Knowledge Graph Embedding Research Articles

Knowledge Graph Embedding for Hierarchical Entities Based on Auto-Embedding Size

Knowledge graph embedding represents entities and relations as low-dimensional continuous vectors. Recently, researchers have attempted to leverage the potential semantic connections between entities with hierarchical relationships in the knowledge graph. However, existing knowledge embedding methods that model entity hierarchical structures face the following challenges: (1) Setting the same embedding dimension for entities at different hierarchical levels can lead to overfitting issues and the waste of storage and computational resources; (2) Manually searching the embedding dimension in discrete space makes it easy to miss the optimal parameters and increases training costs. Therefore, we propose a knowledge embedding method, HEAES, that automatically learns the embedding dimensions for entities based on their hierarchical structure. Specifically, we first propose a new modeling method to capture the hierarchical relationships of entities, and we then train the model on a triple classification task. Then, we adaptively learn the pruning threshold to trim the embedding vectors, automatically learning different embedding dimensions for entities at different hierarchical levels. Experiments on the YAGO26K and DB111K datasets verify that introducing entity hierarchical information helps boost the model performance.

GeoEntity-type constrained knowledge graph embedding for predicting natural-language spatial relations

Natural-language spatial relations between geographic entities (geoentities) reflect diverse perceptions influenced by factors like location, culture, and linguistic conventions. These relations play a crucial role in supporting geospatial tasks, such as question answering and cognitive reasoning. While prior studies focused on a limited set of human-selected spatial terms and geometric attributes, they often overlooked essential semantic attributes. To overcome this limitation, we developed a Spatial Relation-based Knowledge Graph Embedding framework, SR-KGE, with new KG fusion functions to predict spatial relation terms among distinct geoentities. This method not only considers graph structures and the diversity of natural language expressions in the embedding and learning process, but also incorporates geoentity types as a constraint to capture spatial and semantic relations more accurately. Our experiments on two knowledge graph datasets, one small-scale and one large-scale, have both shown its superior performance in spatial relation inference compared to popular KGE models, including TransE, RotatE, and HAKE. We hope our research will advance the classic study of natural language described spatial relations in a more automated and intelligent way.

A knowledge graph-based inspection items recommendation method for port state control inspection of LNG carriers

The safe navigation and operation of Liquified natural gas (LNG) carriers is crucial in maritime transportation. The Port State Control (PSC) inspection is the primary method for identifying deficiencies in vessels. Different from other vessels, the PSC inspection of LNG carriers requires knowledge of specialized transport equipment. Therefore, effective management of inspection knowledge and precise targeting of inspection items are particularly crucial. Knowledge graph is an efficient way to manage knowledge in the context of artificial intelligence. In this study, an LNG carrier PSC inspection knowledge graph is constructed for fusing multisource knowledge data from PSC inspection. Additionally, a knowledge graph-based recommendation model, namely the improved knowledge graph convolutional network combined with pretrained translation embedding (PT-KGCN), is developed to recommend inspection items and knowledge. The PT-KGCN model first carries out knowledge graph embedding. It then predicts possible deficiencies on the basis of historical PSC inspection data. Finally, it recommends inspection items by correlating the predicted deficiencies with knowledge from the knowledge graph. The results show that more than 87% of defective items in historical data are correctly predicted. The research findings can provide ideas for the practical application of knowledge data in the inspection fields.

HGCGE: hyperbolic graph convolutional networks-based knowledge graph embedding for link prediction

HGCGE: hyperbolic graph convolutional networks-based knowledge graph embedding for link prediction

TarKG: a comprehensive biomedical knowledge graph for target discovery.

Target discovery is a crucial step in drug development, as it directly affects the success rate of clinical trials. Knowledge graphs (KGs) offer unique advantages in processing complex biological data and inferring new relationships. Existing biomedical KGs primarily focus on tasks such as drug repositioning and drug-target interactions, leaving a gap in the construction of KGs tailored for target discovery. We established a comprehensive biomedical KG focusing on target discovery, termed TarKG, by integrating seven existing biomedical KGs, nine public databases, and traditional Chinese medicine knowledge databases. TarKG consists of 1143313 entities and 32806467 relations across 15 entity categories and 171 relation types, all centered around 3 core entity types: Disease, Gene, and Compound. TarKG provides specialized knowledges for the core entities including chemical structures, protein sequences, or text descriptions. By using different KG embedding algorithms, we assessed the knowledge completion capabilities of TarKG, particularly for disease-target link prediction. In case studies, we further examined TarKG's ability to predict potential protein targets for Alzheimer's disease (AD) and to identify diseases potentially associated with the metallo-deubiquitinase CSN5, using literature analysis for validation. Furthermore, we provided a user-friendly web server (https://tarkg.ddtmlab.org) that enables users to perform knowledge retrieval and relation inference using TarKG. TarKG is accessible at https://tarkg.ddtmlab.org.

A multi-entity reinforced main path analysis: Heterogeneous network embedding considering knowledge proximity

Main path analysis (MPA) is an important approach in detecting the trajectory of knowledge diffusion in a specific research domain. Previous studies always focus on citation-based relationships, overlooking other structural forms in citation network. This study introduces a multi-entity reinforced MPA model by constructing a knowledge graph from paper metadata, including citations, authors, journals, and keywords. We construct heterogeneous network to reveal relationships among various entities. Different knowledge graph embedding models are employed to train the network, thereby obtaining entity and relation embeddings. The cosine similarity algorithm is adopted to measure the knowledge proximity between these embeddings. We take the Internet of Thing domain as an example to verify the performance of the multi-entity reinforced MPA through both quantitative and qualitative analysis. Our findings indicate that the adjusted MPA exhibits stronger topic relevance, demonstrating the effectiveness of the method in capturing complex knowledge relationships.

Recommender systems based on neuro-symbolic knowledge graph embeddings encoding first-order logic rules

Recommender systems based on neuro-symbolic knowledge graph embeddings encoding first-order logic rules

FuseLinker: Leveraging LLM’s pre-trained text embeddings and domain knowledge to enhance GNN-based link prediction on biomedical knowledge graphs

ObjectiveTo develop the FuseLinker, a novel link prediction framework for biomedical knowledge graphs (BKGs), which fully exploits the graph’s structural, textual and domain knowledge information. We evaluated the utility of FuseLinker in the graph-based drug repurposing task through detailed case studies. MethodsFuseLinker leverages fused pre-trained text embedding and domain knowledge embedding to enhance the graph neural network (GNN)-based link prediction model tailored for BKGs. This framework includes three parts: a) obtain text embeddings for BKGs using embedding-visible large language models (LLMs), b) learn the representations of medical ontology as domain knowledge information by employing the Poincaré graph embedding method, and c) fuse these embeddings and further learn the graph structure representations of BKGs by applying a GNN-based link prediction model. We evaluated FuseLinker against traditional knowledge graph embedding models and a conventional GNN-based link prediction model across four public BKG datasets. Additionally, we examined the impact of using different embedding-visible LLMs on FuseLinker’s performance. Finally, we investigated FuseLinker’s ability to generate medical hypotheses through two drug repurposing case studies for Sorafenib and Parkinson’s disease. ResultsBy comparing FuseLinker with baseline models on four BKGs, our method demonstrates superior performance. The Mean Reciprocal Rank (MRR) and Area Under receiver operating characteristic Curve (AUROC) for KEGG50k, Hetionet, SuppKG and ADInt are 0.969 and 0.987, 0.548 and 0.903, 0.739 and 0.928, and 0.831 and 0.890, respectively. ConclusionOur study demonstrates that FuseLinker is an effective novel link prediction framework that integrates multiple graph information and shows significant potential for practical applications in biomedical and clinical tasks. Source code and data are available at https://github.com/YKXia0/FuseLinker.

Research Progresses and Applications of Knowledge Graph Embedding Technique in Chemistry.

A knowledge graph (KG) is a technique for modeling entities and their interrelations. Knowledge graph embedding (KGE) translates these entities and relationships into a continuous vector space to facilitate dense and efficient representations. In the domain of chemistry, applying KG and KGE techniques integrates heterogeneous chemical information into a coherent and user-friendly framework, enhances the representation of chemical data features, and is beneficial for downstream tasks, such as chemical property prediction. This paper begins with a comprehensive review of classical and contemporary KGE methodologies, including distance-based models, semantic matching models, and neural network-based approaches. We then catalogue the primary databases employed in chemistry and biochemistry that furnish the KGs with essential chemical data. Subsequently, we explore the latest applications of KG and KGE in chemistry, focusing on risk assessment, property prediction, and drug discovery. Finally, we discuss the current challenges to KG and KGE techniques and provide a perspective on their potential future developments.

A robotic manipulation framework for industrial human–robot collaboration based on continual knowledge graph embedding

A robotic manipulation framework for industrial human–robot collaboration based on continual knowledge graph embedding

Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics

The emergence of perturbation transcriptomics provides a new perspective for drug discovery, but existing analysis methods suffer from inadequate performance and limited applicability. In this work, we present PertKGE, a method designed to deconvolute compound-protein interactions from perturbation transcriptomics with knowledge graph embedding. By considering multi-level regulatory events within biological systems that share the same semantic context, PertKGE significantly improves deconvoluting accuracy in two critical "cold-start" settings: inferring targets for new compounds and conducting virtual screening for new targets. We further demonstrate the pivotal role of incorporating multi-level regulatory events in alleviating representational biases. Notably, it enables the identification of ectonucleotide pyrophosphatase/phosphodiesterase-1 as the target responsible for the unique anti-tumor immunotherapy effect of tankyrase inhibitor K-756 and the discovery of five novel hits targeting the emerging cancer therapeutic targetaldehyde dehydrogenase 1B1 with a remarkable hit rate of 10.2%. These findings highlight the potential of PertKGE to accelerate drug discovery.

Decoupled semantic graph neural network for knowledge graph embedding

Knowledge graph embedding (KGE) learns an embedding space for a more accurate representation of entities and relations. Although the KGE model has proliferated, it often fails to fully capture the rich semantics in knowledge graphs. Some studies attempt to apply decoupling methods to decompose node representations, yet they neglect the semantic noise generated during the decoupled process. To address these issues, we introduce the decoupled semantic graph network for KGE (named DSGNet), which employs a novel approach that combines semantic decoupling with structural awareness. DSGNet begins by projecting the knowledge graph into distinct semantic spaces, ensuring minimal correlation between them to achieve effective semantic decoupling. To mitigate semantic noise, a top-k sampling technique is applied to the decoupled graphs. DSGNet then aggregates these different semantic graphs using a relation-aware aggregation module, followed by a multi-layer aggregation process for enhanced node representation. The extensive experiments demonstrate that DSGNet performs competitively on two popular datasets. We make our code publicly available at https://github.com/HubuKG/DSGNet.

Intelligent Asset Allocation Portfolio Division and Recommendation

With the continuous development of financial markets, intelligent asset allocation has become a topic of great concern in the investment field. However, traditional asset allocation methods often face difficulties in grasping the relationship between diversity, risk and return, which limits its application in complex market environments. To solve this problem, this study introduces deep learning and knowledge graphs and proposes an intelligent asset allocation model. Our model makes full use of the advantages of the Knowledge Graph Embedding Model (KGE), LSTM, and Genetic Algorithm (GA) to build a multi-level and multi-dimensional asset allocation model. KGE helps capture the complex relationships between different assets, LSTM is used to learn key patterns of historical portfolio performance, and GA finds the optimal asset allocation combination by simulating natural selection and genetic mechanisms. Experimental findings indicate that our model has demonstrated substantial improvements across various performance metrics and outperforms conventional approaches.

Knowledge Graph Embedding Using a Multi-Channel Interactive Convolutional Neural Network with Triple Attention

Knowledge Graph Embedding Using a Multi-Channel Interactive Convolutional Neural Network with Triple Attention

Community knowledge graph abstraction for enhanced link prediction: A study on PubMed knowledge graph

Objective:As new knowledge is produced at a rapid pace in the biomedical field, existing biomedical Knowledge Graphs (KGs) cannot be manually updated in a timely manner. Previous work in Natural Language Processing (NLP) has leveraged link prediction to infer the missing knowledge in general-purpose KGs. Inspired by this, we propose to apply link prediction to existing biomedical KGs to infer missing knowledge. Although Knowledge Graph Embedding (KGE) methods are effective in link prediction tasks, they are less capable of capturing relations between communities of entities with specific attributes (Fanourakis et al., 2023). Methods:To address this challenge, we proposed an entity distance-based method for abstracting a Community Knowledge Graph (CKG) from a simplified version of the pre-existing PubMed Knowledge Graph (PKG) (Xu et al., 2020). For link prediction on the abstracted CKG, we proposed an extension approach for the existing KGE models by linking the information in the PKG to the abstracted CKG. The applicability of this extension was proved by employing six well-known KGE models: TransE, TransH, DistMult, ComplEx, SimplE, and RotatE. Evaluation metrics including Mean Rank (MR), Mean Reciprocal Rank (MRR), and Hits@k were used to assess the link prediction performance. In addition, we presented a backtracking process that traces the results of CKG link prediction back to the PKG scale for further comparison. Results:Six different CKGs were abstracted from the PKG by using embeddings of the six KGE methods. The results of link prediction in these abstracted CKGs indicate that our proposed extension can improve the existing KGE methods, achieving a top-10 accuracy of 0.69 compared to 0.5 for TransE, 0.7 compared to 0.54 for TransH, 0.67 compared to 0.6 for DistMult, 0.73 compared to 0.57 for ComplEx, 0.73 compared to 0.63 for SimplE, and 0.85 compared to 0.76 for RotatE on their CKGs, respectively. These improved performances also highlight the wide applicability of the extension approach. Conclusion:This study proposed novel insights into abstracting CKGs from the PKG. The extension approach indicated enhanced performance of the existing KGE methods and has applicability. As an interesting future extension, we plan to conduct link prediction for entities that are newly introduced to the PKG.

A survey on temporal knowledge graph embedding: Models and applications

Knowledge graph embedding (KGE), as a pivotal technology in artificial intelligence, plays a significant role in enhancing the logical reasoning and management efficiency of downstream tasks in knowledge graphs (KGs). It maps the intricate structure of a KG to a continuous vector space. Conventional KGE techniques primarily focus on representing static data within a KG. However, in the real world, facts frequently change over time, as exemplified by evolving social relationships and news events. The effective utilization of embedding technologies to represent KGs that integrate temporal data has gained significant scholarly interest. This paper comprehensively reviews the existing methods for learning KG representations that incorporate temporal data. It offers a highly intuitive perspective by categorizing temporal KGE (TKGE) methods into seven main classes based on dynamic evolution models and extensions of static KGE. The review covers various aspects of TKGE, including the background, problem definition, symbolic representation, training process, commonly used datasets, evaluation schemes, and relevant research. Furthermore, detailed descriptions of related embedding models are provided, followed by an introduction to typical downstream tasks in temporal KG scenarios. Finally, the paper concludes by summarizing the challenges faced in TKGE and outlining future research directions.

Continual knowledge graph embedding enhancement for joint interaction-based next click recommendation

Knowledge Graph Embedding (KGE) based deep neural networks contribute to recommender systems in diverse application scenarios. However, Catastrophic Forgetting (CForg) significantly degrades their performance. Although exemplar replay is commonly adopted as a possible remedy to alleviate the intensity of CForg, a trade-off between performance and complexity occurs in this process. Therefore, in this work, we introduce Continual Knowledge graph embedding enhancement for joint Interaction-based Next click recommendation (CKIN) to defy the CForg and assuage the complexity. Typically, we introduce the Semantic Relevance Estimation (SRE) technique to ensure information relevance by filtering out irrelevant-data and reducing the space complexity. We introduce the SRE-enhanced deep probabilistic technique to probably replay the most relevant exemplars to defy the CForg and reduce the time complexity. Moreover, we introduce the integration of locality-preserving loss into the KGE framework to optimize the loss. In substantial experiments on real-world datasets, CKIN outperforms the baseline methods by effectively meeting the highlighted challenges.

Predicting drug-target interactions by measuring confidence with consistent causal neighborhood interventions

Predicting drug-target interactions (DTI) is a crucial stage in drug discovery and development. Understanding the interaction between drugs and targets is essential for pinpointing the specific relationship between drug molecules and targets, akin to solving a link prediction problem using information technology. While knowledge graph (KG) and knowledge graph embedding (KGE) methods have been rapid advancements and demonstrated impressive performance in drug discovery, they often lack authenticity and accuracy in identifying DTI. This leads to increased misjudgment rates and reduced efficiency in drug development. To address these challenges, our focus lies in refining the accuracy of DTI prediction models through KGE, with a specific emphasis on causal intervention confidence measures (CI). These measures aim to assess triplet scores, enhancing the precision of the predictions. Comparative experiments conducted on three datasets and utilizing 9 KGE models reveal that our proposed confidence measure approach via causal intervention, significantly improves the accuracy of DTI link prediction compared to traditional approaches. Furthermore, our experimental analysis delves deeper into the embedding of intervention values, offering valuable insights for guiding the design and development of subsequent drug development experiments. As a result, our predicted outcomes serve as valuable guidance in the pursuit of more efficient drug development processes.

TAP with ease: a generic recommendation system for trigger-action programming based on multi-modal representation learning

The escalating popularity of smart devices has given rise to an increasing trend wherein users leverage customized trigger-action programming (TAP) rules within the Internet of Things (IoT) to automate various aspects of their lives. This article addresses the challenge of effectively combining functions provided by many smart devices and online services by introducing a novel multi-modal representation learning model called TAP-TAG. This model integrates both textual and graph structures inherent in TAP rules, offering a holistic method to rule recommendation. TAP-TAG comprises two branches: the Knowledge Graph Embedding model, which projects triplets extracted from the TAP dataset into embeddings, and convolution neural networks that extract semantic features from the textual content of TAP rules. Extensive experiments are conducted on real-world TAP datasets to evaluate our model’s ability to recommend relevant rules based on user preferences. The experimental results show that TAP-TAG can outperform the state-of-the-art method by 5% in Precision@5, indicating that TAP-TAG is highly effective in providing accurate and diverse recommendations for TAP rules.

Evaluating the Predictive Features of Person-Centric Knowledge Graph Embeddings: Unfolding Ablation Studies.

Developing novel predictive models with complex biomedical information is challenging due to various idiosyncrasies related to heterogeneity, standardization or sparseness of the data. We previously introduced a person-centric ontology to organize information about individual patients, and a representation learning framework to extract person-centric knowledge graphs (PKGs) and to train Graph Neural Networks (GNNs). In this paper, we propose a systematic approach to examine the results of GNN models trained with both structured and unstructured information from the MIMIC-III dataset. Through ablation studies on different clinical, demographic, and social data, we show the robustness of this approach in identifying predictive features in PKGs for the task of readmission prediction.