Survey on AI-Drug Discovery with Knowledge Graphs: Data, Algorithm, and Application

Recently, large-scale knowledge graphs (KGs) have become a key asset for search, analytics, recommendations and data integration. Large-scale KGs provide millions of facts about the real world. Each fact is composed as (subject, relation, object), e.g., the triplet (“Cristiano Ronaldo”, playFor, “Real Madrid”). However, these facts are blind to the temporal dimension. Actually, knowledge in practice is time-variant and many relations are only valid for a certain period of time. This phenomenon highlights the importance of building temporal knowledge graphs. In particular, knowledge in temporal KG is represented as (subject, relation, object, valid time), e.g., (“Cristiano Ronaldo”, playFor, “Real Madrid”, “[2009, 2018]”. However, research on temporal KG is very current and there are still many problems needed to be addressed. One obvious problem is that the size of temporal KG is still very small. For example, only 6.6% of the facts are time-aware in one of the largest knowledge graphs, YAGO3. In addition, 71% of people have no known place of birth, and 75% have no known nationality in Freebase. Furthermore, over 87.7% of the facts are uncovered in Japanese DBpedia compared with English DBpedia. Therefore, in this thesis, we study how to enlarge and enrich temporal knowledge graphs from three aspects, namely, temporal KG enrichment. In particular, we study the enrichment problem from the following aspects: (1) volume, (2) completeness, and (3) coverage.Our first solution is temporal knowledge harvesting which extracts temporal knowledge from free text directly. However, text corpus is noisy, and extracting structured temporal facts with high accuracy and coverage is very challenging. Inspired by pattern-based systems, we propose a temporal knowledge harvesting framework. In particular, we propose various techniques to extract temporal patterns, including corpus annotation, pattern generation, scoring and clustering. These techniques can reduce ambiguity in the text corpus and can improve both the accuracy and coverage of the extracted patterns. Second, we leverage the extracted patterns to harvest temporal knowledge. To improve the accuracy, we propose a parse-tree-based method. And to increase the coverage, we consider the relationships between tree components, including part of speech (POS), clause types, constituency and dependency. Experiments on real-world datasets verify the effectiveness of our proposed framework.Our second solution is temporal knowledge graph completion. Temporal KG completion is the task of inferring unobserved edges between entity pairs. Generally, temporal KG completion relies on the temporal KG embeddings technique, which learns the low-dimensional representations of all KG components. As research on temporal KG embedding is very current, we study both the embedding and the completion problems. In particular, we observe that contexts are extremely useful for learning the representations of entities and for inferring the unknown time intervals. As a result, we propose a context-aware embedding model for KG embeddings and a context-based temporal inference model for KG completion. In our embedding model, we not only capture factual plausibility as traditional methods did, but also propose a new measure on contexts, named temporal consistency. It measures how well the target entity interacts with its surrounding contexts on the temporal dimension. Our completion model is based on the embedding model, and further captures the interactions on the entity dimension. Extensive experiments verify the effectiveness of our models.Our third solution is temporal knowledge graph alignment which aims to discover the SameAs edges across two temporal KGs. Not like previous attribute-based alignment models, we further divide attribute facts into character facts, digit facts and time facts. In particular, we observe that the context information is extremely useful for the identification of the same entities. Therefore, we propose an alignment model on leveraging temporal contexts to represent entities. However, contexts of the same object can be very different. For example, the value of career predicate changed from “football player” to “coach” for the football player “Zidane”. This is because entities are evolving over time and thus the predicate values can be different. In our framework, we propose an alignment module that simulates the entity evolving process. Specifically, this module captures the interactions between contexts and aggregates context information to represent the entity. Lastly, we found that not all contexts are relevant, e.g., height v.s. career. Actually, only the relevant contexts are useful for capturing the evolving. Therefore, we propose a clustering approach for grouping relevant contexts together. Our experimental results validate the superiority of our proposed alignment model.

A knowledge graph (KG) consists of numerous triples, in which each triple, i.e., (head entity, relation, tail entity), denotes a real-world assertion. Many large-scale KGs have been developed, e.g., general-purpose KGs Freebase and YAGO. Also, lots of domain-specific KGs are emerging, e.g., COVID-19 KGs, biomedical KGs, and agricultural KGs. By embedding KGs into low-dimensional vectors, i.e., representations of entities and relations, we could integrate KGs into machine learning models and enhance the performance of many prediction tasks, including search, recommendations, and question answering. During the construction, refinement, embedding, and application of KGs, a variety of KG learning algorithms have been developed to handle challenges in various real-world scenarios. Moreover, graph neural networks have also brought new opportunities to KG learning. This workshop aims to engage with active researchers from KG communities, recommendation communities, natural language processing communities, and other communities, and deliver state-of-the-art research insights into the core challenges in KG learning.

This systematic literature review investigates how evolvable knowledge graphs (KGs) enhance manufacturing. Evolvable KGs adapt to changing knowledge by leveraging machine learning algorithms and human expertise to improve decision-making, operational efficiency, and predictive maintenance capabilities beyond the capabilities of prevailing solutions enabled by dynamic KGs. This review maps the existing literature based on the stages of the KG development process. The main results are an updated model of the creation and maintenance of evolvable KGs in manufacturing and a literature-based synthesis of learning approaches for enabling KG evolution through knowledge processing and knowledge utilization. The results contribute to updating the KG development process model and synthesizing an understanding of evolvable KGs that utilize the observed learning approaches on knowledge processing to change KG relations and nodes, and three learning approaches through knowledge utilization (human-guided, machine-driven, and human-machine collaborative knowledge updates). Despite emerging advances, challenges persist in quality assurance, process planning, and integration of human expertise. The findings advocate addressing these issues to promote greater adoption and optimization of KGs in manufacturing. By deepening the understanding of how KGs can evolve through learning, this review sets a conceptual basis for future research to develop more dynamic and intelligent KG-based manufacturing systems.

Knowledge Graph (KG) embedding approaches have been proved effective to infer new facts for a KG based on the existing ones–a problem known as KG completion. However, most of them have focused on static KGs, in fact, relational facts in KGs often show temporal dynamics, e.g., the fact (US, has president, Barack Obama, [2009–2017]) is only valid from 2009 to 2017. Therefore, utilizing available time information to develop temporal KG embedding models is an increasingly important problem. In this paper, we propose a new hyperplane-based time-aware KG embedding model for temporal KG completion. By employing the method of time-specific hyperplanes, our model could explicitly incorporate time information in the entity-relation space to predict missing elements in the KG more effectively, especially temporal scopes for facts with missing time information. Moreover, in order to model and infer four important relation patterns including symmetry, antisymmetry, inversion and composition, we map facts happened at the same time into a polar coordinate system. During training procedure, a time-enhanced negative sampling strategy is proposed to get more effective negative samples. Experimental results on datasets extracted from real-world temporal KGs show that our model significantly outperforms existing state-of-the-art approaches for the KG completion task.

Finding similar entities among knowledge graphs is an essential research problem for knowledge integration and knowledge graph connection. This paper aims at finding semantically similar entities between two knowledge graphs. This can help end users and search agents more effectively and easily access pertinent information across knowledge graphs. Given a query entity in one knowledge graph, the proposed approach tries to find the most similar entity in another knowledge graph. The main idea is to leverage graph embedding, clustering, regression and sentence embedding. In this approach, RDF2Vec has been employed to generate vector representations of all entities of the second knowledge graph and then the vectors have been clustered based on cosine similarity using K medoids algorithm. Then, an artificial neural network with multilayer perception topology has been used as a regression model to predict the corresponding vector in the second knowledge graph for a given vector from the first knowledge graph. After determining the cluster of the predicated vector, the entities of the detected cluster are ranked through sentence-BERT method and finally the entity with the highest rank is chosen as the most similar one. To evaluate the proposed approach, experiments have been conducted on real-world knowledge graphs. The experimental results demonstrate the effectiveness of the proposed approach.

Multitype view of knowledge contrastive learning for recommendation

In recent years, the related research of entity alignment has mainly focused on entity alignment via knowledge embeddings and graph neural networks; however, these proposed models usually suffer from structural heterogeneity and the large-scale problem of knowledge graph. A novel entity alignment model based on graph isomorphic network and compressed sensing is proposed. First, for the problem of structural heterogeneity, graph isomorphic network encoder is applied in knowledge graph to capture structural similarity of entity relation. Second, for the problem of large scale, key node and community are integrated for priority entity alignment to improve execution speed. However, the exiting node importance ranking algorithm cannot accurately identify key node in knowledge graph. So the compressed sensing is adopted in node importance ranking to improve the accuracy of identifying key node. The authors have carried out several experiments to test the effect and efficiency of the proposed entity alignment model.

Imagine having a knowledge graph that can extract medical health knowledge related to patient diagnosis solutions and treatments from thousands of research papers, distilled using machine learning techniques in healthcare applications. Medical doctors can quickly determine treatments and medications for urgent patients, while researchers can discover innovative treatments for existing and unknown diseases. This would be incredible! Our approach serves as an all-in-one solution, enabling users to employ a unified design methodology for creating their own knowledge graphs. Our rigorous validation process involves multiple stages of refinement, ensuring that the resulting answers are of the utmost professionalism and solidity, surpassing the capabilities of other solutions. However, building a high-quality knowledge graph from scratch, with complete triplets consisting of subject entities, relations, and object entities, is a complex and important task that requires a systematic approach. To address this, we have developed a comprehensive design flow for knowledge graph development and a high-quality entities database. We also developed knowledge distillation schemes that allow you to input a keyword (entity) and display all related entities and relations. Our proprietary methodology, multiple levels refinement (MLR), is a novel approach to constructing knowledge graphs and refining entities level-by-level. This ensures the generation of high-quality triplets and a readable knowledge graph through keyword searching. We have generated multiple knowledge graphs and developed a scheme to find the corresponding inputs and outputs of entity linking. Entities with multiple inputs and outputs are referred to as joints, and we have created a joint-version knowledge graph based on this. Additionally, we developed an interactive knowledge graph, providing a user-friendly environment for medical professionals to explore entities related to existing or unknown treatments/diseases. Finally, we have advanced knowledge distillation techniques.

Knowledge graphs (KGs) are essential resources for many applications including Web search and question answering. As KGs are often automatically constructed, they may contain incorrect facts. Detecting them is a crucial, yet extremely expensive task. Prominent solutions detect and explain inconsistency in KGs with respect to accompanying ontologies that describe the KG domain of interest. Compared to machine learning methods they are more reliable and human-interpretable but scale poorly on large KGs. In this paper, we present a novel approach to dramatically speed up the process of detecting and explaining inconsistency in large KGs by exploiting KG abstractions that capture prominent data patterns. Though much smaller, KG abstractions preserve inconsistency and their explanations. Our experiments with large KGs (e.g., DBpedia and Yago) demonstrate the feasibility of our approach and show that it significantly outperforms the popular baseline.

Clinical decision support system for hypertension medication based on knowledge graph

Recently, there has been an upsurge in the number of knowledge graphs (KG) that can only be accessed by experts. Non-expert users lack an adequate understanding of the queried knowledge graph's vocabulary and structure, as well as the syntax of the structured query language used to express the user's information needs. To increase the user base of these KGs, a set of Question Answering (QA) systems that use natural language to query these knowledge graphs have been introduced. However, finding a benchmark that accurately evaluates the quality of a QA system is a difficult task due to (1) the high degree of variation in the fine-grained properties among the existing benchmarks, (2) the static nature of the existing benchmarks versus the evolving nature of KGs, and (3) the limited number of KGs targeted by existing benchmarks, which hinders the usability of QA systems in real-world deployment over KGs that are different from those that were used in the evaluation of the QA systems. In this paper, we introduce Maestro, a benchmark generation system for question answering over knowledge graphs. Maestro can generate a new benchmark for any KG given the KG and, optionally, a text corpus that covers this KG. The benchmark generated by Maestro is guaranteed to cover all the properties of the natural language questions and queries that were encountered in the literature as long as the targeted KG includes these properties. Maestro also generates high-quality natural language questions with various utterances that are on par with manually-generated ones to better evaluate QA systems.

Effectively integrating and correlating multisource data involved in the bridge construction process is crucial for the improvement of the bridge informatization level. In the current issues of dynamic numerous data and low information sharing between different engineering departments, the traditional information management methods are inefficient in providing comprehensive and accurate data support for construction safety. Focusing on the bridge construction stage, this article proposes a dynamic data‐driven construction method of railway bridge construction knowledge graph (KG) in combination with dynamic data (materials, personnel, equipment and sensors) in the construction process and KG technology. By taking a railway bridge as a case, the study develops a prototype system and analyzes the effectiveness of bridge construction KG in material traceability, personnel and equipment management and construction safety guidance, which can provide comprehensive and accurate data support for bridge construction management and construction optimization. The results show that: (1) bridge construction KG that takes into account the dynamic features of bridge projects can effectively integrate multiple elements; (2) the bridge construction KG is dynamically updated through real‐time comparison and advance prediction based on the dynamic data collected by multi‐sensing equipment at the construction site, and can provide effective data support for guiding bridge construction safety; and (3) the construction management prototype system based on railway bridge construction KG can provide accurate data support for material traceability, personnel and equipment management and assisted risk event decision‐making. The results of the comparative experiment between the KG group and the spreadsheet group showed that utilizing the KG saved approximately 50% of time and achieved a 20% higher accuracy rate in the material traceability task compared to the spreadsheet group. In general, this study proposes a dynamic data‐driven construction method of railway bridge construction KG, which can effectively realize the effective integration and management of multisource data in the bridge construction process, provide the necessary scientific basis for fine bridge management, and help to improve bridge informatization management level.

Knowledge graphs exhibit a typical hierarchical structure and find extensive applications in various artificial intelligence domains. However, large-scale knowledge graphs need to be completed, which limits the performance of knowledge graphs in downstream tasks. Knowledge graph embedding methods have emerged as a primary solution to enhance knowledge graph completeness. These methods aim to represent entities and relations as low-dimensional vectors, focusing on handling relation patterns and multi-relation types. Researchers need to pay more attention to the crucial feature of hierarchical relationships in real-world knowledge graphs. We propose a novel knowledge graph embedding model called Hierarchy-Aware Paired Relation Vectors Knowledge Graph Embedding (HPRE) to bridge this gap. By leveraging the power of 2D coordinates, HPRE adeptly model relation patterns, multi-relation types, and hierarchical features in the knowledge graph. Specifically, HPRE employs paired relation vectors to capture the distinct characteristics of head and tail entities, facilitating a better fit for relational patterns and multi-relation scenarios. Additionally, HPRE employs angular coordinates to differentiate entities at various levels of the hierarchy, effectively representing the hierarchical nature of the knowledge graph. The experimental results show that the HPRE model can effectively learn the hierarchical features of the knowledge graph and achieve state-of-the-art experimental results on multiple real-world datasets for the link prediction task.

Video2Entities: A computer vision-based entity extraction framework for updating the architecture, engineering and construction industry knowledge graphs

EASC: An exception-aware semantic compression framework for real-world knowledge graphs