoS data feedback results are limited. Therefore, effectively predicting the Qos value to provide users with high-quality services has become a key issue. In this paper, we propose a truncated nuclear norm Low-rank Tensor Completion method for the QoS data prediction. This method represents complex multivariate QoS data by constructing tensors. Furthermore, the truncated nuclear norm is introduced in the QoS data tensor completion in order to mine the correlation between QoS data and improve the prediction accuracy. At the same time, the general rate parameter is introduced to control the truncation degree of tensor mode. Finally, the prediction approximate tensor is obtained by the Alternating Direction Multiplier Method iterative optimization algorithm. Numerical experiments are conducted based on the public QoS dataset WS-Dream. The results indicate that our QoS prediction method has better prediction accuracy than other methods under different missing density QoS data.

A List-Ranking Framework Based on Linear and Non-Linear Fusion for Recommendation from Implicit Feedback.

Although most list-ranking frameworks are based on multilayer perceptrons (MLP), they still face limitations within the method itself in the field of recommender systems in two respects: (1) MLP suffer from overfitting when dealing with sparse vectors. At the same time, the model itself tends to learn in-depth features of user-item interaction behavior but ignores some low-rank and shallow information present in the matrix. (2) Existing ranking methods cannot effectively deal with the problem of ranking between items with the same rating value and the problem of inconsistent independence in reality. We propose a list ranking framework based on linear and non-linear fusion for recommendation from implicit feedback, named RBLF. First, the model uses dense vectors to represent users and items through one-hot encoding and embedding. Second, to jointly learn shallow and deep user-item interaction, we use the interaction grabbing layer to capture the user-item interaction behavior through dense vectors of users and items. Finally, RBLF uses the Bayesian collaborative ranking to better fit the characteristics of implicit feedback. Eventually, the experiments show that the performance of RBLF obtains a significant improvement.

MIGAN: Mutual-Interaction Graph Attention Network for Collaborative Filtering.

Many web platforms now include recommender systems. Network representation learning has been a successful approach for building these efficient recommender systems. However, learning the mutual influence of nodes in the network is challenging. Indeed, it carries collaborative signals accounting for complex user-item interactions on user decisions. For this purpose, in this paper, we develop a Mutual Interaction Graph Attention Network "MIGAN", a new algorithm based on self-supervised representation learning on a large-scale bipartite graph (BGNN). Experimental investigation with real-world data demonstrates that MIGAN compares favorably with the baselines in terms of prediction accuracy and recommendation efficiency.

Hybrid collaborative filtering methods for recommending search terms to clinicians.

With increasing and extensive use of electronic health records (EHR), clinicians are often challenged in retrieving relevant patient information efficiently and effectively to arrive at a diagnosis. While using the search function built into an EHR can be more useful than browsing in a voluminous patient record, it is cumbersome and repetitive to search for the same or similar information on similar patients. To address this challenge, there is a critical need to build effective recommender systems that can recommend search terms to clinicians accurately. In this study, we developed a hybrid collaborative filtering model to recommend search terms for a specific patient to a clinician. The model draws on information from patients' clinical encounters and the searches that were performed during them. To generate recommendations, the model uses search terms which are (1) frequently co-occurring with the ICD codes recorded for the patient and (2) highly relevant to the most recent search terms. In one variation of the model (Hybrid Collaborative Filtering Method for Healthcare, or HCFMH), we use only the most recent ICD codes assigned to the patient, and in the other (Co-occurrence Pattern based HCFMH, or cpHCFMH), all ICD codes. We have conducted comprehensive experiments to evaluate the proposed model. These experiments demonstrate that our model outperforms state-of-the-art baseline methods for top-N search term recommendation on different data sets.

Efficient framework for predicting MiRNA-disease associations based on improved hybrid collaborative filtering.

BACKGROUND: Accumulating studies indicates that microRNAs (miRNAs) play vital roles in the process of development and progression of many human complex diseases. However, traditional biochemical experimental methods for identifying disease-related miRNAs cost large amount of time, manpower, material and financial resources. METHODS: In this study, we developed a framework named hybrid collaborative filtering for miRNA-disease association prediction (HCFMDA) by integrating heterogeneous data, e.g., miRNA functional similarity, disease semantic similarity, known miRNA-disease association networks, and Gaussian kernel similarity of miRNAs and diseases. To capture the intrinsic interaction patterns embedded in the sparse association matrix, we prioritized the predictive score by fusing three types of information: similar disease associations, similar miRNA associations, and similar disease-miRNA associations. Meanwhile, singular value decomposition was adopted to reduce the impact of noise and accelerate predictive speed. RESULTS: We then validated HCFMDA with leave-one-out cross-validation (LOOCV) and two types of case studies. In the LOOCV, we achieved 0.8379 of AUC (area under the curve). To evaluate the performance of HCFMDA on real diseases, we further implemented the first type of case validation over three important human diseases: Colon Neoplasms, Esophageal Neoplasms and Prostate Neoplasms. As a result, 44, 46 and 44 out of the top 50 predicted disease-related miRNAs were confirmed by experimental evidence. Moreover, the second type of case validation on Breast Neoplasms indicates that HCFMDA could also be applied to predict potential miRNAs towards those diseases without any known associated miRNA. CONCLUSIONS: The satisfactory prediction performance demonstrates that our model could serve as a reliable tool to guide the following research for identifying candidate miRNAs associated with human diseases.

A Systematic Review of Recommender Systems and Their Applications in Cybersecurity.

This paper discusses the valuable role recommender systems may play in cybersecurity. First, a comprehensive presentation of recommender system types is presented, as well as their advantages and disadvantages, possible applications and security concerns. Then, the paper collects and presents the state of the art concerning the use of recommender systems in cybersecurity; both the existing solutions and future ideas are presented. The contribution of this paper is two-fold: to date, to the best of our knowledge, there has been no work collecting the applications of recommenders for cybersecurity. Moreover, this paper attempts to complete a comprehensive survey of recommender types, after noticing that other works usually mention two-three types at once and neglect the others.

Efficient Graph Collaborative Filtering via Contrastive Learning.

Collaborative filtering (CF) aims to make recommendations for users by detecting user's preference from the historical user-item interactions. Existing graph neural networks (GNN) based methods achieve satisfactory performance by exploiting the high-order connectivity between users and items, however they suffer from the poor training efficiency problem and easily introduce bias for information propagation. Moreover, the widely applied Bayesian personalized ranking (BPR) loss is insufficient to provide supervision signals for training due to the extremely sparse observed interactions. To deal with the above issues, we propose the Efficient Graph Collaborative Filtering (EGCF) method. Specifically, EGCF adopts merely one-layer graph convolution to model the collaborative signal for users and items from the first-order neighbors in the user-item interactions. Moreover, we introduce contrastive learning to enhance the representation learning of users and items by deriving the self-supervisions, which is jointly trained with the supervised learning. Extensive experiments are conducted on two benchmark datasets, i.e., Yelp2018 and Amazon-book, and the experimental results demonstrate that EGCF can achieve the state-of-the-art performance in terms of Recall and normalized discounted cumulative gain (NDCG), especially on ranking the target items at right positions. In addition, EGCF shows obvious advantages in the training efficiency compared with the competitive baselines, making it practicable for potential applications.

Edge Caching Based on Collaborative Filtering for Heterogeneous ICN-IoT Applications.

The substantial advancements offered by the edge computing has indicated serious evolutionary improvements for the internet of things (IoT) technology. The rigid design philosophy of the traditional network architecture limits its scope to meet future demands. However, information centric networking (ICN) is envisioned as a promising architecture to bridge the huge gaps and maintain IoT networks, mostly referred as ICN-IoT. The edge-enabled ICN-IoT architecture always demands efficient in-network caching techniques for supporting better user's quality of experience (QoE). In this paper, we propose an enhanced ICN-IoT content caching strategy by enabling artificial intelligence (AI)-based collaborative filtering within the edge cloud to support heterogeneous IoT architecture. This collaborative filtering-based content caching strategy would intelligently cache content on edge nodes for traffic management at cloud databases. The evaluations has been conducted to check the performance of the proposed strategy over various benchmark strategies, such as LCE, LCD, CL4M, and ProbCache. The analytical results demonstrate the better performance of our proposed strategy with average gain of 15% for cache hit ratio, 12% reduction in content retrieval delay, and 28% reduced average hop count in comparison to best considered LCD. We believe that the proposed strategy will contribute an effective solution to the related studies in this domain.

Modeling of Recommendation System Based on Emotional Information and Collaborative Filtering.

Emotion information represents a user's current emotional state and can be used in a variety of applications, such as cultural content services that recommend music according to user emotional states and user emotion monitoring. To increase user satisfaction, recommendation methods must understand and reflect user characteristics and circumstances, such as individual preferences and emotions. However, most recommendation methods do not reflect such characteristics accurately and are unable to increase user satisfaction. In this paper, six human emotions (neutral, happy, sad, angry, surprised, and bored) are broadly defined to consider user speech emotion information and recommend matching content. The "genetic algorithms as a feature selection method" (GAFS) algorithm was used to classify normalized speech according to speech emotion information. We used a support vector machine (SVM) algorithm and selected an optimal kernel function for recognizing the six target emotions. Performance evaluation results for each kernel function revealed that the radial basis function (RBF) kernel function yielded the highest emotion recognition accuracy of 86.98%. Additionally, content data (images and music) were classified based on emotion information using factor analysis, correspondence analysis, and Euclidean distance. Finally, speech information that was classified based on emotions and emotion information that was recognized through a collaborative filtering technique were used to predict user emotional preferences and recommend content that matched user emotions in a mobile application.