Recently, knowledge graph embeddings (KGEs) received significant attention, and several software libraries have been developed for training and evaluating KGEs. While each of them addresses specific needs, we re-designed and re-implemented PyKEEN, one of the first KGE libraries, in a community effort. PyKEEN 1.0 enables users to compose knowledge graph embedding models (KGEMs) based on a wide range of interaction models, training approaches, loss functions, and permits the explicit modeling of inverse relations. Besides, an automatic memory optimization has been realized in order to exploit the provided hardware optimally, and through the integration of Optuna extensive hyper-parameter optimization (HPO) functionalities are provided.
Knowledge Graphs (KG) are gaining increasing attention in both academia and industry. Despite their diverse benefits, recent research have identified social and cultural biases embedded in the representations learned from KGs. Such biases can have detrimental consequences on different population and minority groups as applications of KG begin to intersect and interact with social spheres. This paper aims at identifying and mitigating such biases in Knowledge Graph (KG) embeddings. As a first step, we explore popularity bias -- the relationship between node popularity and link prediction accuracy. In case of node2vec graph embeddings, we find that prediction accuracy of the embedding is negatively correlated with the degree of the node. However, in case of knowledge-graph embeddings (KGE), we observe an opposite trend. As a second step, we explore gender bias in KGE, and a careful examination of popular KGE algorithms suggest that sensitive attribute like the gender of a person can be predicted from the embedding. This implies that such biases in popular KGs is captured by the structural properties of the embedding. As a preliminary solution to debiasing KGs, we introduce a novel framework to filter out the sensitive attribute information from the KG embeddings, which we call FAN (Filtering Adversarial Network). We also suggest the applicability of FAN for debiasing other network embeddings which could be explored in future work.
Much of biomedical and healthcare data is encoded in discrete, symbolic form such as text and medical codes. There is a wealth of expert-curated biomedical domain knowledge stored in knowledge bases and ontologies, but the lack of reliable methods for learning knowledge representation has limited their usefulness in machine learning applications. While text-based representation learning has significantly improved in recent years through advances in natural language processing, attempts to learn biomedical concept embeddings so far have been lacking. A recent family of models called knowledge graph embeddings have shown promising results on general domain knowledge graphs, and we explore their capabilities in the biomedical domain. We train several state-of-the-art knowledge graph embedding models on the SNOMED-CT knowledge graph, provide a benchmark with comparison to existing methods and in-depth discussion on best practices, and make a case for the importance of leveraging the multi-relational nature of knowledge graphs for learning biomedical knowledge representation. The embeddings, code, and materials will be made available to the communitY.
Performing link prediction using knowledge graph embedding models has become a popular approach for knowledge graph completion. Such models employ a transformation function that maps nodes via edges into a vector space in order to measure the likelihood of the links. While mapping the individual nodes, the structure of subgraphs is also transformed. Most of the embedding models designed in Euclidean geometry usually support a single transformation type - often translation or rotation, which is suitable for learning on graphs with small differences in neighboring subgraphs. However, multi-relational knowledge graphs often include multiple sub-graph structures in a neighborhood (e.g. combinations of path and loop structures), which current embedding models do not capture well. To tackle this problem, we propose a novel KGE model (5*E) in projective geometry, which supports multiple simultaneous transformations - specifically inversion, reflection, translation, rotation, and homothety. The model has several favorable theoretical properties and subsumes the existing approaches. It outperforms them on the most widely used link prediction benchmarks
Industry~4.0 (I4.0) standards and standardization frameworks have been proposed with the goal of \emph{empowering interoperability} in smart factories. These standards enable the description and interaction of the main components, systems, and processes inside of a smart factory. Due to the growing number of frameworks and standards, there is an increasing need for approaches that automatically analyze the landscape of I4.0 standards. Standardization frameworks classify standards according to their functions into layers and dimensions. However, similar standards can be classified differently across the frameworks, producing, thus, interoperability conflicts among them. Semantic-based approaches that rely on ontologies and knowledge graphs, have been proposed to represent standards, known relations among them, as well as their classification according to existing frameworks. Albeit informative, the structured modeling of the I4.0 landscape only provides the foundations for detecting interoperability issues. Thus, graph-based analytical methods able to exploit knowledge encoded by these approaches, are required to uncover alignments among standards. We study the relatedness among standards and frameworks based on community analysis to discover knowledge that helps to cope with interoperability conflicts between standards. We use knowledge graph embeddings to automatically create these communities exploiting the meaning of the existing relationships. In particular, we focus on the identification of similar standards, i.e., communities of standards, and analyze their properties to detect unknown relations. We empirically evaluate our approach on a knowledge graph of I4.0 standards using the Trans$^*$ family of embedding models for knowledge graph entities. Our results are promising and suggest that relations among standards can be detected accurately.
Knowledge graph (KG) embeddings learn low-dimensional representations of entities and relations to predict missing facts. KGs often exhibit hierarchical and logical patterns which must be preserved in the embedding space. For hierarchical data, hyperbolic embedding methods have shown promise for high-fidelity and parsimonious representations. However, existing hyperbolic embedding methods do not account for the rich logical patterns in KGs. In this work, we introduce a class of hyperbolic KG embedding models that simultaneously capture hierarchical and logical patterns. Our approach combines hyperbolic reflections and rotations with attention to model complex relational patterns. Experimental results on standard KG benchmarks show that our method improves over previous Euclidean- and hyperbolic-based efforts by up to 6.1% in mean reciprocal rank (MRR) in low dimensions. Furthermore, we observe that different geometric transformations capture different types of relations while attention-based transformations generalize to multiple relations. In high dimensions, our approach yields new state-of-the-art MRRs of 49.6% on WN18RR and 57.7% on YAGO3-10.
Knowledge graph embeddings are now a widely adopted approach to knowledge representation in which entities and relationships are embedded in vector spaces. In this chapter, we introduce the reader to the concept of knowledge graph embeddings by explaining what they are, how they can be generated and how they can be evaluated. We summarize the state-of-the-art in this field by describing the approaches that have been introduced to represent knowledge in the vector space. In relation to knowledge representation, we consider the problem of explainability, and discuss models and methods for explaining predictions obtained via knowledge graph embeddings.
``Classical'' word embeddings, such as Word2Vec, have been shown to capture the semantics of words based on their distributional properties. However, their ability to represent the different meanings that a word may have is limited. Such approaches also do not explicitly encode relations between entities, as denoted by words. Embeddings of knowledge bases (KB) capture the explicit relations between entities denoted by words, but are not able to directly capture the syntagmatic properties of these words. To our knowledge, recent research have focused on representation learning that augment the strengths of one with the other. In this work, we begin exploring another approach using contextual and KB embeddings jointly at the same level and propose two tasks -- an entity typing and a relation typing task -- that evaluate the performance of contextual and KB embeddings. We also evaluated a concatenated model of contextual and KB embeddings with these two tasks, and obtain conclusive results on the first task. We hope our work may contribute as a basis for models and datasets that develop in the direction of this approach.
Interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDI) is one of the key tasks in public health and drug development. Recently, several knowledge graph embedding approaches have received increasing attention in the DDI domain due to their capability of projecting drugs and interactions into a low-dimensional feature space for predicting links and classifying triplets. However, existing methods only apply a uniformly random mode to construct negative samples. As a consequence, these samples are often too simplistic to train an effective model. In this paper, we propose a new knowledge graph embedding framework by introducing adversarial autoencoders (AAE) based on Wasserstein distances and Gumbel-Softmax relaxation for drug-drug interactions tasks. In our framework, the autoencoder is employed to generate high-quality negative samples and the hidden vector of the autoencoder is regarded as a plausible drug candidate. Afterwards, the discriminator learns the embeddings of drugs and interactions based on both positive and negative triplets. Meanwhile, in order to solve vanishing gradient problems on the discrete representation--an inherent flaw in traditional generative models--we utilize the Gumbel-Softmax relaxation and the Wasserstein distance to train the embedding model steadily. We empirically evaluate our method on two tasks, link prediction and DDI classification. The experimental results show that our framework can attain significant improvements and noticeably outperform competitive baselines.
Little is known about the trustworthiness of predictions made by knowledge graph embedding (KGE) models. In this paper we take initial steps toward this direction by investigating the calibration of KGE models, or the extent to which they output confidence scores that reflect the expected correctness of predicted knowledge graph triples. We first conduct an evaluation under the standard closed-world assumption (CWA), in which predicted triples not already in the knowledge graph are considered false, and show that existing calibration techniques are effective for KGE under this common but narrow assumption. Next, we introduce the more realistic but challenging open-world assumption (OWA), in which unobserved predictions are not considered true or false until ground-truth labels are obtained. Here, we show that existing calibration techniques are much less effective under the OWA than the CWA, and provide explanations for this discrepancy. Finally, to motivate the utility of calibration for KGE from a practitioner's perspective, we conduct a unique case study of human-AI collaboration, showing that calibrated predictions can improve human performance in a knowledge graph completion task.
In this paper, we present KGvec2go, a Web API for accessing and consuming graph embeddings in a light-weight fashion in downstream applications. Currently, we serve pre-trained embeddings for four knowledge graphs. We introduce the service and its usage, and we show further that the trained models have semantic value by evaluating them on multiple semantic benchmarks. The evaluation also reveals that the combination of multiple models can lead to a better outcome than the best individual model.
The autonomous driving (AD) industry is exploring the use of knowledge graphs (KGs) to manage the vast amount of heterogeneous data generated from vehicular sensors. The various types of equipped sensors include video, LIDAR and RADAR. Scene understanding is an important topic in AD which requires consideration of various aspects of a scene, such as detected objects, events, time and location. Recent work on knowledge graph embeddings (KGEs) - an approach that facilitates neuro-symbolic fusion - has shown to improve the predictive performance of machine learning models. With the expectation that neuro-symbolic fusion through KGEs will improve scene understanding, this research explores the generation and evaluation of KGEs for autonomous driving data. We also present an investigation of the relationship between the level of informational detail in a KG and the quality of its derivative embeddings. By systematically evaluating KGEs along four dimensions -- i.e. quality metrics, KG informational detail, algorithms, and datasets -- we show that (1) higher levels of informational detail in KGs lead to higher quality embeddings, (2) type and relation semantics are better captured by the semantic transitional distance-based TransE algorithm, and (3) some metrics, such as coherence measure, may not be suitable for intrinsically evaluating KGEs in this domain. Additionally, we also present an (early) investigation of the usefulness of KGEs for two use-cases in the AD domain.
Entity linking - connecting entity mentions in a natural language utterance to knowledge graph (KG) entities is a crucial step for question answering over KGs. It is often based on measuring the string similarity between the entity label and its mention in the question. The relation referred to in the question can help to disambiguate between entities with the same label. This can be misleading if an incorrect relation has been identified in the relation linking step. However, an incorrect relation may still be semantically similar to the relation in which the correct entity forms a triple within the KG; which could be captured by the similarity of their KG embeddings. Based on this idea, we propose the first end-to-end neural network approach that employs KG as well as word embeddings to perform joint relation and entity classification of simple questions while implicitly performing entity disambiguation with the help of a novel gating mechanism. An empirical evaluation shows that the proposed approach achieves a performance comparable to state-of-the-art entity linking while requiring less post-processing.
There is an emerging trend of embedding knowledge graphs (KGs) in continuous vector spaces in order to use those for machine learning tasks. Recently, many knowledge graph embedding (KGE) models have been proposed that learn low dimensional representations while trying to maintain the structural properties of the KGs such as the similarity of nodes depending on their edges to other nodes. KGEs can be used to address tasks within KGs such as the prediction of novel links and the disambiguation of entities. They can also be used for downstream tasks like question answering and fact-checking. Overall, these tasks are relevant for the semantic web community. Despite their popularity, the reproducibility of KGE experiments and the transferability of proposed KGE models to research fields outside the machine learning community can be a major challenge. Therefore, we present the KEEN Universe, an ecosystem for knowledge graph embeddings that we have developed with a strong focus on reproducibility and transferability. The KEEN Universe currently consists of the Python packages PyKEEN (Python KnowlEdge EmbeddiNgs), BioKEEN (Biological KnowlEdge EmbeddiNgs), and the KEEN Model Zoo for sharing trained KGE models with the community.
Knowledge graph embedding methods learn continuous vector representations for entities in knowledge graphs and have been used successfully in a large number of applications. We present a novel and scalable paradigm for the computation of knowledge graph embeddings, which we dub PYKE . Our approach combines a physical model based on Hooke's law and its inverse with ideas from simulated annealing to compute embeddings for knowledge graphs efficiently. We prove that PYKE achieves a linear space complexity. While the time complexity for the initialization of our approach is quadratic, the time complexity of each of its iterations is linear in the size of the input knowledge graph. Hence, PYKE's overall runtime is close to linear. Consequently, our approach easily scales up to knowledge graphs containing millions of triples. We evaluate our approach against six state-of-the-art embedding approaches on the DrugBank and DBpedia datasets in two series of experiments. The first series shows that the cluster purity achieved by PYKE is up to 26% (absolute) better than that of the state of art. In addition, PYKE is more than 22 times faster than existing embedding solutions in the best case. The results of our second series of experiments show that PYKE is up to 23% (absolute) better than the state of art on the task of type prediction while maintaining its superior scalability. Our implementation and results are open-source and are available at http://github.com/dice-group/PYKE.
It has recently been shown that word embeddings encode social biases, with a harmful impact on downstream tasks. However, to this point there has been no similar work done in the field of graph embeddings. We present the first study on social bias in knowledge graph embeddings, and propose a new metric suitable for measuring such bias. We conduct experiments on Wikidata and Freebase, and show that, as with word embeddings, harmful social biases related to professions are encoded in the embeddings with respect to gender, religion, ethnicity and nationality. For example, graph embeddings encode the information that men are more likely to be bankers, and women more likely to be homekeepers. As graph embeddings become increasingly utilized, we suggest that it is important the existence of such biases are understood and steps taken to mitigate their impact.
Knowledge graph embedding, which aims to represent entities and relations as low dimensional vectors (or matrices, tensors, etc.), has been shown to be a powerful technique for predicting missing links in knowledge graphs. Existing knowledge graph embedding models mainly focus on modeling relation patterns such as symmetry/antisymmetry, inversion, and composition. However, many existing approaches fail to model semantic hierarchies, which are common in real-world applications. To address this challenge, we propose a novel knowledge graph embedding model -- namely, Hierarchy-Aware Knowledge Graph Embedding (HAKE) -- which maps entities into the polar coordinate system. HAKE is inspired by the fact that concentric circles in the polar coordinate system can naturally reflect the hierarchy. Specifically, the radial coordinate aims to model entities at different levels of the hierarchy, and entities with smaller radii are expected to be at higher levels; the angular coordinate aims to distinguish entities at the same level of the hierarchy, and these entities are expected to have roughly the same radii but different angles. Experiments demonstrate that HAKE can effectively model the semantic hierarchies in knowledge graphs, and significantly outperforms existing state-of-the-art methods on benchmark datasets for the link prediction task.
Pre-trained language representation models (PLMs) cannot well capture factual knowledge from text. In contrast, knowledge embedding (KE) methods can effectively represent the relational facts in knowledge graphs (KGs) with informative entity embeddings, but conventional KE models cannot take full advantage of the abundant textual information. In this paper, we propose a unified model for Knowledge Embedding and Pre-trained LanguagE Representation (KEPLER), which can not only better integrate factual knowledge into PLMs but also produce effective text-enhanced KE with the strong PLMs. In KEPLER, we encode textual entity descriptions with a PLM as their embeddings, and then jointly optimize the KE and language modeling objectives. Experimental results show that KEPLER achieves state-of-the-art performances on various NLP tasks, and also works remarkably well as an inductive KE model on KG link prediction. Furthermore, for pre-training and evaluating KEPLER, we construct Wikidata5M, a large-scale KG dataset with aligned entity descriptions, and benchmark state-of-the-art KE methods on it. It shall serve as a new KE benchmark and facilitate the research on large KG, inductive KE, and KG with text. The source code can be obtained from https://github.com/THU-KEG/KEPLER.
Most existing knowledge graphs suffer from incompleteness, which can be alleviated by inferring missing links based on known facts. One popular way to accomplish this is to generate low-dimensional embeddings of entities and relations, and use these to make inferences. ConvE, a recently proposed approach, applies convolutional filters on 2D reshapings of entity and relation embeddings in order to capture rich interactions between their components. However, the number of interactions that ConvE can capture is limited. In this paper, we analyze how increasing the number of these interactions affects link prediction performance, and utilize our observations to propose InteractE. InteractE is based on three key ideas -- feature permutation, a novel feature reshaping, and circular convolution. Through extensive experiments, we find that InteractE outperforms state-of-the-art convolutional link prediction baselines on FB15k-237. Further, InteractE achieves an MRR score that is 9%, 7.5%, and 23% better than ConvE on the FB15k-237, WN18RR and YAGO3-10 datasets respectively. The results validate our central hypothesis -- that increasing feature interaction is beneficial to link prediction performance. We make the source code of InteractE available to encourage reproducible research.
Knowledge Graphs (KGs) are composed of structured information about a particular domain in the form of entities and relations. In addition to the structured information KGs help in facilitating interconnectivity and interoperability between different resources represented in the Linked Data Cloud. KGs have been used in a variety of applications such as entity linking, question answering, recommender systems, etc. However, KG applications suffer from high computational and storage costs. Hence, there arises the necessity for a representation able to map the high dimensional KGs into low dimensional spaces, i.e., embedding space, preserving structural as well as relational information. This paper conducts a survey of KG embedding models which not only consider the structured information contained in the form of entities and relations in a KG but also the unstructured information represented as literals such as text, numerical values, images, etc. Along with a theoretical analysis and comparison of the methods proposed so far for generating KG embeddings with literals, an empirical evaluation of the different methods under identical settings has been performed for the general task of link prediction.