Knowledge graphs (KGs) have emerged as a prominent data representation and management paradigm. Being usually underpinned by a schema (e.g. an ontology), KGs capture not only factual information but also contextual knowledge. In some tasks, a few KGs established themselves as standard benchmarks. However, recent works outline that relying on a limited collection of datasets is not sufficient to assess the generalization capability of an approach. In some data-sensitive fields such as education or medicine, access to public datasets is even more limited. To remedy the aforementioned issues, we release PyGraft, a Python-based tool that generates highly customized, domain-agnostic schemas and knowledge graphs. The synthesized schemas encompass various RDFS and OWL constructs, while the synthesized KGs emulate the characteristics and scale of real-world KGs. Logical consistency of the generated resources is ultimately ensured by running a description logic (DL) reasoner. By providing a way of generating both a schema and KG in a single pipeline, PyGraft's aim is to empower the generation of a more diverse array of KGs for benchmarking novel approaches in areas such as graph-based machine learning (ML), or more generally KG processing. In graph-based ML in particular, this should foster a more holistic evaluation of model performance and generalization capability, thereby going beyond the limited collection of available benchmarks. PyGraft is available at: https://github.com/nicolas-hbt/pygraft.

Knowledge graph embeddings are dense numerical representations of entities in a knowledge graph (KG). While the majority of approaches concentrate only on relational information, i.e., relations between entities, fewer approaches exist which also take information about literal values (e.g., textual descriptions or numerical information) into account. Those which exist are typically tailored towards a particular modality of literal and a particular embedding method. In this paper, we propose a set of universal preprocessing operators which can be used to transform KGs with literals for numerical, temporal, textual, and image information, so that the transformed KGs can be embedded with any method. The results on the kgbench dataset with three different embedding methods show promising results.

This study presents insights from interviews with nineteen Knowledge Graph (KG) practitioners who work in both enterprise and academic settings on a wide variety of use cases. Through this study, we identify critical challenges experienced by KG practitioners when creating, exploring, and analyzing KGs that could be alleviated through visualization design. Our findings reveal three major personas among KG practitioners - KG Builders, Analysts, and Consumers - each of whom have their own distinct expertise and needs. We discover that KG Builders would benefit from schema enforcers, while KG Analysts need customizable query builders that provide interim query results. For KG Consumers, we identify a lack of efficacy for node-link diagrams, and the need for tailored domain-specific visualizations to promote KG adoption and comprehension. Lastly, we find that implementing KGs effectively in practice requires both technical and social solutions that are not addressed with current tools, technologies, and collaborative workflows. From the analysis of our interviews, we distill several visualization research directions to improve KG usability, including knowledge cards that balance digestibility and discoverability, timeline views to track temporal changes, interfaces that support organic discovery, and semantic explanations for AI and machine learning predictions.

Drug repositioning-a promising strategy for discovering new therapeutic uses for existing drugs-has been increasingly explored in the computational science literature using biomedical databases. However, the technological potential of drug repositioning candidates has often been overlooked. This study presents a novel protocol to comprehensively analyse various sources such as pharmaceutical patents and biomedical databases, and identify drug repositioning candidates with both technological potential and scientific evidence. To this end, first, we constructed a scientific biomedical knowledge graph (s-BKG) comprising relationships between drugs, diseases, and genes derived from biomedical databases. Our protocol involves identifying drugs that exhibit limited association with the target disease but are closely located in the s-BKG, as potential drug candidates. We constructed a patent-informed biomedical knowledge graph (p-BKG) by adding pharmaceutical patent information. Finally, we developed a graph embedding protocol to ascertain the structure of the p-BKG, thereby calculating the relevance scores of those candidates with target disease-related patents to evaluate their technological potential. Our case study on Alzheimer's disease demonstrates its efficacy and feasibility, while the quantitative outcomes and systematic methods are expected to bridge the gap between computational discoveries and successful market applications in drug repositioning research.

Knowledge graphs enable data scientists to learn end-to-end on heterogeneous knowledge. However, most end-to-end models solely learn from the relational information encoded in graphs' structure: raw values, encoded as literal nodes, are either omitted completely or treated as regular nodes without consideration for their values. In either case we lose potentially relevant information which could have otherwise been exploited by our learning methods. We propose a multimodal message passing network which not only learns end-to-end from the structure of graphs, but also from their possibly divers set of multimodal node features. Our model uses dedicated (neural) encoders to naturally learn embeddings for node features belonging to five different types of modalities, including numbers, texts, dates, images and geometries, which are projected into a joint representation space together with their relational information. We implement and demonstrate our model on node classification and link prediction for artificial and real-worlds datasets, and evaluate the effect that each modality has on the overall performance in an inverse ablation study. Our results indicate that end-to-end multimodal learning from any arbitrary knowledge graph is indeed possible, and that including multimodal information can significantly affect performance, but that much depends on the characteristics of the data.

Rule learning approaches for knowledge graph completion are efficient, interpretable and competitive to purely neural models. The rule aggregation problem is concerned with finding one plausibility score for a candidate fact which was simultaneously predicted by multiple rules. Although the problem is ubiquitous, as data-driven rule learning can result in noisy and large rulesets, it is underrepresented in the literature and its theoretical foundations have not been studied before in this context. In this work, we demonstrate that existing aggregation approaches can be expressed as marginal inference operations over the predicting rules. In particular, we show that the common Max-aggregation strategy, which scores candidates based on the rule with the highest confidence, has a probabilistic interpretation. Finally, we propose an efficient and overlooked baseline which combines the previous strategies and is competitive to computationally more expensive approaches.

Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.

Knowledge graph (KG) embedding has been used to benefit the diagnosis of animal diseases by analyzing electronic medical records (EMRs), such as notes and veterinary records. However, learning representations to capture entities and relations with literal information in KGs is challenging as the KGs show heterogeneous properties and various types of literal information. Meanwhile, the existing methods mostly aim to preserve graph structures surrounding target nodes without considering different types of literals, which could also carry significant information. In this paper, we propose a knowledge graph embedding model for the efficient diagnosis of animal diseases, which could learn various types of literal information and graph structure and fuse them into unified representations, namely LiteralKG. Specifically, we construct a knowledge graph that is built from EMRs along with literal information collected from various animal hospitals. We then fuse different types of entities and node feature information into unified vector representations through gate networks. Finally, we propose a self-supervised learning task to learn graph structure in pretext tasks and then towards various downstream tasks. Experimental results on link prediction tasks demonstrate that our model outperforms the baselines that consist of state-of-the-art models. The source code is available at https://github.com/NSLab-CUK/LiteralKG.

Knowledge graph entity typing (KGET) is a task to predict the missing entity types in knowledge graphs (KG). Previously, KG embedding (KGE) methods tried to solve the KGET task by introducing an auxiliary relation, 'hasType', to model the relationship between entities and their types. However, a single auxiliary relation has limited expressiveness for diverse entity-type patterns. We improve the expressiveness of KGE methods by introducing multiple auxiliary relations in this work. Similar entity types are grouped to reduce the number of auxiliary relations and improve their capability to model entity-type patterns with different granularities. With the presence of multiple auxiliary relations, we propose a method adopting an Asynchronous learning scheme for Entity Typing, named AsyncET, which updates the entity and type embeddings alternatively to keep the learned entity embedding up-to-date and informative for entity type prediction. Experiments are conducted on two commonly used KGET datasets to show that the performance of KGE methods on the KGET task can be substantially improved by the proposed multiple auxiliary relations and asynchronous embedding learning. Furthermore, our method has a significant advantage over state-of-the-art methods in model sizes and time complexity.

Symbolic knowledge graphs (KGs) play a pivotal role in knowledge-centric applications such as search, question answering and recommendation. As contemporary language models (LMs) trained on extensive textual data have gained prominence, researchers have extensively explored whether the parametric knowledge within these models can match up to that present in knowledge graphs. Various methodologies have indicated that enhancing the size of the model or the volume of training data enhances its capacity to retrieve symbolic knowledge, often with minimal or no human supervision. Despite these advancements, there is a void in comprehensively evaluating whether LMs can encompass the intricate topological and semantic attributes of KGs, attributes crucial for reasoning processes. In this work, we provide an exhaustive evaluation of language models of varying sizes and capabilities. We construct nine qualitative benchmarks that encompass a spectrum of attributes including symmetry, asymmetry, hierarchy, bidirectionality, compositionality, paths, entity-centricity, bias and ambiguity. Additionally, we propose novel evaluation metrics tailored for each of these attributes. Our extensive evaluation of various LMs shows that while these models exhibit considerable potential in recalling factual information, their ability to capture intricate topological and semantic traits of KGs remains significantly constrained. We note that our proposed evaluation metrics are more reliable in evaluating these abilities than the existing metrics. Lastly, some of our benchmarks challenge the common notion that larger LMs (e.g., GPT-4) universally outshine their smaller counterparts (e.g., BERT).