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.
Computing latent representations for graph-structured data is an ubiquitous learning task in many industrial and academic applications ranging from molecule synthetization to social network analysis and recommender systems. Knowledge graphs are among the most popular and widely used data representations related to the Semantic Web. Next to structuring factual knowledge in a machine-readable format, knowledge graphs serve as the backbone of many artificial intelligence applications and allow the ingestion of context information into various learning algorithms. Graph neural networks attempt to encode graph structures in low-dimensional vector spaces via a message passing heuristic between neighboring nodes. Over the recent years, a multitude of different graph neural network architectures demonstrated ground-breaking performances in many learning tasks. In this work, we propose a strategy to map deep graph learning architectures for knowledge graph reasoning to neuromorphic architectures. Based on the insight that randomly initialized and untrained (i.e., frozen) graph neural networks are able to preserve local graph structures, we compose a frozen neural network with shallow knowledge graph embedding models. We experimentally show that already on conventional computing hardware, this leads to a significant speedup and memory reduction while maintaining a competitive performance level. Moreover, we extend the frozen architecture to spiking neural networks, introducing a novel, event-based and highly sparse knowledge graph embedding algorithm that is suitable for implementation in neuromorphic hardware.
In the search for knowledge graph embeddings that could capture ontological knowledge, geometric models of existential rules have been recently introduced. It has been shown that convex geometric regions capture the so-called quasi-chained rules. Attributed description logics (DL) have been defined to bridge the gap between DL languages and knowledge graphs, whose facts often come with various kinds of annotations that may need to be taken into account for reasoning. In particular, temporally attributed DLs are enriched by specific attributes whose semantics allows for some temporal reasoning. Considering that geometric models and (temporally) attributed DLs are promising tools designed for knowledge graphs, this paper investigates their compatibility, focusing on the attributed version of a Horn dialect of the DL-Lite family. We first adapt the definition of geometric models to attributed DLs and show that every satisfiable ontology has a convex geometric model. Our second contribution is a study of the impact of temporal attributes. We show that a temporally attributed DL may not have a convex geometric model in general but we can recover geometric satisfiability by imposing some restrictions on the use of the temporal attributes.
This paper presents the participation of the MiniTrue team in the FinSim-3 shared task on learning semantic similarities for the financial domain in English language. Our approach combines contextual embeddings learned by transformer-based language models with network structures embeddings extracted on external knowledge sources, to create more meaningful representations of financial domain entities and terms. For this, two BERT based language models and a knowledge graph embedding model are used. Besides, we propose a voting function to joint three basic models for the final inference. Experimental results show that the model with the knowledge graph embeddings has achieved a superior result than these models with only contextual embeddings. Nevertheless, we also observe that our voting function brings an extra benefit to the final system.
Knowledge Graph (KG) completion has been excessively studied with a massive number of models proposed for the Link Prediction (LP) task. The main limitation of such models is their insensitivity to time. Indeed, the temporal aspect of stored facts is often ignored. To this end, more and more works consider time as a parameter to complete KGs. In this paper, we first demonstrate that, by simply increasing the number of negative samples, the recent AttH model can achieve competitive or even better performance than the state-of-the-art on Temporal KGs (TKGs), albeit its nontemporality. We further propose Hercules, a time-aware extension of AttH model, which defines the curvature of a Riemannian manifold as the product of both relation and time. Our experiments show that both Hercules and AttH achieve competitive or new state-of-the-art performances on ICEWS04 and ICEWS05-15 datasets. Therefore, one should raise awareness when learning TKGs representations to identify whether time truly boosts performances.
The drug discovery and development process is a long and expensive one, costing over 1 billion USD on average per drug and taking 10-15 years. To reduce the high levels of attrition throughout the process, there has been a growing interest in applying machine learning methodologies to various stages of drug discovery and development in the recent decade, especially at the earliest stage identification of druggable disease genes. In this paper, we have developed a new tensor factorisation model to predict potential drug targets (genes or proteins) for treating diseases. We created a three dimensional data tensor consisting of 1,048 gene targets, 860 diseases and 230,011 evidence attributes and clinical outcomes connecting them, using data extracted from the Open Targets and PharmaProjects databases. We enriched the data with gene target representations learned from a drug discovery oriented knowledge graph and applied our proposed method to predict the clinical outcomes for unseen gene target and disease pairs. We designed three evaluation strategies to measure the prediction performance and benchmarked several commonly used machine learning classifiers together with Bayesian matrix and tensor factorisation methods. The result shows that incorporating knowledge graph embeddings significantly improves the prediction accuracy and that training tensor factorisation alongside a dense neural network outperforms all other baselines. In summary, our framework combines two actively studied machine learning approaches to disease target identification, namely tensor factorisation and knowledge graph representation learning, which could be a promising avenue for further exploration in data driven drug discovery.
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.
Ontology-based approaches for predicting gene-disease associations include the more classical semantic similarity methods and more recently knowledge graph embeddings. While semantic similarity is typically restricted to hierarchical relations within the ontology, knowledge graph embeddings consider their full breadth. However, embeddings are produced over a single graph and complex tasks such as gene-disease association may require additional ontologies. We investigate the impact of employing richer semantic representations that are based on more than one ontology, able to represent both genes and diseases and consider multiple kinds of relations within the ontologies. Our experiments demonstrate the value of employing knowledge graph embeddings based on random-walks and highlight the need for a closer integration of different ontologies.
Requiring multiple demonstrations of a task plan presents a burden to end-users of robots. However, robustly executing tasks plans from a single end-user demonstration is an ongoing challenge in robotics. We address the problem of one-shot task execution, in which a robot must generalize a single demonstration or prototypical example of a task plan to a new execution environment. Our approach integrates task plans with domain knowledge to infer task plan constituents for new execution environments. Our experimental evaluations show that our knowledge representation makes more relevant generalizations that result in significantly higher success rates over tested baselines. We validated the approach on a physical platform, which resulted in the successful generalization of initial task plans to 38 of 50 execution environments with errors resulting from autonomous robot operation included.
Contextualized entity representations learned by state-of-the-art transformer-based language models (TLMs) like BERT, GPT, T5, etc., leverage the attention mechanism to learn the data context from training data corpus. However, these models do not use the knowledge context. Knowledge context can be understood as semantics about entities and their relationship with neighboring entities in knowledge graphs. We propose a novel and effective technique to infuse knowledge context from multiple knowledge graphs for conceptual and ambiguous entities into TLMs during fine-tuning. It projects knowledge graph embeddings in the homogeneous vector-space, introduces new token-types for entities, aligns entity position ids, and a selective attention mechanism. We take BERT as a baseline model and implement the "Knowledge-Infused BERT" by infusing knowledge context from ConceptNet and WordNet, which significantly outperforms BERT and other recent knowledge-aware BERT variants like ERNIE, SenseBERT, and BERT_CS over eight different subtasks of GLUE benchmark. The KI-BERT-base model even significantly outperforms BERT-large for domain-specific tasks like SciTail and academic subsets of QQP, QNLI, and MNLI.
Knowledge graphs suffer from sparsity which degrades the quality of representations generated by various methods. While there is an abundance of textual information throughout the web and many existing knowledge bases, aligning information across these diverse data sources remains a challenge in the literature. Previous work has partially addressed this issue by enriching knowledge graph entities based on "hard" co-occurrence of words present in the entities of the knowledge graphs and external text, while we achieve "soft" augmentation by proposing a knowledge graph enrichment and embedding framework named Edge. Given an original knowledge graph, we first generate a rich but noisy augmented graph using external texts in semantic and structural level. To distill the relevant knowledge and suppress the introduced noise, we design a graph alignment term in a shared embedding space between the original graph and augmented graph. To enhance the embedding learning on the augmented graph, we further regularize the locality relationship of target entity based on negative sampling. Experimental results on four benchmark datasets demonstrate the robustness and effectiveness of Edge in link prediction and node classification.
Among the top approaches of recent years, link prediction using knowledge graph embedding (KGE) models has gained significant attention for knowledge graph completion. Various embedding models have been proposed so far, among which, some recent KGE models obtain state-of-the-art performance on link prediction tasks by using embeddings with a high dimension (e.g. 1000) which accelerate the costs of training and evaluation considering the large scale of KGs. In this paper, we propose a simple but effective performance boosting strategy for KGE models by using multiple low dimensions in different repetition rounds of the same model. For example, instead of training a model one time with a large embedding size of 1200, we repeat the training of the model 6 times in parallel with an embedding size of 200 and then combine the 6 separate models for testing while the overall numbers of adjustable parameters are same (6*200=1200) and the total memory footprint remains the same. We show that our approach enables different models to better cope with their expressiveness issues on modeling various graph patterns such as symmetric, 1-n, n-1 and n-n. In order to justify our findings, we conduct experiments on various KGE models. Experimental results on standard benchmark datasets, namely FB15K, FB15K-237 and WN18RR, show that multiple low-dimensional models of the same kind outperform the corresponding single high-dimensional models on link prediction in a certain range and have advantages in training efficiency by using parallel training while the overall numbers of adjustable parameters are same.
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.
Recent knowledge graph embedding (KGE) models based on hyperbolic geometry have shown great potential in a low-dimensional embedding space. However, the necessity of hyperbolic space in KGE is still questionable, because the calculation based on hyperbolic geometry is much more complicated than Euclidean operations. In this paper, based on the state-of-the-art hyperbolic-based model RotH, we develop two lightweight Euclidean-based models, called RotL and Rot2L. The RotL model simplifies the hyperbolic operations while keeping the flexible normalization effect. Utilizing a novel two-layer stacked transformation and based on RotL, the Rot2L model obtains an improved representation capability, yet costs fewer parameters and calculations than RotH. The experiments on link prediction show that Rot2L achieves the state-of-the-art performance on two widely-used datasets in low-dimensional knowledge graph embeddings. Furthermore, RotL achieves similar performance as RotH but only requires half of the training time.
Conventional Machine Reading Comprehension (MRC) has been well-addressed by pattern matching, but the ability of commonsense reasoning remains a gap between humans and machines. Previous methods tackle this problem by enriching word representations via pre-trained Knowledge Graph Embeddings (KGE). However, they make limited use of a large number of connections between nodes in Knowledge Graphs (KG), which could be pivotal cues to build the commonsense reasoning chains. In this paper, we propose a Plug-and-play module to IncorporatE Connection information for commonsEnse Reasoning (PIECER). Beyond enriching word representations with knowledge embeddings, PIECER constructs a joint query-passage graph to explicitly guide commonsense reasoning by the knowledge-oriented connections between words. Further, PIECER has high generalizability since it can be plugged into suitable positions in any MRC model. Experimental results on ReCoRD, a large-scale public MRC dataset requiring commonsense reasoning, show that PIECER introduces stable performance improvements for four representative base MRC models, especially in low-resource settings.
Medical knowledge graphs (KGs) constructed from Electronic Medical Records (EMR) contain abundant information about patients and medical entities. The utilization of KG embedding models on these data has proven to be efficient for different medical tasks. However, existing models do not properly incorporate patient demographics and most of them ignore the probabilistic features of the medical KG. In this paper, we propose DARLING (Demographic Aware pRobabiListic medIcal kNowledge embeddinG), a demographic-aware medical KG embedding framework that explicitly incorporates demographics in the medical entities space by associating patient demographics with a corresponding hyperplane. Our framework leverages the probabilistic features within the medical entities for learning their representations through demographic guidance. We evaluate DARLING through link prediction for treatments and medicines, on a medical KG constructed from EMR data, and illustrate its superior performance compared to existing KG embedding models.
Embedding entities and relations of a knowledge graph in a low-dimensional space has shown impressive performance in predicting missing links between entities. Although progresses have been achieved, existing methods are heuristically motivated and theoretical understanding of such embeddings is comparatively underdeveloped. This paper extends the random walk model (Arora et al., 2016a) of word embeddings to Knowledge Graph Embeddings (KGEs) to derive a scoring function that evaluates the strength of a relation R between two entities h (head) and t (tail). Moreover, we show that marginal loss minimisation, a popular objective used in much prior work in KGE, follows naturally from the log-likelihood ratio maximisation under the probabilities estimated from the KGEs according to our theoretical relationship. We propose a learning objective motivated by the theoretical analysis to learn KGEs from a given knowledge graph. Using the derived objective, accurate KGEs are learnt from FB15K237 and WN18RR benchmark datasets, providing empirical evidence in support of the theory.
In recent years, there has been a resurgence in methods that use distributed (neural) representations to represent and reason about semantic knowledge for robotics applications. However, while robots often observe previously unknown concepts, these representations typically assume that all concepts are known a priori, and incorporating new information requires all concepts to be learned afresh. Our work relaxes this limiting assumption of existing representations and tackles the incremental knowledge graph embedding problem by leveraging the principles of a range of continual learning methods. Through an experimental evaluation with several knowledge graphs and embedding representations, we provide insights about trade-offs for practitioners to match a semantics-driven robotics applications to a suitable continual knowledge graph embedding method.