Gene Ontology (GO) and its Annotations (GOA) provide a controlled and evolving vocabulary for gene products and gene functions widely used in molecular biology. GO \& GOA are updated and maintained both automatically from biological publications and manually by curators. These knowledge bases however are often incomplete for two reasons: 1) Research in biological domain itself is still ongoing; 2) The amount of experimental evidence might not be yet sufficient to validate annotations. In this paper, we address the gap in evidence between gene products and their annotations by making link predictions using Knowledge Graph Embedding (KGE) methods. Through the application of the True Path Rule (TPR) in the training stage of KGE, we were able to improve the performance of traditional KGE methods. We report two experimental scenarios with GO and GO Chicken Annotation datasets to show the contribution of embedding TPR to prediction accuracy.
Knowledge graph (KG) embedding methods map entities and relations into continuous vector spaces, improving performance in tasks like link prediction and question answering. With rising privacy concerns, machine unlearning (MU) has emerged as a critical AI technology, enabling models to eliminate the influence of specific data. Existing MU approaches often rely on data obfuscation and adjustments to training loss but lack generalization across unlearning tasks. This paper introduces MetaEU, a Meta-Learning-Based Knowledge Graph Embedding Unlearning framework. MetaEU leverages meta-learning to unlearn specific embeddings, mitigating their impact while preserving model performance on remaining data. Experiments on benchmark datasets demonstrate its effectiveness in KG embedding unlearning.
Knowledge Graph Embedding models, representing entities and edges in a low-dimensional space, have been extremely successful at solving tasks related to completing and exploring Knowledge Graphs (KGs). One of the key aspects of training most of these models is teaching to discriminate between true statements positives and false ones (negatives). However, the way in which negatives can be defined is not trivial, as facts missing from the KG are not necessarily false and a set of ground truth negatives is hardly ever given. This makes synthetic negative generation a necessity. Different generation strategies can heavily affect the quality of the embeddings, making it a primary aspect to consider. We revamp a strategy that generates corruptions during training respecting the domain and range of relations, we extend its capabilities and we show our methods bring substantial improvement (+10% MRR) for standard benchmark datasets and over +150% MRR for a larger ontology-backed dataset.
Hyperbolic rotation is commonly used to effectively model knowledge graphs and their inherent hierarchies. However, existing hyperbolic rotation models rely on logarithmic and exponential mappings for feature transformation. These models only project data features into hyperbolic space for rotation, limiting their ability to fully exploit the hyperbolic space. To address this problem, we propose a novel fully hyperbolic model designed for knowledge graph embedding. Instead of feature mappings, we define the model directly in hyperbolic space with the Lorentz model. Our model considers each relation in knowledge graphs as a Lorentz rotation from the head entity to the tail entity. We adopt the Lorentzian version distance as the scoring function for measuring the plausibility of triplets. Extensive results on standard knowledge graph completion benchmarks demonstrated that our model achieves competitive results with fewer parameters. In addition, our model get the state-of-the-art performance on datasets of CoDEx-s and CoDEx-m, which are more diverse and challenging than before. Our code is available at https://github.com/llqy123/FHRE.
Introduction: Tracing the spread of ideas and the presence of influence is a question of special importance across a wide range of disciplines, ranging from intellectual history to cultural analytics, computational social science, and the science of science. Method: We collect a corpus of open source journal articles, generate Knowledge Graph representations using the Gemini LLM, and attempt to predict the existence of citations between sampled pairs of articles using previously published methods and a novel Graph Neural Network based embedding model. Results: We demonstrate that our knowledge graph embedding method is superior at distinguishing pairs of articles with and without citation. Once trained, it runs efficiently and can be fine-tuned on specific corpora to suit individual researcher needs. Conclusion(s): This experiment demonstrates that the relationships encoded in a knowledge graph, especially the types of concepts brought together by specific relations can encode information capable of revealing intellectual influence. This suggests that further work in analyzing document level knowledge graphs to understand latent structures could provide valuable insights.
Understanding the complex dynamics of high-dimensional, contingent, and strongly nonlinear economic data, often shaped by multiplicative processes, poses significant challenges for traditional regression methods as such methods offer limited capacity to capture the structural changes they feature. To address this, we propose leveraging the potential of knowledge graph embeddings for economic trade data, in particular, to predict international trade relationships. We implement KonecoKG, a knowledge graph representation of economic trade data with multidimensional relationships using SDM-RDFizer, and transform the relationships into a knowledge graph embedding using AmpliGraph.
In recent years, knowledge graphs have gained interest and witnessed widespread applications in various domains, such as information retrieval, question-answering, recommendation systems, amongst others. Large-scale knowledge graphs to this end have demonstrated their utility in effectively representing structured knowledge. To further facilitate the application of machine learning techniques, knowledge graph embedding (KGE) models have been developed. Such models can transform entities and relationships within knowledge graphs into vectors. However, these embedding models often face challenges related to noise, missing information, distribution shift, adversarial attacks, etc. This can lead to sub-optimal embeddings and incorrect inferences, thereby negatively impacting downstream applications. While the existing literature has focused so far on adversarial attacks on KGE models, the challenges related to the other critical aspects remain unexplored. In this paper, we, first of all, give a unified definition of resilience, encompassing several factors such as generalisation, performance consistency, distribution adaption, and robustness. After formalizing these concepts for machine learning in general, we define them in the context of knowledge graphs. To find the gap in the existing works on resilience in the context of knowledge graphs, we perform a systematic survey, taking into account all these aspects mentioned previously. Our survey results show that most of the existing works focus on a specific aspect of resilience, namely robustness. After categorizing such works based on their respective aspects of resilience, we discuss the challenges and future research directions.
Geospatial Knowledge Graphs (GeoKGs) model geoentities (e.g., places and natural features) and spatial relationships in an interconnected manner, providing strong knowledge support for geographic applications, including data retrieval, question-answering, and spatial reasoning. However, existing methods for mining and reasoning from GeoKGs, such as popular knowledge graph embedding (KGE) techniques, lack geographic awareness. This study aims to enhance general-purpose KGE by developing new strategies and integrating geometric features of spatial relations, including topology, direction, and distance, to infuse the embedding process with geographic intuition. The new model is tested on downstream link prediction tasks, and the results show that the inclusion of geometric features, particularly topology and direction, improves prediction accuracy for both geoentities and spatial relations. Our research offers new perspectives for integrating spatial concepts and principles into the GeoKG mining process, providing customized GeoAI solutions for geospatial challenges.
Knowledge Graph Embedding (KGE) techniques play a pivotal role in transforming symbolic Knowledge Graphs (KGs) into numerical representations, thereby enhancing various deep learning models for knowledge-augmented applications. Unlike entities, relations in KGs are the carriers of semantic meaning, and their accurate modeling is crucial for the performance of KGE models. Firstly, we address the complex mapping properties inherent in relations, such as one-to-one, one-to-many, many-to-one, and many-to-many mappings. We provide a comprehensive summary of relation-aware mapping-based models, models that utilize specific representation spaces, tensor decomposition-based models, and neural network-based models. Next, focusing on capturing various relation patterns like symmetry, asymmetry, inversion, and composition, we review models that employ modified tensor decomposition, those based on modified relation-aware mappings, and those that leverage rotation operations. Subsequently, considering the implicit hierarchical relations among entities, we introduce models that incorporate auxiliary information, models based on hyperbolic spaces, and those that utilize the polar coordinate system. Finally, in response to more complex scenarios such as sparse and dynamic KGs, this paper discusses potential future research directions. We explore innovative ideas such as integrating multimodal information into KGE, enhancing relation pattern modeling with rules, and developing models to capture relation characteristics in dynamic KGE settings.
In knowledge graph embedding, aside from positive triplets (ie: facts in the knowledge graph), the negative triplets used for training also have a direct influence on the model performance. In reality, since knowledge graphs are sparse and incomplete, negative triplets often lack explicit labels, and thus they are often obtained from various sampling strategies (eg: randomly replacing an entity in a positive triplet). An ideal sampled negative triplet should be informative enough to help the model train better. However, existing methods often ignore diversity and adaptiveness in their sampling process, which harms the informativeness of negative triplets. As such, we propose a generative adversarial approach called Diversified and Adaptive Negative Sampling DANS on knowledge graphs. DANS is equipped with a two-way generator that generates more diverse negative triplets through two pathways, and an adaptive mechanism that produces more fine-grained examples by localizing the global generator for different entities and relations. On the one hand, the two-way generator increase the overall informativeness with more diverse negative examples; on the other hand, the adaptive mechanism increases the individual sample-wise informativeness with more fine-grained sampling. Finally, we evaluate the performance of DANS on three benchmark knowledge graphs to demonstrate its effectiveness through quantitative and qualitative experiments.
In recent years, knowledge graph embedding models have been successfully applied in the transductive setting to tackle various challenging tasks including link prediction, and query answering. Yet, the transductive setting does not allow for reasoning over unseen entities, relations, let alone numerical or non-numerical literals. Although increasing efforts are put into exploring inductive scenarios, inference over unseen entities, relations, and literals has yet to come. This limitation prohibits the existing methods from handling real-world dynamic knowledge graphs involving heterogeneous information about the world. Here, we propose a remedy to this limitation. We propose the attentive byte-pair encoding layer (BytE) to construct a triple embedding from a sequence of byte-pair encoded subword units of entities and relations. Compared to the conventional setting, BytE leads to massive feature reuse via weight tying, since it forces a knowledge graph embedding model to learn embeddings for subword units instead of entities and relations directly. Consequently, the size of the embedding matrices are not anymore bound to the unique number of entities and relations of a knowledge graph. Experimental results show that BytE improves the link prediction performance of 4 knowledge graph embedding models on datasets where the syntactic representations of triples are semantically meaningful. However, benefits of training a knowledge graph embedding model with BytE dissipate on knowledge graphs where entities and relations are represented with plain numbers or URIs. We provide an open source implementation of BytE to foster reproducible research.
Knowledge graph completion (KGC) tasks aim to infer missing facts in a knowledge graph (KG) for many knowledge-intensive applications. However, existing embedding-based KGC approaches primarily rely on factual triples, potentially leading to outcomes inconsistent with common sense. Besides, generating explicit common sense is often impractical or costly for a KG. To address these challenges, we propose a pluggable common sense-enhanced KGC framework that incorporates both fact and common sense for KGC. This framework is adaptable to different KGs based on their entity concept richness and has the capability to automatically generate explicit or implicit common sense from factual triples. Furthermore, we introduce common sense-guided negative sampling and a coarse-to-fine inference approach for KGs with rich entity concepts. For KGs without concepts, we propose a dual scoring scheme involving a relation-aware concept embedding mechanism. Importantly, our approach can be integrated as a pluggable module for many knowledge graph embedding (KGE) models, facilitating joint common sense and fact-driven training and inference. The experiments illustrate that our framework exhibits good scalability and outperforms existing models across various KGC tasks.
A key to knowledge graph embedding (KGE) is to choose a proper representation space, e.g., point-wise Euclidean space and complex vector space. In this paper, we propose a unified perspective of embedding and introduce uncertainty into KGE from the view of group theory. Our model can incorporate existing models (i.e., generality), ensure the computation is tractable (i.e., efficiency) and enjoy the expressive power of complex random variables (i.e., expressiveness). The core idea is that we embed entities/relations as elements of a symmetric group, i.e., permutations of a set. Permutations of different sets can reflect different properties of embedding. And the group operation of symmetric groups is easy to compute. In specific, we show that the embedding of many existing models, point vectors, can be seen as elements of a symmetric group. To reflect uncertainty, we first embed entities/relations as permutations of a set of random variables. A permutation can transform a simple random variable into a complex random variable for greater expressiveness, called a normalizing flow. We then define scoring functions by measuring the similarity of two normalizing flows, namely NFE. We construct several instantiating models and prove that they are able to learn logical rules. Experimental results demonstrate the effectiveness of introducing uncertainty and our model. The code is available at https://github.com/changyi7231/NFE.
We introduce a novel embedding method diverging from conventional approaches by operating within function spaces of finite dimension rather than finite vector space, thus departing significantly from standard knowledge graph embedding techniques. Initially employing polynomial functions to compute embeddings, we progress to more intricate representations using neural networks with varying layer complexities. We argue that employing functions for embedding computation enhances expressiveness and allows for more degrees of freedom, enabling operations such as composition, derivatives and primitive of entities representation. Additionally, we meticulously outline the step-by-step construction of our approach and provide code for reproducibility, thereby facilitating further exploration and application in the field.
Knowledge Graph Completion has been increasingly adopted as a useful method for several tasks in biomedical research, like drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models has been proposed over the years. However, little is known about the properties that render a dataset useful for a given task and, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. We conduct a comprehensive investigation into the topological properties of publicly available biomedical Knowledge Graphs and establish links to the accuracy observed in real-world applications. By releasing all model predictions and a new suite of analysis tools we invite the community to build upon our work and continue improving the understanding of these crucial applications.
Knowledge graph embedding (KGE) constitutes a foundational task, directed towards learning representations for entities and relations within knowledge graphs (KGs), with the objective of crafting representations comprehensive enough to approximate the logical and symbolic interconnections among entities. In this paper, we define a metric Z-counts to measure the difficulty of training each triple ($<$head entity, relation, tail entity$>$) in KGs with theoretical analysis. Based on this metric, we propose \textbf{CL4KGE}, an efficient \textbf{C}urriculum \textbf{L}earning based training strategy for \textbf{KGE}. This method includes a difficulty measurer and a training scheduler that aids in the training of KGE models. Our approach possesses the flexibility to act as a plugin within a wide range of KGE models, with the added advantage of adaptability to the majority of KGs in existence. The proposed method has been evaluated on popular KGE models, and the results demonstrate that it enhances the state-of-the-art methods. The use of Z-counts as a metric has enabled the identification of challenging triples in KGs, which helps in devising effective training strategies.
Knowledge graph embeddings (KGE) apply machine learning methods on knowledge graphs (KGs) to provide non-classical reasoning capabilities based on similarities and analogies. The learned KG embeddings are typically used to answer queries by ranking all potential answers, but rankings often lack a meaningful probabilistic interpretation - lower-ranked answers do not necessarily have a lower probability of being true. This limitation makes it difficult to quantify uncertainty of model's predictions, posing challenges for the application of KGE methods in high-stakes domains like medicine. We address this issue by applying the theory of conformal prediction that allows generating answer sets, which contain the correct answer with probabilistic guarantees. We explain how conformal prediction can be used to generate such answer sets for link prediction tasks. Our empirical evaluation on four benchmark datasets using six representative KGE methods validates that the generated answer sets satisfy the probabilistic guarantees given by the theory of conformal prediction. We also demonstrate that the generated answer sets often have a sensible size and that the size adapts well with respect to the difficulty of the query.
Knowledge graph embedding (KGE) models are often used to predict missing links for knowledge graphs (KGs). However, multiple KG embeddings can perform almost equally well for link prediction yet give conflicting predictions for unseen queries. This phenomenon is termed \textit{predictive multiplicity} in the literature. It poses substantial risks for KGE-based applications in high-stake domains but has been overlooked in KGE research. We define predictive multiplicity in link prediction, introduce evaluation metrics and measure predictive multiplicity for representative KGE methods on commonly used benchmark datasets. Our empirical study reveals significant predictive multiplicity in link prediction, with $8\%$ to $39\%$ testing queries exhibiting conflicting predictions. We address this issue by leveraging voting methods from social choice theory, significantly mitigating conflicts by $66\%$ to $78\%$ in our experiments.
Temporal knowledge graph completion aims to infer the missing facts in temporal knowledge graphs. Current approaches usually embed factual knowledge into continuous vector space and apply geometric operations to learn potential patterns in temporal knowledge graphs. However, these methods only adopt a single operation, which may have limitations in capturing the complex temporal dynamics present in temporal knowledge graphs. Therefore, we propose a simple but effective method, i.e. TCompoundE, which is specially designed with two geometric operations, including time-specific and relation-specific operations. We provide mathematical proofs to demonstrate the ability of TCompoundE to encode various relation patterns. Experimental results show that our proposed model significantly outperforms existing temporal knowledge graph embedding models. Our code is available at https://github.com/nk-ruiying/TCompoundE.
Federated Knowledge Graph Embedding (FKGE) aims to facilitate collaborative learning of entity and relation embeddings from distributed Knowledge Graphs (KGs) across multiple clients, while preserving data privacy. Training FKGE models with higher dimensions is typically favored due to their potential for achieving superior performance. However, high-dimensional embeddings present significant challenges in terms of storage resource and inference speed. Unlike traditional KG embedding methods, FKGE involves multiple client-server communication rounds, where communication efficiency is critical. Existing embedding compression methods for traditional KGs may not be directly applicable to FKGE as they often require multiple model trainings which potentially incur substantial communication costs. In this paper, we propose a light-weight component based on Knowledge Distillation (KD) which is titled FedKD and tailored specifically for FKGE methods. During client-side local training, FedKD facilitates the low-dimensional student model to mimic the score distribution of triples from the high-dimensional teacher model using KL divergence loss. Unlike traditional KD way, FedKD adaptively learns a temperature to scale the score of positive triples and separately adjusts the scores of corresponding negative triples using a predefined temperature, thereby mitigating teacher over-confidence issue. Furthermore, we dynamically adjust the weight of KD loss to optimize the training process. Extensive experiments on three datasets support the effectiveness of FedKD.