Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new Bio-ML track at OAEI 2022.

Knowledge graphs represent facts about real-world entities. Most of these facts are defined as positive statements. The negative statements are scarce but highly relevant under the open-world assumption. Furthermore, they have been demonstrated to improve the performance of several applications, namely in the biomedical domain. However, no benchmark dataset supports the evaluation of the methods that consider these negative statements. We present a collection of datasets for three relation prediction tasks - protein-protein interaction prediction, gene-disease association prediction and disease prediction - that aim at circumventing the difficulties in building benchmarks for knowledge graphs with negative statements. These datasets include data from two successful biomedical ontologies, Gene Ontology and Human Phenotype Ontology, enriched with negative statements. We also generate knowledge graph embeddings for each dataset with two popular path-based methods and evaluate the performance in each task. The results show that the negative statements can improve the performance of knowledge graph embeddings.

In the age of Industry 4.0 and Cyber-Physical Production Systems (CPPSs) vast amounts of potentially valuable data are being generated. Methods from Machine Learning (ML) and Data Mining (DM) have proven to be promising in extracting complex and hidden patterns from the data collected. The knowledge obtained can in turn be used to improve tasks like diagnostics or maintenance planning. However, such data-driven projects, usually performed with the Cross-Industry Standard Process for Data Mining (CRISP-DM), often fail due to the disproportionate amount of time needed for understanding and preparing the data. The application of domain-specific ontologies has demonstrated its advantageousness in a wide variety of Industry 4.0 application scenarios regarding the aforementioned challenges. However, workflows and artifacts from ontology design for CPPSs have not yet been systematically integrated into the CRISP-DM. Accordingly, this contribution intends to present an integrated approach so that data scientists are able to more quickly and reliably gain insights into the CPPS. The result is exemplarily applied to an anomaly detection use case.

We investigate the impact of non-regular path expressions on the decidability of satisfiability checking and querying in description logics extending ALC. Our primary objects of interest are ALCreg and ALCvpl, the extensions of with path expressions employing, respectively, regular and visibly-pushdown languages. The first one, ALCreg, is a notational variant of the well-known Propositional Dynamic Logic of Fischer and Ladner. The second one, ALCvpl, was introduced and investigated by Loding and Serre in 2007. The logic ALCvpl generalises many known decidable non-regular extensions of ALCreg. We provide a series of undecidability results. First, we show that decidability of the concept satisfiability problem for ALCvpl is lost upon adding the seemingly innocent Self operator. Second, we establish undecidability for the concept satisfiability problem for ALCvpl extended with nominals. Interestingly, our undecidability proof relies only on one single non-regular (visibly-pushdown) language, namely on r#s# := { r^n s^n | n in N } for fixed role names r and s. Finally, in contrast to the classical database setting, we establish undecidability of query entailment for queries involving non-regular atoms from r#s#, already in the case of ALC-TBoxes.

Taxonomies are an essential knowledge representation, yet most studies on automatic taxonomy construction (ATC) resort to manual evaluation to score proposed algorithms. We argue that automatic taxonomy evaluation (ATE) is just as important as taxonomy construction. We propose RaTE, an automatic label-free taxonomy scoring procedure, which relies on a large pre-trained language model. We apply our evaluation procedure to three state-of-the-art ATC algorithms with which we built seven taxonomies from the Yelp domain, and show that 1) RaTE correlates well with human judgments and 2) artificially degrading a taxonomy leads to decreasing RaTE score.

Engineering knowledge-based (or expert) systems require extensive manual effort and domain knowledge. As Large Language Models (LLMs) are trained using an enormous amount of cross-domain knowledge, it becomes possible to automate such engineering processes. This paper presents an empirical automation and semi-automation framework for domain knowledge distillation using prompt engineering and the LLM ChatGPT. We assess the framework empirically in the autonomous driving domain and present our key observations. In our implementation, we construct the domain knowledge ontology by "chatting" with ChatGPT. The key finding is that while fully automated domain ontology construction is possible, human supervision and early intervention typically improve efficiency and output quality as they lessen the effects of response randomness and the butterfly effect. We, therefore, also develop a web-based distillation assistant enabling supervision and flexible intervention at runtime. We hope our findings and tools could inspire future research toward revolutionizing the engineering of knowledge-based systems across application domains.

Biomedical datasets are often modeled as knowledge graphs (KGs) because they capture the multi-relational, heterogeneous, and dynamic natures of biomedical systems. KG completion (KGC), can, therefore, help researchers make predictions to inform tasks like drug repositioning. While previous approaches for KGC were either rule-based or embedding-based, hybrid approaches based on neurosymbolic artificial intelligence are becoming more popular. Many of these methods possess unique characteristics which make them even better suited toward biomedical challenges. Here, we survey such approaches with an emphasis on their utilities and prospective benefits for biomedicine.

Clinical Practice Guidelines (CPGs) for cancer diseases evolve rapidly due to new evidence generated by active research. Currently, CPGs are primarily published in a document format that is ill-suited for managing this developing knowledge. A knowledge model of the guidelines document suitable for programmatic interaction is required. This work proposes an automated method for extraction of knowledge from National Comprehensive Cancer Network (NCCN) CPGs in Oncology and generating a structured model containing the retrieved knowledge. The proposed method was tested using two versions of NCCN Non-Small Cell Lung Cancer (NSCLC) CPG to demonstrate the effectiveness in faithful extraction and modeling of knowledge. Three enrichment strategies using Cancer staging information, Unified Medical Language System (UMLS) Metathesaurus & National Cancer Institute thesaurus (NCIt) concepts, and Node classification are also presented to enhance the model towards enabling programmatic traversal and querying of cancer care guidelines. The Node classification was performed using a Support Vector Machine (SVM) model, achieving a classification accuracy of 0.81 with 10-fold cross-validation.

Presently, knowledge graph-based recommendation algorithms have garnered considerable attention among researchers. However, these algorithms solely consider knowledge graphs with single relationships and do not effectively model exercise-rich features, such as exercise representativeness and informativeness. Consequently, this paper proposes a framework, namely the Knowledge-Graph-Exercise Representativeness and Informativeness Framework, to address these two issues. The framework consists of four intricate components and a novel cognitive diagnosis model called the Neural Attentive cognitive diagnosis model. These components encompass the informativeness component, exercise representation component, knowledge importance component, and exercise representativeness component. The informativeness component evaluates the informational value of each question and identifies the candidate question set that exhibits the highest exercise informativeness. Furthermore, the skill embeddings are employed as input for the knowledge importance component. This component transforms a one-dimensional knowledge graph into a multi-dimensional one through four class relations and calculates skill importance weights based on novelty and popularity. Subsequently, the exercise representativeness component incorporates exercise weight knowledge coverage to select questions from the candidate question set for the tested question set. Lastly, the cognitive diagnosis model leverages exercise representation and skill importance weights to predict student performance on the test set and estimate their knowledge state. To evaluate the effectiveness of our selection strategy, extensive experiments were conducted on two publicly available educational datasets. The experimental results demonstrate that our framework can recommend appropriate exercises to students, leading to improved student performance.