A fundamental task for knowledge graphs (KGs) is knowledge graph completion (KGC). It aims to predict unseen edges by learning representations for all the entities and relations in a KG. A common concern when learning representations on traditional graphs is degree bias. It can affect graph algorithms by learning poor representations for lower-degree nodes, often leading to low performance on such nodes. However, there has been limited research on whether there exists degree bias for embedding-based KGC and how such bias affects the performance of KGC. In this paper, we validate the existence of degree bias in embedding-based KGC and identify the key factor to degree bias. We then introduce a novel data augmentation method, KG-Mixup, to generate synthetic triples to mitigate such bias. Extensive experiments have demonstrated that our method can improve various embedding-based KGC methods and outperform other methods tackling the bias problem on multiple benchmark datasets.

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Entity alignment (EA) is a fundamental data integration task that identifies equivalent entities between different knowledge graphs (KGs). Temporal Knowledge graphs (TKGs) extend traditional knowledge graphs by introducing timestamps, which have received increasing attention. State-of-the-art time-aware EA studies have suggested that the temporal information of TKGs facilitates the performance of EA. However, existing studies have not thoroughly exploited the advantages of temporal information in TKGs. Also, they perform EA by pre-aligning entity pairs, which can be labor-intensive and thus inefficient. In this paper, we present DualMatch which effectively fuses the relational and temporal information for EA. DualMatch transfers EA on TKGs into a weighted graph matching problem. More specifically, DualMatch is equipped with an unsupervised method, which achieves EA without necessitating seed alignment. DualMatch has two steps: (i) encoding temporal and relational information into embeddings separately using a novel label-free encoder, Dual-Encoder; and (ii) fusing both information and transforming it into alignment using a novel graph-matching-based decoder, GM-Decoder. DualMatch is able to perform EA on TKGs with or without supervision, due to its capability of effectively capturing temporal information. Extensive experiments on three real-world TKG datasets offer the insight that DualMatch outperforms the state-of-the-art methods in terms of H@1 by 2.4% - 10.7% and MRR by 1.7% - 7.6%, respectively.

Learning hyperbolic embeddings for knowledge graph (KG) has gained increasing attention due to its superiority in capturing hierarchies. However, some important operations in hyperbolic space still lack good definitions, making existing methods unable to fully leverage the merits of hyperbolic space. Specifically, they suffer from two main limitations: 1) existing Graph Convolutional Network (GCN) methods in hyperbolic space rely on tangent space approximation, which would incur approximation error in representation learning, and 2) due to the lack of inner product operation definition in hyperbolic space, existing methods can only measure the plausibility of facts (links) with hyperbolic distance, which is difficult to capture complex data patterns. In this work, we contribute: 1) a Full Poincar\'{e} Multi-relational GCN that achieves graph information propagation in hyperbolic space without requiring any approximation, and 2) a hyperbolic generalization of Euclidean inner product that is beneficial to capture both hierarchical and complex patterns. On this basis, we further develop a \textbf{F}ully and \textbf{F}lexible \textbf{H}yperbolic \textbf{R}epresentation framework (\textbf{FFHR}) that is able to transfer recent Euclidean-based advances to hyperbolic space. We demonstrate it by instantiating FFHR with four representative KGC methods. Extensive experiments on benchmark datasets validate the superiority of our FFHRs over their Euclidean counterparts as well as state-of-the-art hyperbolic embedding methods.

Multimodal learning has been a field of increasing interest, aiming to combine various modalities in a single joint representation. Especially in the area of visiolinguistic (VL) learning multiple models and techniques have been developed, targeting a variety of tasks that involve images and text. VL models have reached unprecedented performances by extending the idea of Transformers, so that both modalities can learn from each other. Massive pre-training procedures enable VL models to acquire a certain level of real-world understanding, although many gaps can be identified: the limited comprehension of commonsense, factual, temporal and other everyday knowledge aspects questions the extendability of VL tasks. Knowledge graphs and other knowledge sources can fill those gaps by explicitly providing missing information, unlocking novel capabilities of VL models. In the same time, knowledge graphs enhance explainability, fairness and validity of decision making, issues of outermost importance for such complex implementations. The current survey aims to unify the fields of VL representation learning and knowledge graphs, and provides a taxonomy and analysis of knowledge-enhanced VL models.

Knowledge graph embedding (KGE), which maps entities and relations in a knowledge graph into continuous vector spaces, has achieved great success in predicting missing links in knowledge graphs. However, knowledge graphs often contain incomplete triples that are difficult to inductively infer by KGEs. To address this challenge, we resort to analogical inference and propose a novel and general self-supervised framework AnKGE to enhance KGE models with analogical inference capability. We propose an analogical object retriever that retrieves appropriate analogical objects from entity-level, relation-level, and triple-level. And in AnKGE, we train an analogy function for each level of analogical inference with the original element embedding from a well-trained KGE model as input, which outputs the analogical object embedding. In order to combine inductive inference capability from the original KGE model and analogical inference capability enhanced by AnKGE, we interpolate the analogy score with the base model score and introduce the adaptive weights in the score function for prediction. Through extensive experiments on FB15k-237 and WN18RR datasets, we show that AnKGE achieves competitive results on link prediction task and well performs analogical inference.

We propose an entity-agnostic representation learning method for handling the problem of inefficient parameter storage costs brought by embedding knowledge graphs. Conventional knowledge graph embedding methods map elements in a knowledge graph, including entities and relations, into continuous vector spaces by assigning them one or multiple specific embeddings (i.e., vector representations). Thus the number of embedding parameters increases linearly as the growth of knowledge graphs. In our proposed model, Entity-Agnostic Representation Learning (EARL), we only learn the embeddings for a small set of entities and refer to them as reserved entities. To obtain the embeddings for the full set of entities, we encode their distinguishable information from their connected relations, k-nearest reserved entities, and multi-hop neighbors. We learn universal and entity-agnostic encoders for transforming distinguishable information into entity embeddings. This approach allows our proposed EARL to have a static, efficient, and lower parameter count than conventional knowledge graph embedding methods. Experimental results show that EARL uses fewer parameters and performs better on link prediction tasks than baselines, reflecting its parameter efficiency.

Developing personalized diagnostic strategies and targeted treatments requires a deep understanding of disease biology and the ability to dissect the relationship between molecular and genetic factors and their phenotypic consequences. However, such knowledge is fragmented across publications, non-standardized repositories, and evolving ontologies describing various scales of biological organization between genotypes and clinical phenotypes. Here, we present PrimeKG, a multimodal knowledge graph for precision medicine analyses. PrimeKG integrates 20 high-quality resources to describe 17,080 diseases with 4,050,249 relationships representing ten major biological scales, including disease-associated protein perturbations, biological processes and pathways, anatomical and phenotypic scales, and the entire range of approved drugs with their therapeutic action, considerably expanding previous efforts in disease-rooted knowledge graphs. PrimeKG contains an abundance of ‘indications’, ‘contradictions’, and ‘off-label use’ drug-disease edges that lack in other knowledge graphs and can support AI analyses of how drugs affect disease-associated networks. We supplement PrimeKG’s graph structure with language descriptions of clinical guidelines to enable multimodal analyses and provide instructions for continual updates of PrimeKG as new data become available.

Reasoning over Temporal Knowledge Graphs (TKGs) aims to predict future facts based on given history. One of the key challenges for prediction is to learn the evolution of facts. Most existing works focus on exploring evolutionary information in history to obtain effective temporal embeddings for entities and relations, but they ignore the variation in evolution patterns of facts, which makes them struggle to adapt to future data with different evolution patterns. Moreover, new entities continue to emerge along with the evolution of facts over time. Since existing models highly rely on historical information to learn embeddings for entities, they perform poorly on such entities with little historical information. To tackle these issues, we propose a novel Temporal Meta-learning framework for TKG reasoning, MetaTKG for brevity. Specifically, our method regards TKG prediction as many temporal meta-tasks, and utilizes the designed Temporal Meta-learner to learn evolutionary meta-knowledge from these meta-tasks. The proposed method aims to guide the backbones to learn to adapt quickly to future data and deal with entities with little historical information by the learned meta-knowledge. Specially, in temporal meta-learner, we design a Gating Integration module to adaptively establish temporal correlations between meta-tasks. Extensive experiments on four widely-used datasets and three backbones demonstrate that our method can greatly improve the performance.

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of knowledge graphs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of knowledge graphs. Features include a simple, modular extract-transform-load (ETL) pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate knowledge graphs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph machine learning, including node embeddings and training of models for link prediction and node classification.