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.
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.
Knowledge graph embedding models learn the representations of entities and relations in the knowledge graphs for predicting missing links (relations) between entities. Their effectiveness are deeply affected by the ability of modeling and inferring different relation patterns such as symmetry, asymmetry, inversion, composition and transitivity. Although existing models are already able to model many of these relations patterns, transitivity, a very common relation pattern, is still not been fully supported. In this paper, we first theoretically show that the transitive relations can be modeled with projections. We then propose the Rot-Pro model which combines the projection and relational rotation together. We prove that Rot-Pro can infer all the above relation patterns. Experimental results show that the proposed Rot-Pro model effectively learns the transitivity pattern and achieves the state-of-the-art results on the link prediction task in the datasets containing transitive relations.
Knowledge graphs (KGs) consisting of a large number of triples have become widespread recently, and many knowledge graph embedding (KGE) methods are proposed to embed entities and relations of a KG into continuous vector spaces. Such embedding methods simplify the operations of conducting various in-KG tasks (e.g., link prediction) and out-of-KG tasks (e.g., question answering). They can be viewed as general solutions for representing KGs. However, existing KGE methods are not applicable to inductive settings, where a model trained on source KGs will be tested on target KGs with entities unseen during model training. Existing works focusing on KGs in inductive settings can only solve the inductive relation prediction task. They can not handle other out-of-KG tasks as general as KGE methods since they don't produce embeddings for entities. In this paper, to achieve inductive knowledge graph embedding, we propose a model MorsE, which does not learn embeddings for entities but learns transferable meta-knowledge that can be used to produce entity embeddings. Such meta-knowledge is modeled by entity-independent modules and learned by meta-learning. Experimental results show that our model significantly outperforms corresponding baselines for in-KG and out-of-KG tasks in inductive settings.
Logical reasoning over Knowledge Graphs (KGs) is a fundamental technique that can provide efficient querying mechanism over large and incomplete databases. Current approaches employ spatial geometries such as boxes to learn query representations that encompass the answer entities and model the logical operations of projection and intersection. However, their geometry is restrictive and leads to non-smooth strict boundaries, which further results in ambiguous answer entities. Furthermore, previous works propose transformation tricks to handle unions which results in non-closure and, thus, cannot be chained in a stream. In this paper, we propose a Probabilistic Entity Representation Model (PERM) to encode entities as a Multivariate Gaussian density with mean and covariance parameters to capture its semantic position and smooth decision boundary, respectively. Additionally, we also define the closed logical operations of projection, intersection, and union that can be aggregated using an end-to-end objective function. On the logical query reasoning problem, we demonstrate that the proposed PERM significantly outperforms the state-of-the-art methods on various public benchmark KG datasets on standard evaluation metrics. We also evaluate PERM's competence on a COVID-19 drug-repurposing case study and show that our proposed work is able to recommend drugs with substantially better F1 than current methods. Finally, we demonstrate the working of our PERM's query answering process through a low-dimensional visualization of the Gaussian representations.
Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of \textit{cellular sheaves}: a knowledge graph embedding can be described as an approximate global section of an appropriate \textit{knowledge sheaf} over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.
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 Embedding (KGE) aims to learn representations for entities and relations. Most KGE models have gained great success, especially on extrapolation scenarios. Specifically, given an unseen triple (h, r, t), a trained model can still correctly predict t from (h, r, ?), or h from (?, r, t), such extrapolation ability is impressive. However, most existing KGE works focus on the design of delicate triple modeling function, which mainly tells us how to measure the plausibility of observed triples, but offers limited explanation of why the methods can extrapolate to unseen data, and what are the important factors to help KGE extrapolate. Therefore in this work, we attempt to study the KGE extrapolation of two problems: 1. How does KGE extrapolate to unseen data? 2. How to design the KGE model with better extrapolation ability? For the problem 1, we first discuss the impact factors for extrapolation and from relation, entity and triple level respectively, propose three Semantic Evidences (SEs), which can be observed from train set and provide important semantic information for extrapolation. Then we verify the effectiveness of SEs through extensive experiments on several typical KGE methods. For the problem 2, to make better use of the three levels of SE, we propose a novel GNN-based KGE model, called Semantic Evidence aware Graph Neural Network (SE-GNN). In SE-GNN, each level of SE is modeled explicitly by the corresponding neighbor pattern, and merged sufficiently by the multi-layer aggregation, which contributes to obtaining more extrapolative knowledge representation. Finally, through extensive experiments on FB15k-237 and WN18RR datasets, we show that SE-GNN achieves state-of-the-art performance on Knowledge Graph Completion task and performs a better extrapolation ability. Our code is available at https://github.com/renli1024/SE-GNN.
Knowledge graph completion (KGC) has become a focus of attention across deep learning community owing to its excellent contribution to numerous downstream tasks. Although recently have witnessed a surge of work on KGC, they are still insufficient to accurately capture complex relations, since they adopt the single and static representations. In this work, we propose a novel Disentangled Knowledge Graph Attention Network (DisenKGAT) for KGC, which leverages both micro-disentanglement and macro-disentanglement to exploit representations behind Knowledge graphs (KGs). To achieve micro-disentanglement, we put forward a novel relation-aware aggregation to learn diverse component representation. For macro-disentanglement, we leverage mutual information as a regularization to enhance independence. With the assistance of disentanglement, our model is able to generate adaptive representations in terms of the given scenario. Besides, our work has strong robustness and flexibility to adapt to various score functions. Extensive experiments on public benchmark datasets have been conducted to validate the superiority of DisenKGAT over existing methods in terms of both accuracy and explainability.
Recently, several Knowledge Graph Embedding (KGE) approaches have been devised to represent entities and relations in dense vector space and employed in downstream tasks such as link prediction. A few KGE techniques address interpretability, i.e., mapping the connectivity patterns of the relations (i.e., symmetric/asymmetric, inverse, and composition) to a geometric interpretation such as rotations. Other approaches model the representations in higher dimensional space such as four-dimensional space (4D) to enhance the ability to infer the connectivity patterns (i.e., expressiveness). However, modeling relation and entity in a 4D space often comes at the cost of interpretability. This paper proposes HopfE, a novel KGE approach aiming to achieve the interpretability of inferred relations in the four-dimensional space. We first model the structural embeddings in 3D Euclidean space and view the relation operator as an SO(3) rotation. Next, we map the entity embedding vector from a 3D space to a 4D hypersphere using the inverse Hopf Fibration, in which we embed the semantic information from the KG ontology. Thus, HopfE considers the structural and semantic properties of the entities without losing expressivity and interpretability. Our empirical results on four well-known benchmarks achieve state-of-the-art performance for the KG completion task.
Collaborative Metric Learning (CML) recently emerged as a powerful paradigm for recommendation based on implicit feedback collaborative filtering. However, standard CML methods learn fixed user and item representations, which fails to capture the complex interests of users. Existing extensions of CML also either ignore the heterogeneity of user-item relations, i.e. that a user can simultaneously like very different items, or the latent item-item relations, i.e. that a user's preference for an item depends, not only on its intrinsic characteristics, but also on items they previously interacted with. In this paper, we present a hierarchical CML model that jointly captures latent user-item and item-item relations from implicit data. Our approach is inspired by translation mechanisms from knowledge graph embedding and leverages memory-based attention networks. We empirically show the relevance of this joint relational modeling, by outperforming existing CML models on recommendation tasks on several real-world datasets. Our experiments also emphasize the limits of current CML relational models on very sparse datasets.
Entity alignment (EA) plays an important role in automatically integrating knowledge graphs (KGs) from multiple sources. Recent approaches based on Graph Neural Network (GNN) obtain entity representation from relation information and have achieved promising results. Besides, more and more methods introduce semi-supervision to ask for more labeled training data. However, two challenges still exist in GNN-based EA methods: (1) Deeper GNN Encoder: The GNN encoder of current methods has limited depth (usually 2-layers). (2) Low-quality Bootstrapping: The generated semi-supervised data is of low quality. In this paper, we propose a novel framework, Echo Entity Alignment (EchoEA), which leverages 4-levels self-attention mechanism to spread entity information to relations and echo back to entities. Furthermore, we propose attribute-combined bi-directional global-filtered strategy (ABGS) to improve bootstrapping, reduce false samples and generate high-quality training data. The experimental results on three real-world cross-lingual datasets are stable at around 96\% at hits@1 on average, showing that our approach not only significantly outperforms the state-of-the-art GNN-based methods, but also is universal and transferable for existing EA methods.
Learning embeddings for entities and relations in knowledge graph (KG) have benefited many downstream tasks. In recent years, scoring functions, the crux of KG learning, have been human-designed to measure the plausibility of triples and capture different kinds of relations in KGs. However, as relations exhibit intricate patterns that are hard to infer before training, none of them consistently perform the best on benchmark tasks. In this paper, inspired by the recent success of automated machine learning (AutoML), we search bilinear scoring functions for different KG tasks through the AutoML techniques. However, it is non-trivial to explore domain-specific information here. We first set up a search space for AutoBLM by analyzing existing scoring functions. Then, we propose a progressive algorithm (AutoBLM) and an evolutionary algorithm (AutoBLM+), which are further accelerated by filter and predictor to deal with the domain-specific properties for KG learning. Finally, we perform extensive experiments on benchmarks in KG completion, multi-hop query, and entity classification tasks. Empirical results show that the searched scoring functions are KG dependent, new to the literature, and outperform the existing scoring functions. AutoBLM+ is better than AutoBLM as the evolutionary algorithm can flexibly explore better structures in the same budget.
Knowledge graph embedding research has mainly focused on the two smallest normed division algebras, $\mathbb{R}$ and $\mathbb{C}$. Recent results suggest that trilinear products of quaternion-valued embeddings can be a more effective means to tackle link prediction. In addition, models based on convolutions on real-valued embeddings often yield state-of-the-art results for link prediction. In this paper, we investigate a composition of convolution operations with hypercomplex multiplications. We propose the four approaches QMult, OMult, ConvQ and ConvO to tackle the link prediction problem. QMult and OMult can be considered as quaternion and octonion extensions of previous state-of-the-art approaches, including DistMult and ComplEx. ConvQ and ConvO build upon QMult and OMult by including convolution operations in a way inspired by the residual learning framework. We evaluated our approaches on seven link prediction datasets including WN18RR, FB15K-237 and YAGO3-10. Experimental results suggest that the benefits of learning hypercomplex-valued vector representations become more apparent as the size and complexity of the knowledge graph grows. ConvO outperforms state-of-the-art approaches on FB15K-237 in MRR, Hit@1 and Hit@3, while QMult, OMult, ConvQ and ConvO outperform state-of-the-approaches on YAGO3-10 in all metrics. Results also suggest that link prediction performances can be further improved via prediction averaging. To foster reproducible research, we provide an open-source implementation of approaches, including training and evaluation scripts as well as pretrained models.
In knowledge graph embedding, the theoretical relationship between the softmax cross-entropy and negative sampling loss functions has not been investigated. This makes it difficult to fairly compare the results of the two different loss functions. We attempted to solve this problem by using the Bregman divergence to provide a unified interpretation of the softmax cross-entropy and negative sampling loss functions. Under this interpretation, we can derive theoretical findings for fair comparison. Experimental results on the FB15k-237 and WN18RR datasets show that the theoretical findings are valid in practical settings.
Knowledge graph embedding techniques are key to making knowledge graphs amenable to the plethora of machine learning approaches based on vector representations. Link prediction is often used as a proxy to evaluate the quality of these embeddings. Given that the creation of benchmarks for link prediction is a time-consuming endeavor, most work on the subject matter uses only a few benchmarks. As benchmarks are crucial for the fair comparison of algorithms, ensuring their quality is tantamount to providing a solid ground for developing better solutions to link prediction and ipso facto embedding knowledge graphs. First studies of benchmarks pointed to limitations pertaining to information leaking from the development to the test fragments of some benchmark datasets. We spotted a further common limitation of three of the benchmarks commonly used for evaluating link prediction approaches: out-of-vocabulary entities in the test and validation sets. We provide an implementation of an approach for spotting and removing such entities and provide corrected versions of the datasets WN18RR, FB15K-237, and YAGO3-10. Our experiments on the corrected versions of WN18RR, FB15K-237, and YAGO3-10 suggest that the measured performance of state-of-the-art approaches is altered significantly with p-values <1%, <1.4%, and <1%, respectively. Overall, state-of-the-art approaches gain on average absolute $3.29 \pm 0.24\%$ in all metrics on WN18RR. This means that some of the conclusions achieved in previous works might need to be revisited. We provide an open-source implementation of our experiments and corrected datasets at at https://github.com/dice-group/OOV-In-Link-Prediction.
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 embedding has been an active research topic for knowledge base completion (KGC), with progressive improvement from the initial TransE, TransH, RotatE et al to the current state-of-the-art QuatE. However, QuatE ignores the multi-faceted nature of the entity and the complexity of the relation, only using rigorous operation on quaternion space to capture the interaction between entitiy pair and relation, leaving opportunities for better knowledge representation which will finally help KGC. In this paper, we propose a novel model, QuatDE, with a dynamic mapping strategy to explicitly capture the variety of relational patterns and separate different semantic information of the entity, using transition vectors to adjust the point position of the entity embedding vectors in the quaternion space via Hamilton product, enhancing the feature interaction capability between elements of the triplet. Experiment results show QuatDE achieves state-of-the-art performance on three well-established knowledge graph completion benchmarks. In particular, the MR evaluation has relatively increased by 26% on WN18 and 15% on WN18RR, which proves the generalization of QuatDE.
Numeric values associated to edges of a knowledge graph have been used to represent uncertainty, edge importance, and even out-of-band knowledge in a growing number of scenarios, ranging from genetic data to social networks. Nevertheless, traditional knowledge graph embedding models are not designed to capture such information, to the detriment of predictive power. We propose a novel method that injects numeric edge attributes into the scoring layer of a traditional knowledge graph embedding architecture. Experiments with publicly available numeric-enriched knowledge graphs show that our method outperforms traditional numeric-unaware baselines as well as the recent UKGE model.
Knowledge graph embedding plays an important role in knowledge representation, reasoning, and data mining applications. However, for multiple cross-domain knowledge graphs, state-of-the-art embedding models cannot make full use of the data from different knowledge domains while preserving the privacy of exchanged data. In addition, the centralized embedding model may not scale to the extensive real-world knowledge graphs. Therefore, we propose a novel decentralized scalable learning framework, \emph{Federated Knowledge Graphs Embedding} (FKGE), where embeddings from different knowledge graphs can be learnt in an asynchronous and peer-to-peer manner while being privacy-preserving. FKGE exploits adversarial generation between pairs of knowledge graphs to translate identical entities and relations of different domains into near embedding spaces. In order to protect the privacy of the training data, FKGE further implements a privacy-preserving neural network structure to guarantee no raw data leakage. We conduct extensive experiments to evaluate FKGE on 11 knowledge graphs, demonstrating a significant and consistent improvement in model quality with at most 17.85\% and 7.90\% increases in performance on triple classification and link prediction tasks.