KGRACDA: A Model Based on Knowledge Graph from Recursion and Attention Aggregation for CircRNA-Disease Association Prediction.

Graph neural networks (GNN) have recently been applied to exploit knowledge graph (KG) for recommendation. Existing GNN-based methods explicitly model the dependency between an entity and its local graph context in KG (i.e., the set of its first-order neighbors), but may not be effective in capturing its non-local graph context (i.e., the set of most related high-order neighbors). In this paper, we propose a novel recommendation framework, named Contextualized Graph Attention Network (CGAT), which can explicitly exploit both local and non-local graph context information of an entity in KG. More specifically, CGAT captures the local context information by a user-specific graph attention mechanism, considering a user's personalized preferences on entities. In addition, CGAT employs a biased random walk sampling process to extract the non-local context of an entity, and utilizes a Recurrent Neural Network (RNN) to model the dependency between the entity and its non-local contextual entities. To capture the user's personalized preferences on items, an item-specific attention mechanism is also developed to model the dependency between a target item and the contextual items extracted from the user's historical behaviors. We compared CGAT with state-of-the-art KG-based recommendation methods on real datasets, and the experimental results demonstrate the effectiveness of CGAT.

Detecting rail surface anomalies has become crucial for ensuring the safety of train operations. However, manual detection methods are time-consuming and labor-intensive. Although traditional detection models based on one-dimensional signals or two-dimensional images can effectively identify the existence of defects, they are difficult to use to obtain local depth characteristic information, leading to difficulties in accurately assessing the extent of damage in abnormal regions. Rail track maintenance strategies are typically developed based on the detected different depth ranges of defects. To address this issue, this paper proposes a local depth estimation method based on the point cloud of the target rail surface reconstructed by PatchmatchNet. Firstly, according to the acquisition method of multi-view images and the sampling environment at the site, a practical data collection protocol is established for generating a multi-view dataset of rail surface. Next, dense point cloud of the target rail surface were reconstructed by PatchmatchNet. Subsequently, a method for estimating the local anomaly depth is developed based on the point cloud. Experimental results demonstrate that the proposed method achieves a minimum error of approximately 5.5% within a maximum depth range of 0.35mm, when compared to depth measurements obtained using a structured light camera. Finally, this paper presents a more comprehensive three-dimensional representation of the local abnormal physical structure, surpassing traditional one-dimensional and two-dimensional forms. This enhanced representation offers richer information for the effective determination of whether the anomalies constitute defects and aids in distinguishing true defects from other surface irregularities. Such advancement significantly improves the precision of defect assessment and supports the development of highly precise repair strategies.

Large-scale Knowledge Graphs (KGs) have recently gained considerable research attention for their ability to model the inter- and intra- relationships of data. However, the huge scale of KGs has necessitated the use of querying methods to facilitate human use. Question Answering (QA) systems have shown much promise in breaking down this human-machine barrier. A recent QA model that achieved state-of-the-art performance, Query2box, modelled queries on a KG using box embeddings with an attention mechanism backend to compute the intersections of boxes for query resolution. In this paper, we introduce a new model, Query2Geom, which replaces the Query2box attention mechanism with a novel, exact geometric calculation. Our findings show that Query2Geom generally matches the performance of Query2box while having many fewer parameters. Our analysis of the two models leads us to formally describe the interaction between knowledge graph data and box embeddings with the concepts of semantic-geometric alignment and mismatch. We create the Attention Deviation Metric as a measure of how well the geometry of box embeddings captures the semantics of a knowledge graph, and apply it to explain the difference in performance between Query2box and Query2Geom. We conclude that Query2box’s attention mechanism operates using “latent intersections” that attend to the semantic properties in embeddings not expressed in box geometry, acting as a limit on model interpretability. Finally, we generalise our results and propose that semantic-geometric mismatch is a more general property of attention mechanisms, and provide future directions on how to formally model the interaction between attention and latent semantics.

Knowledge Graph Embeddings (KGE) aim to map entities and relations to low dimensional spaces and have become the de-facto standard for knowledge graph completion. Most existing KGE methods suffer from the sparsity challenge, where it is harder to predict entities that appear less frequently in knowledge graphs. In this work, we propose a novel framework KRACL1 to alleviate the widespread sparsity in KGs with graph context and contrastive learning. Firstly, we propose the Knowledge Relational Attention Network (KRAT) to leverage the graph context by simultaneously projecting neighboring triples to different latent spaces and jointly aggregating messages with the attention mechanism. KRAT is capable of capturing the subtle semantic information and importance of different context triples as well as leveraging multi-hop information in knowledge graphs. Secondly, we propose the knowledge contrastive loss by combining the contrastive loss with cross entropy loss, which introduces more negative samples and thus enriches the feedback to sparse entities. Our experiments demonstrate that KRACL achieves superior results across various standard knowledge graph benchmarks, especially on WN18RR and NELL-995 which have large numbers of low in-degree entities. Extensive experiments also bear out KRACL’s effectiveness in handling sparse knowledge graphs and robustness against noisy triples.

Circular RNAs (circRNAs) are involved in the regulatory mechanisms of multiple complex diseases, and the identification of their associations is critical to the diagnosis and treatment of diseases. In recent years, many computational methods have been designed to predict circRNA-disease associations. However, most of the existing methods rely on single correlation data. Here, we propose a machine learning framework for circRNA-disease association prediction, called MLCDA, which effectively fuses multiple sources of heterogeneous information including circRNA sequences and disease ontology. Comprehensive evaluation in the gold standard dataset showed that MLCDA can successfully capture the complex relationships between circRNAs and diseases and accurately predict their potential associations. In addition, the results of case studies on real data show that MLCDA significantly outperforms other existing methods. MLCDA can serve as a useful tool for circRNA-disease association prediction, providing mechanistic insights for disease research and thus facilitating the progress of disease treatment.

Multilingual knowledge graph completion predicts missing facts in the target language knowledge graph by learning and inferring knowledge and rules in other language knowledge graphs. Existing methods tend to use aligned entities between knowledge graphs in different languages as alignment seeds, and receive information from them through alignment seeds to promote entity alignment between different knowledge graphs. However, these methods only consider the local structural information of the knowledge graph by aggregating entity neighborhood information through aligned entities, and ignore the global structural information. At the same time, the methods aboved are hardly to learn the entity representation with sparse neighborhood in isolated subgraphs. To address these two problems, this paper proposes a multilingual knowledge graph completion method based on double-branch graph neural network and self-supervised entity alignment (DBGNN-SSL). The global and local topological structures of the knowledge graph are learned through a double-branch graph attention neural network, and more aligned entities can be iteratively generated through self-supervised learning. The experimental results on datasets DBP-5L and E-PKG verify the effectiveness of the proposed method.

Financial fraud detection has been an urgent technical demand in cyberspace. It highly relies on clear extraction and deep representation toward complex relationships inside financial social networks. As consequence, this study combines both knowledge graph and deep learning to deal with such issue. Thus, an intelligent financial fraud detection model based on knowledge graph guidance and deep neural network is proposed in this paper. First, a new knowledge graph based on financially related systems is constructed, which includes multiple entities and relationships. Then, an adversarial learning-based neural network structure is formulated to extract financial attributes. Finally, the detection results can be output according to the extracted factors. Empirically, the proposal is implemented on a real-world dataset for performance evaluation. The experimental results show that it has higher accuracy and effectiveness compared to traditional fraud detection methods. The proposed detection model can not only identify known fraudulent behaviors, but also predict potential fraud patterns based on consumer habits, thereby improving the security and reliability of financial transactions. It can also update the knowledge graph in real-time, enabling it to cope with emerging fraud methods and variants.

Drug-drug interactions (DDIs) prediction is a challenging task in drug development and clinical application. Due to the extremely large complete set of all possible DDIs, computer-aided DDIs prediction methods are getting lots of attention in the pharmaceutical industry and academia. However, most existing computational methods only use single perspective information and few of them conduct the task based on the biomedical knowledge graph (BKG), which can provide more detailed and comprehensive drug lateral side information flow. To this end, a deep learning framework, namely DeepLGF, is proposed to fully exploit BKG fusing local-global information to improve the performance of DDIs prediction. More specifically, DeepLGF first obtains chemical local information on drug sequence semantics through a natural language processing algorithm. Then a model of BFGNN based on graph neural network is proposed to extract biological local information on drug through learning embedding vector from different biological functional spaces. The global feature information is extracted from the BKG by our knowledge graph embedding method. In DeepLGF, for fusing local-global features well, we designed four aggregating methods to explore the most suitable ones. Finally, the advanced fusing feature vectors are fed into deep neural network to train and predict. To evaluate the prediction performance of DeepLGF, we tested our method in three prediction tasks and compared it with state-of-the-art models. In addition, case studies of three cancer-related and COVID-19-related drugs further demonstrated DeepLGF's superior ability for potential DDIs prediction. The webserver of the DeepLGF predictor is freely available at http://120.77.11.78/DeepLGF/.

Knowledge graph (KG) embedding aims to study the embedding representation to retain the inherent structure of KGs. Graph neural networks (GNNs), as an effective graph representation technique, have shown impressive performance in learning graph embedding. However, KGs have an intrinsic property of heterogeneity, which contains various types of entities and relations. How to address complex graph data and aggregate multiple types of semantic information simultaneously is a critical issue. In this article, a novel heterogeneous GNNs framework based on attention mechanism is proposed. Specifically, the neighbor features of an entity are first aggregated under each relation-path. Then the importance of different relation-paths is learned through the relation features. Finally, each relation-path-based features with the learned weight values are aggregated to generate the embedding representation. Thus, the proposed method not only aggregates entity features from different semantic aspects but also allocates appropriate weights to them. This method can capture various types of semantic information and selectively aggregate informative features. The experiment results on three real-world KGs demonstrate superior performance when compared with several state-of-the-art methods.

Exploring the relationship between circular RNA (circRNA) and disease is beneficial for revealing the mechanisms of disease pathogenesis. However, a blind search for all possible associations between circRNAs and diseases through biological experiments is time-consuming. Although some prediction methods have been proposed, they still have limitations. In this study, a novel computational framework, called GATCL2CD, is proposed to forecast unknown circRNA-disease associations (CDAs). First, we calculate Gaussian interactive profile kernel (GIP) similarity and semantic similarity for diseases, circRNA sequence similarity and function similarity, and GIPs for circRNAs. Then, we combine them to construct a heterogeneous graph. Thereafter, GATCL2CD proposes a feature convolution learning framework, that uses a multi-head dynamic attention mechanism to obtain different aggregated representations of features that correspond to the nodes in the heterogeneous graph. Then, it extracts rich higher-order features from the stacked feature representations of each node by using of a single-layer convolutional neural network with filter kernels of different sizes. Finally, a pairwise element-wise product operation is implemented to capture the interactions of higher-order feature representations, and a multilayer perceptron neural network is introduced as an efficient classifier for inferring potential CDAs. Major experimental results under 5-fold cross-validation (5-fold CV) on three different datasets show that GATCL2CD is superior to five other state-of-the-art methods. Furthermore, case studies demonstrate the suitability of GATCL2CD as a useful tool for identifying potential disease-related circRNAs.

CircRNA is a non-coding RNA that has been considered as a marker of disease and can even be used as a drug target. Exploring the associations between circRNA and disease is beneficial for revealing the mechanisms of disease pathogenesis. Most of the existing computational-based methods do not consider the interaction in multiple features of circRNAs or diseases. Unlike traditional linear models, factorization machines take into account the interaction between features. In this study, we propose a method to Identify the CircRNA-Disease associations based on Feature Graph Factorization (ICDFGF) with graph attention mechanism. After extracting the sequence features, expression features, regulatory features of circRNAs and disease symptom features, disease-miRNA features, disease-gene features, an interactive network of features was constructed and learned by graph factorization. Compared with other existing prediction methods, ICDFGF has higher prediction accuracy. At the same time, the study also analyzes the predicted circRNA-disease associations, which can be corroborated by other studies.

Temporal knowledge graph embedding via sparse transfer matrix

Biomedical knowledge graphs (KGs), which can help with the understanding of complex biological systems and pathologies, have begun to play a critical role in medical practice and research. However, challenges remain in their embedding and use due to their complex nature and the specific demands of their construction. Existing studies often suffer from problems such as sparse and noisy datasets, insufficient modeling methods and non-uniform evaluation metrics. In this work, we established a comprehensive KG system for the biomedical field in an attempt to bridge the gap. Here, we introduced PharmKG, a multi-relational, attributed biomedical KG, composed of more than 500000 individual interconnections between genes, drugs and diseases, with 29 relation types over a vocabulary of ~8000 disambiguated entities. Each entity in PharmKG is attached with heterogeneous, domain-specific information obtained from multi-omics data, i.e. gene expression, chemical structure and disease word embedding, while preserving the semantic and biomedical features. For baselines, we offered nine state-of-the-art KG embedding (KGE) approaches and a new biological, intuitive, graph neural network-based KGE method that uses a combination of both global network structure and heterogeneous domain features. Based on the proposed benchmark, we conducted extensive experiments to assess these KGE models using multiple evaluation metrics. Finally, we discussed our observations across various downstream biological tasks and provide insights and guidelines for how to use a KG in biomedicine. We hope that the unprecedented quality and diversity of PharmKG will lead to advances in biomedical KG construction, embedding and application.

Understanding the 3D structure of the environment is advantageous for many tasks in the field of robotics and autonomous vehicles. From the robot’s point of view, 3D perception is often formulated as a depth image reconstruction problem. In the literature, dense depth images are often recovered deterministically from stereo image disparities. Other systems use an expensive LiDAR sensor to produce accurate, but semi-sparse depth images. With the advent of deep learning there have also been attempts to estimate depth by only using monocular images. In this paper we combine the best of the two worlds, focusing on a combination of monocular images and low cost LiDAR point clouds. We explore the idea that very sparse depth information accurately captures the global scene structure while variations in image patches can be used to reconstruct local depth to a high resolution. The main contribution of this paper is a supervised learning depth reconstruction system based on a deep convolutional neural network. The network is trained on RGB image patches reinforced with sparse depth information and the output is a depth estimate for each pixel. Using image and point cloud data from the KITTI vision dataset we are able to learn a correspondence between local RGB information and local depth, while at the same time preserving the global scene structure. Our results are evaluated on sequences from the KITTI dataset and our own recordings using a low cost camera and LiDAR setup.

AttenE: a knowledge graph completion model based on entity-relation attention embedding