Knowledge graph (KG) embeddings have shown great power in learning representations of entities and relations for link prediction tasks. Previous work usually embeds KGs into a single geometric space such as Euclidean space (zero curved), hyperbolic space (negatively curved) or hyperspherical space (positively curved) to maintain their specific geometric structures (e.g., chain, hierarchy and ring structures). However, the topological structure of KGs appears to be complicated, since it may contain multiple types of geometric structures simultaneously. Therefore, embedding KGs in a single space, no matter the Euclidean space, hyperbolic space or hyperspheric space, cannot capture the complex structures of KGs accurately. To overcome this challenge, we propose Geometry Interaction knowledge graph Embeddings (GIE), which learns spatial structures interactively between the Euclidean, hyperbolic and hyperspherical spaces. Theoretically, our proposed GIE can capture a richer set of relational information, model key inference patterns, and enable expressive semantic matching across entities. Experimental results on three well-established knowledge graph completion benchmarks show that our GIE achieves the state-of-the-art performance with fewer parameters.
Knowledge graph (KG) link prediction is a fundamental task in artificial intelligence, with applications in natural language processing, information retrieval, and biomedicine. Recently, promising results have been achieved by leveraging cross-modal information in KGs, using ensembles that combine knowledge graph embeddings (KGEs) and contextual language models (LMs). However, existing ensembles are either (1) not consistently effective in terms of ranking accuracy gains or (2) impractically inefficient on larger datasets due to the combinatorial explosion problem of pairwise ranking with deep language models. In this paper, we propose a novel tiered ranking architecture CascadER to maintain the ranking accuracy of full ensembling while improving efficiency considerably. CascadER uses LMs to rerank the outputs of more efficient base KGEs, relying on an adaptive subset selection scheme aimed at invoking the LMs minimally while maximizing accuracy gain over the KGE. Extensive experiments demonstrate that CascadER improves MRR by up to 9 points over KGE baselines, setting new state-of-the-art performance on four benchmarks while improving efficiency by one or more orders of magnitude over competitive cross-modal baselines. Our empirical analyses reveal that diversity of models across modalities and preservation of individual models' confidence signals help explain the effectiveness of CascadER, and suggest promising directions for cross-modal cascaded architectures. Code and pretrained models are available at https://github.com/tsafavi/cascader.
Knowledge graph embedding research has mainly focused on learning continuous representations of entities and relations tailored towards the link prediction problem. Recent results indicate an ever increasing predictive ability of current approaches on benchmark datasets. However, this effectiveness often comes with the cost of over-parameterization and increased computationally complexity. The former induces extensive hyperparameter optimization to mitigate malicious overfitting. The latter magnifies the importance of winning the hardware lottery. Here, we investigate a remedy for the first problem. We propose a technique based on Kronecker decomposition to reduce the number of parameters in a knowledge graph embedding model, while retaining its expressiveness. Through Kronecker decomposition, large embedding matrices are split into smaller embedding matrices during the training process. Hence, embeddings of knowledge graphs are not plainly retrieved but reconstructed on the fly. The decomposition ensures that elementwise interactions between three embedding vectors are extended with interactions within each embedding vector. This implicitly reduces redundancy in embedding vectors and encourages feature reuse. To quantify the impact of applying Kronecker decomposition on embedding matrices, we conduct a series of experiments on benchmark datasets. Our experiments suggest that applying Kronecker decomposition on embedding matrices leads to an improved parameter efficiency on all benchmark datasets. Moreover, empirical evidence suggests that reconstructed embeddings entail robustness against noise in the input knowledge graph. To foster reproducible research, we provide an open-source implementation of our approach, including training and evaluation scripts as well as pre-trained models in our knowledge graph embedding framework (https://github.com/dice-group/dice-embeddings).
Ontology matching is a core task when creating interoperable and linked open datasets. In this paper, we explore a novel structure-based mapping approach which is based on knowledge graph embeddings: The ontologies to be matched are embedded, and an approach known as absolute orientation is used to align the two embedding spaces. Next to the approach, the paper presents a first, preliminary evaluation using synthetic and real-world datasets. We find in experiments with synthetic data, that the approach works very well on similarly structured graphs; it handles alignment noise better than size and structural differences in the ontologies.
Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.
Scholarly data is growing continuously containing information about the articles from a plethora of venues including conferences, journals, etc. Many initiatives have been taken to make scholarly data available as Knowledge Graphs (KGs). These efforts to standardize these data and make them accessible have also led to many challenges such as exploration of scholarly articles, ambiguous authors, etc. This study more specifically targets the problem of Author Name Disambiguation (AND) on Scholarly KGs and presents a novel framework, Literally Author Name Disambiguation (LAND), which utilizes Knowledge Graph Embeddings (KGEs) using multimodal literal information generated from these KGs. This framework is based on three components: 1) Multimodal KGEs, 2) A blocking procedure, and finally, 3) Hierarchical Agglomerative Clustering. Extensive experiments have been conducted on two newly created KGs: (i) KG containing information from Scientometrics Journal from 1978 onwards (OC-782K), and (ii) a KG extracted from a well-known benchmark for AND provided by AMiner (AMiner-534K). The results show that our proposed architecture outperforms our baselines of 8-14% in terms of the F1 score and shows competitive performances on a challenging benchmark such as AMiner. The code and the datasets are publicly available through Github: https://github.com/sntcristian/and-kge and Zenodo:https://doi.org/10.5281/zenodo.6309855 respectively.
Previous knowledge graph embedding approaches usually map entities to representations and utilize score functions to predict the target entities, yet they typically struggle to reason rare or emerging unseen entities. In this paper, we propose kNN-KGE, a new knowledge graph embedding approach with pre-trained language models, by linearly interpolating its entity distribution with k-nearest neighbors. We compute the nearest neighbors based on the distance in the entity embedding space from the knowledge store. Our approach can allow rare or emerging entities to be memorized explicitly rather than implicitly in model parameters. Experimental results demonstrate that our approach can improve inductive and transductive link prediction results and yield better performance for low-resource settings with only a few triples, which might be easier to reason via explicit memory. Code is available at https://github.com/zjunlp/KNN-KG.
A few models have tried to tackle the link prediction problem, also known as knowledge graph completion, by embedding knowledge graphs in comparably lower dimensions. However, the state-of-the-art results are attained at the cost of considerably increasing the dimensionality of embeddings which causes scalability issues in the case of huge knowledge bases. Transformers have been successfully used recently as powerful encoders for knowledge graphs, but available models still have scalability issues. To address this limitation, we introduce a Transformer-based model to gain expressive low-dimensional embeddings. We utilize a large number of self-attention heads as the key to applying query-dependent projections to capture mutual information between entities and relations. Empirical results on WN18RR and FB15k-237 as standard link prediction benchmarks demonstrate that our model has favorably comparable performance with the current state-of-the-art models. Notably, we yield our promising results with a significant reduction of 66.9% in the dimensionality of embeddings compared to the five best recent state-of-the-art competitors on average.
Adoption of recently developed methods from machine learning has given rise to creation of drug-discovery knowledge graphs (KG) that utilize the interconnected nature of the domain. Graph-based modelling of the data, combined with KG embedding (KGE) methods, are promising as they provide a more intuitive representation and are suitable for inference tasks such as predicting missing links. One common application is to produce ranked lists of genes for a given disease, where the rank is based on the perceived likelihood of association between the gene and the disease. It is thus critical that these predictions are not only pertinent but also biologically meaningful. However, KGs can be biased either directly due to the underlying data sources that are integrated or due to modeling choices in the construction of the graph, one consequence of which is that certain entities can get topologically overrepresented. We demonstrate the effect of these inherent structural imbalances, resulting in densely-connected entities being highly ranked no matter the context. We provide support for this observation across different datasets, models as well as predictive tasks. Further, we present various graph perturbation experiments which yield more support to the observation that KGE models can be more influenced by the frequency of entities rather than any biological information encoded within the relations. Our results highlight the importance of data modeling choices, and emphasizes the need for practitioners to be mindful of these issues when interpreting model outputs and during KG composition.
Learning the embeddings of knowledge graphs (KG) is vital in artificial intelligence, and can benefit various downstream applications, such as recommendation and question answering. In recent years, many research efforts have been proposed for knowledge graph embedding (KGE). However, most previous KGE methods ignore the semantic similarity between the related entities and entity-relation couples in different triples since they separately optimize each triple with the scoring function. To address this problem, we propose a simple yet efficient contrastive learning framework for tensor decomposition based (TDB) KGE, which can shorten the semantic distance of the related entities and entity-relation couples in different triples and thus improve the performance of KGE. We evaluate our proposed method on three standard KGE datasets: WN18RR, FB15k-237 and YAGO3-10. Our method can yield some new state-of-the-art results, achieving 51.2% MRR, 46.8% Hits@1 on the WN18RR dataset, 37.8% MRR, 28.6% Hits@1 on FB15k-237 dataset, and 59.1% MRR, 51.8% Hits@1 on the YAGO3-10 dataset.
We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on this prediction task. We show that using knowledge graph embeddings can increase the accuracy of effect prediction with neural networks. Furthermore, we have implemented a fine-tuning architecture that adapts the knowledge graph embeddings to the effect prediction task and leads to better performance. Finally, we evaluate certain characteristics of the knowledge graph embedding models to shed light on the individual model performance.
Recent advances in neural networks have solved common graph problems such as link prediction, node classification, node clustering, node recommendation by developing embeddings of entities and relations into vector spaces. Graph embeddings encode the structural information present in a graph. The encoded embeddings then can be used to predict the missing links in a graph. However, obtaining the optimal embeddings for a graph can be a computationally challenging task specially in an embedded system. Two techniques which we focus on in this work are 1) node embeddings from random walk based methods and 2) knowledge graph embeddings. Random walk based embeddings are computationally inexpensive to obtain but are sub-optimal whereas knowledge graph embeddings perform better but are computationally expensive. In this work, we investigate a transformation model which converts node embeddings obtained from random walk based methods to embeddings obtained from knowledge graph methods directly without an increase in the computational cost. Extensive experimentation shows that the proposed transformation model can be used for solving link prediction in real-time.
We study the problem of generating data poisoning attacks against Knowledge Graph Embedding (KGE) models for the task of link prediction in knowledge graphs. To poison KGE models, we propose to exploit their inductive abilities which are captured through the relationship patterns like symmetry, inversion and composition in the knowledge graph. Specifically, to degrade the model's prediction confidence on target facts, we propose to improve the model's prediction confidence on a set of decoy facts. Thus, we craft adversarial additions that can improve the model's prediction confidence on decoy facts through different inference patterns. Our experiments demonstrate that the proposed poisoning attacks outperform state-of-art baselines on four KGE models for two publicly available datasets. We also find that the symmetry pattern based attacks generalize across all model-dataset combinations which indicates the sensitivity of KGE models to this pattern.
Despite the widespread use of Knowledge Graph Embeddings (KGE), little is known about the security vulnerabilities that might disrupt their intended behaviour. We study data poisoning attacks against KGE models for link prediction. These attacks craft adversarial additions or deletions at training time to cause model failure at test time. To select adversarial deletions, we propose to use the model-agnostic instance attribution methods from Interpretable Machine Learning, which identify the training instances that are most influential to a neural model's predictions on test instances. We use these influential triples as adversarial deletions. We further propose a heuristic method to replace one of the two entities in each influential triple to generate adversarial additions. Our experiments show that the proposed strategies outperform the state-of-art data poisoning attacks on KGE models and improve the MRR degradation due to the attacks by up to 62% over the baselines.
Learning good representations on multi-relational graphs is essential to knowledge base completion (KBC). In this paper, we propose a new self-supervised training objective for multi-relational graph representation learning, via simply incorporating relation prediction into the commonly used 1vsAll objective. The new training objective contains not only terms for predicting the subject and object of a given triple, but also a term for predicting the relation type. We analyse how this new objective impacts multi-relational learning in KBC: experiments on a variety of datasets and models show that relation prediction can significantly improve entity ranking, the most widely used evaluation task for KBC, yielding a 6.1% increase in MRR and 9.9% increase in Hits@1 on FB15k-237 as well as a 3.1% increase in MRR and 3.4% in Hits@1 on Aristo-v4. Moreover, we observe that the proposed objective is especially effective on highly multi-relational datasets, i.e. datasets with a large number of predicates, and generates better representations when larger embedding sizes are used.
Knowledge graph embeddings (KGEs) compactly encode multi-relational knowledge graphs (KGs). Existing KGE models rely on geometric operations to model relational patterns. Euclidean (circular) rotation is useful for modeling patterns such as symmetry, but cannot represent hierarchical semantics. In contrast, hyperbolic models are effective at modeling hierarchical relations, but do not perform as well on patterns on which circular rotation excels. It is crucial for KGE models to unify multiple geometric transformations so as to fully cover the multifarious relations in KGs. To do so, we propose BiQUE, a novel model that employs biquaternions to integrate multiple geometric transformations, viz., scaling, translation, Euclidean rotation, and hyperbolic rotation. BiQUE makes the best trade-offs among geometric operators during training, picking the best one (or their best combination) for each relation. Experiments on five datasets show BiQUE's effectiveness.
With the recent surge in social applications relying on knowledge graphs, the need for techniques to ensure fairness in KG based methods is becoming increasingly evident. Previous works have demonstrated that KGs are prone to various social biases, and have proposed multiple methods for debiasing them. However, in such studies, the focus has been on debiasing techniques, while the relations to be debiased are specified manually by the user. As manual specification is itself susceptible to human cognitive bias, there is a need for a system capable of quantifying and exposing biases, that can support more informed decisions on what to debias. To address this gap in the literature, we describe a framework for identifying biases present in knowledge graph embeddings, based on numerical bias metrics. We illustrate the framework with three different bias measures on the task of profession prediction, and it can be flexibly extended to further bias definitions and applications. The relations flagged as biased can then be handed to decision makers for judgement upon subsequent debiasing.
Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug discovery domain, KGs can be employed as part of a process which can result in lab-based experiments being performed, or impact on other decisions, incurring significant time and financial costs and most importantly, ultimately influencing patient healthcare. For KGE models to have impact in this domain, a better understanding of not only of performance, but also the various factors which determine it, is required. In this study we investigate, over the course of many thousands of experiments, the predictive performance of five KGE models on two public drug discovery-oriented KGs. Our goal is not to focus on the best overall model or configuration, instead we take a deeper look at how performance can be affected by changes in the training setup, choice of hyperparameters, model parameter initialisation seed and different splits of the datasets. Our results highlight that these factors have significant impact on performance and can even affect the ranking of models. Indeed these factors should be reported along with model architectures to ensure complete reproducibility and fair comparisons of future work, and we argue this is critical for the acceptance of use, and impact of KGEs in a biomedical setting.
Knowledge Graph Embeddings (KGEs) have been intensively explored in recent years due to their promise for a wide range of applications. However, existing studies focus on improving the final model performance without acknowledging the computational cost of the proposed approaches, in terms of execution time and environmental impact. This paper proposes a simple yet effective KGE framework which can reduce the training time and carbon footprint by orders of magnitudes compared with state-of-the-art approaches, while producing competitive performance. We highlight three technical innovations: full batch learning via relational matrices, closed-form Orthogonal Procrustes Analysis for KGEs, and non-negative-sampling training. In addition, as the first KGE method whose entity embeddings also store full relation information, our trained models encode rich semantics and are highly interpretable. Comprehensive experiments and ablation studies involving 13 strong baselines and two standard datasets verify the effectiveness and efficiency of our algorithm.
Parameter servers (PSs) facilitate the implementation of distributed training for large machine learning tasks. In this paper, we argue that existing PSs are inefficient for tasks that exhibit non-uniform parameter access; their performance may even fall behind that of single node baselines. We identify two major sources of such non-uniform access: skew and sampling. Existing PSs are ill-suited for managing skew because they uniformly apply the same parameter management technique to all parameters. They are inefficient for sampling because the PS is oblivious to the associated randomized accesses and cannot exploit locality. To overcome these performance limitations, we introduce NuPS, a novel PS architecture that (i) integrates multiple management techniques and employs a suitable technique for each parameter and (ii) supports sampling directly via suitable sampling primitives and sampling schemes that allow for a controlled quality--efficiency trade-off. In our experimental study, NuPS outperformed existing PSs by up to one order of magnitude and provided up to linear scalability across multiple machine learning tasks.