Recent years have witnessed much interest in temporal reasoning over knowledge graphs (KG) for complex question answering (QA), but there remains a substantial gap in human capabilities. We explore how to generalize relational graph convolutional networks (RGCN) for temporal KGQA. Specifically, we propose a novel, intuitive and interpretable scheme to modulate the messages passed through a KG edge during convolution, based on the relevance of its associated time period to the question. We also introduce a gating device to predict if the answer to a complex temporal question is likely to be a KG entity or time and use this prediction to guide our scoring mechanism. We evaluate the resulting system, which we call TwiRGCN, on TimeQuestions, a recently released, challenging dataset for multi-hop complex temporal QA. We show that TwiRGCN significantly outperforms state-of-the-art systems on this dataset across diverse question types. Notably, TwiRGCN improves accuracy by 9--10 percentage points for the most difficult ordinal and implicit question types.

Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.

Despite being the go-to choice for link prediction on knowledge graphs, research on interpretability of knowledge graph embeddings (KGE) has been relatively unexplored. We present KGEx, a novel post-hoc method that explains individual link predictions by drawing inspiration from surrogate models research. Given a target triple to predict, KGEx trains surrogate KGE models that we use to identify important training triples. To gauge the impact of a training triple, we sample random portions of the target triple neighborhood and we train multiple surrogate KGE models on each of them. To ensure faithfulness, each surrogate is trained by distilling knowledge from the original KGE model. We then assess how well surrogates predict the target triple being explained, the intuition being that those leading to faithful predictions have been trained on "impactful" neighborhood samples. Under this assumption, we then harvest triples that appear frequently across impactful neighborhoods. We conduct extensive experiments on two publicly available datasets, to demonstrate that KGEx is capable of providing explanations faithful to the black-box model.

Published biomedical information has and continues to rapidly increase. The recent advancements in Natural Language Processing (NLP), have generated considerable interest in automating the extraction, normalization, and representation of biomedical knowledge about entities such as genes and diseases. Our study analyzes germline abstracts in the construction of knowledge graphs of the of the immense work that has been done in this area for genes and diseases. This paper presents SimpleGermKG, an automatic knowledge graph construction approach that connects germline genes and diseases. For the extraction of genes and diseases, we employ BioBERT, a pre-trained BERT model on biomedical corpora. We propose an ontology-based and rule-based algorithm to standardize and disambiguate medical terms. For semantic relationships between articles, genes, and diseases, we implemented a part-whole relation approach to connect each entity with its data source and visualize them in a graph-based knowledge representation. Lastly, we discuss the knowledge graph applications, limitations, and challenges to inspire the future research of germline corpora. Our knowledge graph contains 297 genes, 130 diseases, and 46,747 triples. Graph-based visualizations are used to show the results.

Knowledge graphs (KGs) are gaining prominence in Healthcare AI, especially in drug discovery and pharmaceutical research as they provide a structured way to integrate diverse information sources, enhancing AI system interpretability. This interpretability is crucial in healthcare, where trust and transparency matter, and eXplainable AI (XAI) supports decision making for healthcare professionals. This overview summarizes recent literature on the impact of KGs in healthcare and their role in developing explainable AI models. We cover KG workflow, including construction, relationship extraction, reasoning, and their applications in areas like Drug-Drug Interactions (DDI), Drug Target Interactions (DTI), Drug Development (DD), Adverse Drug Reactions (ADR), and bioinformatics. We emphasize the importance of making KGs more interpretable through knowledge-infused learning in healthcare. Finally, we highlight research challenges and provide insights for future directions.

Most knowledge graph completion (KGC) methods learn latent representations of entities and relations of a given graph by mapping them into a vector space. Although the majority of these methods focus on static knowledge graphs, a large number of publicly available KGs contain temporal information stating the time instant/period over which a certain fact has been true. Such graphs are often known as temporal knowledge graphs. Furthermore, knowledge graphs may also contain textual descriptions of entities and relations. Both temporal information and textual descriptions are not taken into account during representation learning by static KGC methods, and only structural information of the graph is leveraged. Recently, some studies have used temporal information to improve link prediction, yet they do not exploit textual descriptions and do not support inductive inference (prediction on entities that have not been seen in training). We propose a novel framework called TEMT that exploits the power of pre-trained language models (PLMs) for text-enhanced temporal knowledge graph completion. The knowledge stored in the parameters of a PLM allows TEMT to produce rich semantic representations of facts and to generalize on previously unseen entities. TEMT leverages textual and temporal information available in a KG, treats them separately, and fuses them to get plausibility scores of facts. Unlike previous approaches, TEMT effectively captures dependencies across different time points and enables predictions on unseen entities. To assess the performance of TEMT, we carried out several experiments including time interval prediction, both in transductive and inductive settings, and triple classification. The experimental results show that TEMT is competitive with the state-of-the-art.

Designing a new clinical trial entails many decisions, such as defining a cohort and setting the study objectives to name a few, and therefore can benefit from recommendations based on exhaustive mining of past clinical trial records. Here, we propose a novel recommendation methodology, based on neural embeddings trained on a first-of-a-kind knowledge graph of clinical trials. We addressed several important research questions in this context, including designing a knowledge graph (KG) for clinical trial data, effectiveness of various KG embedding (KGE) methods for it, a novel inductive inference using KGE, and its use in generating recommendations for clinical trial design. We used publicly available data from clinicaltrials.gov for the study. Results show that our recommendations approach achieves relevance scores of 70%-83%, measured as the text similarity to actual clinical trial elements, and the most relevant recommendation can be found near the top of list. Our study also suggests potential improvement in training KGE using node semantics.

Knowledge graph completion is a task that revolves around filling in missing triples based on the information available in a knowledge graph. Among the current studies, text-based methods complete the task by utilizing textual descriptions of triples. However, this modeling approach may encounter limitations, particularly when the description fails to accurately and adequately express the intended meaning. To overcome these challenges, we propose the augmentation of data through two additional mechanisms. Firstly, we employ ChatGPT as an external knowledge base to generate coherent descriptions to bridge the semantic gap between the queries and answers. Secondly, we leverage inverse relations to create a symmetric graph, thereby creating extra labeling and providing supplementary information for link prediction. This approach offers additional insights into the relationships between entities. Through these efforts, we have observed significant improvements in knowledge graph completion, as these mechanisms enhance the richness and diversity of the available data, leading to more accurate results.

In this work, we present a web application named DBLPLink, which performs entity linking over the DBLP scholarly knowledge graph. DBLPLink uses text-to-text pre-trained language models, such as T5, to produce entity label spans from an input text question. Entity candidates are fetched from a database based on the labels, and an entity re-ranker sorts them based on entity embeddings, such as TransE, DistMult and ComplEx. The results are displayed so that users may compare and contrast the results between T5-small, T5-base and the different KG embeddings used. The demo can be accessed at https://ltdemos.informatik.uni-hamburg.de/dblplink/. Code and data shall be made available at https://github.com/uhh-lt/dblplink.

Bilinear based models are powerful and widely used approaches for Knowledge Graphs Completion (KGC). Although bilinear based models have achieved significant advances, these studies mainly concentrate on posterior properties (based on evidence, e.g. symmetry pattern) while neglecting the prior properties. In this paper, we find a prior property named "the law of identity" that cannot be captured by bilinear based models, which hinders them from comprehensively modeling the characteristics of KGs. To address this issue, we introduce a solution called Unit Ball Bilinear Model (UniBi). This model not only achieves theoretical superiority but also offers enhanced interpretability and performance by minimizing ineffective learning through minimal constraints. Experiments demonstrate that UniBi models the prior property and verify its interpretability and performance.