Knowledge graph (KG) embedding methods which map entities and relations to unique embeddings in the KG have shown promising results on many reasoning tasks. However, the same embedding dimension for both dense entities and sparse entities will cause either over parameterization (sparse entities) or under fitting (dense entities). Normally, a large dimension is set to get better performance. Meanwhile, the inference time grows log-linearly with the number of entities for all entities are traversed and compared. Both the parameter and inference become challenges when working with huge amounts of entities. Thus, we propose PIE, a \textbf{p}arameter and \textbf{i}nference \textbf{e}fficient solution. Inspired from tensor decomposition methods, we find that decompose entity embedding matrix into low rank matrices can reduce more than half of the parameters while maintaining comparable performance. To accelerate model inference, we propose a self-supervised auxiliary task, which can be seen as fine-grained entity typing. By randomly masking and recovering entities' connected relations, the task learns the co-occurrence of entity and relations. Utilizing the fine grained typing, we can filter unrelated entities during inference and get targets with possibly sub-linear time requirement. Experiments on link prediction benchmarks demonstrate the proposed key capabilities. Moreover, we prove effectiveness of the proposed solution on the Open Graph Benchmark large scale challenge dataset WikiKG90Mv2 and achieve the state of the art performance.
Knowledge graph embedding methods are important for the knowledge graph completion (or link prediction) task. One existing efficient method, PairRE, leverages two separate vectors to model complex relations (i.e., 1-to-N, N-to-1, and N-to-N) in knowledge graphs. However, such a method strictly restricts entities on the hyper-ellipsoid surfaces which limits the optimization of entity distribution, leading to suboptimal performance of knowledge graph completion. To address this issue, we propose a novel score function TranSHER, which leverages relation-specific translations between head and tail entities to relax the constraint of hyper-ellipsoid restrictions. By introducing an intuitive and simple relation-specific translation, TranSHER can provide more direct guidance on optimization and capture more semantic characteristics of entities with complex relations. Experimental results show that TranSHER achieves significant performance improvements on link prediction and generalizes well to datasets in different domains and scales. Our codes are public available at https://github.com/yizhilll/TranSHER.
Prior work on integrating text corpora with knowledge graphs (KGs) to improve Knowledge Graph Embedding (KGE) have obtained good performance for entities that co-occur in sentences in text corpora. Such sentences (textual mentions of entity-pairs) are represented as Lexicalised Dependency Paths (LDPs) between two entities. However, it is not possible to represent relations between entities that do not co-occur in a single sentence using LDPs. In this paper, we propose and evaluate several methods to address this problem, where we borrow LDPs from the entity pairs that co-occur in sentences in the corpus (i.e. with mention entity pairs) to represent entity pairs that do not co-occur in any sentence in the corpus (i.e. without mention entity pairs). We propose a supervised borrowing method, SuperBorrow, that learns to score the suitability of an LDP to represent a without-mention entity pair using pre-trained entity embeddings and contextualised LDP representations. Experimental results show that SuperBorrow improves the link prediction performance of multiple widely-used prior KGE methods such as TransE, DistMult, ComplEx and RotatE.
Temporal knowledge graph completion (TKGC) has become a popular approach for reasoning over the event and temporal knowledge graphs, targeting the completion of knowledge with accurate but missing information. In this context, tensor decomposition has successfully modeled interactions between entities and relations. Their effectiveness in static knowledge graph completion motivates us to introduce Time-LowFER, a family of parameter-efficient and time-aware extensions of the low-rank tensor factorization model LowFER. Noting several limitations in current approaches to represent time, we propose a cycle-aware time-encoding scheme for time features, which is model-agnostic and offers a more generalized representation of time. We implement our methods in a unified temporal knowledge graph embedding framework, focusing on time-sensitive data processing. The experiments show that our proposed methods perform on par or better than the state-of-the-art semantic matching models on two benchmarks.
Embedding methods have demonstrated robust performance on the task of link prediction in knowledge graphs, by mostly encoding entity relationships. Recent methods propose to enhance the loss function with a literal-aware term. In this paper, we propose KGA: a knowledge graph augmentation method that incorporates literals in an embedding model without modifying its loss function. KGA discretizes quantity and year values into bins, and chains these bins both horizontally, modeling neighboring values, and vertically, modeling multiple levels of granularity. KGA is scalable and can be used as a pre-processing step for any existing knowledge graph embedding model. Experiments on legacy benchmarks and a new large benchmark, DWD, show that augmenting the knowledge graph with quantities and years is beneficial for predicting both entities and numbers, as KGA outperforms the vanilla models and other relevant baselines. Our ablation studies confirm that both quantities and years contribute to KGA's performance, and that its performance depends on the discretization and binning settings. We make the code, models, and the DWD benchmark publicly available to facilitate reproducibility and future research.
Knowledge graph embedding (KGE) models represent each entity and relation of a knowledge graph (KG) with low-dimensional embedding vectors. These methods have recently been applied to KG link prediction and question answering over incomplete KGs (KGQA). KGEs typically create an embedding for each entity in the graph, which results in large model sizes on real-world graphs with millions of entities. For downstream tasks these atomic entity representations often need to be integrated into a multi stage pipeline, limiting their utility. We show that an off-the-shelf encoder-decoder Transformer model can serve as a scalable and versatile KGE model obtaining state-of-the-art results for KG link prediction and incomplete KG question answering. We achieve this by posing KG link prediction as a sequence-to-sequence task and exchange the triple scoring approach taken by prior KGE methods with autoregressive decoding. Such a simple but powerful method reduces the model size up to 98% compared to conventional KGE models while keeping inference time tractable. After finetuning this model on the task of KGQA over incomplete KGs, our approach outperforms baselines on multiple large-scale datasets without extensive hyperparameter tuning.
In recent years, we have witnessed the proliferation of knowledge graphs (KG) in various domains, aiming to support applications like question answering, recommendations, etc. A frequent task when integrating knowledge from different KGs is to find which subgraphs refer to the same real-world entity. Recently, embedding methods have been used for entity alignment tasks, that learn a vector-space representation of entities which preserves their similarity in the original KGs. A wide variety of supervised, unsupervised, and semi-supervised methods have been proposed that exploit both factual (attribute based) and structural information (relation based) of entities in the KGs. Still, a quantitative assessment of their strengths and weaknesses in real-world KGs according to different performance metrics and KG characteristics is missing from the literature. In this work, we conduct the first meta-level analysis of popular embedding methods for entity alignment, based on a statistically sound methodology. Our analysis reveals statistically significant correlations of different embedding methods with various meta-features extracted by KGs and rank them in a statistically significant way according to their effectiveness across all real-world KGs of our testbed. Finally, we study interesting trade-offs in terms of methods' effectiveness and efficiency.
The link prediction task on knowledge graphs without explicit negative triples in the training data motivates the usage of rank-based metrics. Here, we review existing rank-based metrics and propose desiderata for improved metrics to address lack of interpretability and comparability of existing metrics to datasets of different sizes and properties. We introduce a simple theoretical framework for rank-based metrics upon which we investigate two avenues for improvements to existing metrics via alternative aggregation functions and concepts from probability theory. We finally propose several new rank-based metrics that are more easily interpreted and compared accompanied by a demonstration of their usage in a benchmarking of knowledge graph embedding models.
Knowledge graphs store a large number of factual triples while they are still incomplete, inevitably. The previous knowledge graph completion (KGC) models predict missing links between entities merely relying on fact-view data, ignoring the valuable commonsense knowledge. The previous knowledge graph embedding (KGE) techniques suffer from invalid negative sampling and the uncertainty of fact-view link prediction, limiting KGC's performance. To address the above challenges, we propose a novel and scalable Commonsense-Aware Knowledge Embedding (CAKE) framework to automatically extract commonsense from factual triples with entity concepts. The generated commonsense augments effective self-supervision to facilitate both high-quality negative sampling (NS) and joint commonsense and fact-view link prediction. Experimental results on the KGC task demonstrate that assembling our framework could enhance the performance of the original KGE models, and the proposed commonsense-aware NS module is superior to other NS techniques. Besides, our proposed framework could be easily adaptive to various KGE models and explain the predicted results.
NeuralKG is an open-source Python-based library for diverse representation learning of knowledge graphs. It implements three different series of Knowledge Graph Embedding (KGE) methods, including conventional KGEs, GNN-based KGEs, and Rule-based KGEs. With a unified framework, NeuralKG successfully reproduces link prediction results of these methods on benchmarks, freeing users from the laborious task of reimplementing them, especially for some methods originally written in non-python programming languages. Besides, NeuralKG is highly configurable and extensible. It provides various decoupled modules that can be mixed and adapted to each other. Thus with NeuralKG, developers and researchers can quickly implement their own designed models and obtain the optimal training methods to achieve the best performance efficiently. We built an website in http://neuralkg.zjukg.cn to organize an open and shared KG representation learning community. The source code is all publicly released at https://github.com/zjukg/NeuralKG.
The effectiveness of knowledge graph embedding (KGE) largely depends on the ability to model intrinsic relation patterns and mapping properties. However, existing approaches can only capture some of them with insufficient modeling capacity. In this work, we propose a more powerful KGE framework named HousE, which involves a novel parameterization based on two kinds of Householder transformations: (1) Householder rotations to achieve superior capacity of modeling relation patterns; (2) Householder projections to handle sophisticated relation mapping properties. Theoretically, HousE is capable of modeling crucial relation patterns and mapping properties simultaneously. Besides, HousE is a generalization of existing rotation-based models while extending the rotations to high-dimensional spaces. Empirically, HousE achieves new state-of-the-art performance on five benchmark datasets. Our code is available at https://github.com/anrep/HousE.
Graph convolutional networks (GCNs) -- which are effective in modeling graph structures -- have been increasingly popular in knowledge graph completion (KGC). GCN-based KGC models first use GCNs to generate expressive entity representations and then use knowledge graph embedding (KGE) models to capture the interactions among entities and relations. However, many GCN-based KGC models fail to outperform state-of-the-art KGE models though introducing additional computational complexity. This phenomenon motivates us to explore the real effect of GCNs in KGC. Therefore, in this paper, we build upon representative GCN-based KGC models and introduce variants to find which factor of GCNs is critical in KGC. Surprisingly, we observe from experiments that the graph structure modeling in GCNs does not have a significant impact on the performance of KGC models, which is in contrast to the common belief. Instead, the transformations for entity representations are responsible for the performance improvements. Based on the observation, we propose a simple yet effective framework named LTE-KGE, which equips existing KGE models with linearly transformed entity embeddings. Experiments demonstrate that LTE-KGE models lead to similar performance improvements with GCN-based KGC methods, while being more computationally efficient. These results suggest that existing GCNs are unnecessary for KGC, and novel GCN-based KGC models should count on more ablation studies to validate their effectiveness. The code of all the experiments is available on GitHub at https://github.com/MIRALab-USTC/GCN4KGC.
Recently, increasing efforts are put into learning continual representations for symbolic knowledge bases (KBs). However, these approaches either only embed the data-level knowledge (ABox) or suffer from inherent limitations when dealing with concept-level knowledge (TBox), i.e., they cannot faithfully model the logical structure present in the KBs. We present BoxEL, a geometric KB embedding approach that allows for better capturing the logical structure (i.e., ABox and TBox axioms) in the description logic EL++. BoxEL models concepts in a KB as axis-parallel boxes that are suitable for modeling concept intersection, entities as points inside boxes, and relations between concepts/entities as affine transformations. We show theoretical guarantees (soundness) of BoxEL for preserving logical structure. Namely, the learned model of BoxEL embedding with loss 0 is a (logical) model of the KB. Experimental results on (plausible) subsumption reasonings and a real-world application for protein-protein prediction show that BoxEL outperforms traditional knowledge graph embedding methods as well as state-of-the-art EL++ embedding approaches.
Previous knowledge graph embedding approaches usually map entities to representations and utilize score functions to predict the target entities, yet they typically struggle to reason rare or emerging unseen entities. In this paper, we propose kNN-KGE, a new knowledge graph embedding approach with pre-trained language models, by linearly interpolating its entity distribution with k-nearest neighbors. We compute the nearest neighbors based on the distance in the entity embedding space from the knowledge store. Our approach can allow rare or emerging entities to be memorized explicitly rather than implicitly in model parameters. Experimental results demonstrate that our approach can improve inductive and transductive link prediction results and yield better performance for low-resource settings with only a few triples, which might be easier to reason via explicit memory. Code is available at https://github.com/zjunlp/KNN-KG.
Semantic networks, such as the knowledge graph, can represent the knowledge leveraging the graph structure. Although the knowledge graph shows promising values in natural language processing, it suffers from incompleteness. This paper focuses on knowledge graph completion by predicting linkage between entities, which is a fundamental yet critical task. Semantic matching is a potential solution as it can deal with unseen entities, which the translational distance based methods struggle with. However, to achieve competitive performance as translational distance based methods, semantic matching based methods require large-scale datasets for the training purpose, which are typically unavailable in practical settings. Therefore, we employ the language model and introduce a novel knowledge graph architecture named LP-BERT, which contains two main stages: multi-task pre-training and knowledge graph fine-tuning. In the pre-training phase, three tasks are taken to drive the model to learn the relationship from triples by predicting either entities or relations. While in the fine-tuning phase, inspired by contrastive learning, we design a triple-style negative sampling in a batch, which greatly increases the proportion of negative sampling while keeping the training time almost unchanged. Furthermore, we propose a new data augmentation method utilizing the inverse relationship of triples to improve the performance and robustness of the model. To demonstrate the effectiveness of our method, we conduct extensive experiments on three widely-used datasets, WN18RR, FB15k-237, and UMLS. The experimental results demonstrate the superiority of our methods, and our approach achieves state-of-the-art results on WN18RR and FB15k-237 datasets. Significantly, Hits@10 indicator is improved by 5% from previous state-of-the-art result on the WN18RR dataset while reaching 100% on the UMLS dataset.
Knowledge graphs (KGs) are typically incomplete and we often wish to infer new facts given the existing ones. This can be thought of as a binary classification problem; we aim to predict if new facts are true or false. Unfortunately, we generally only have positive examples (the known facts) but we also need negative ones to train a classifier. To resolve this, it is usual to generate negative examples using a negative sampling strategy. However, this can produce false negatives which may reduce performance, is computationally expensive, and does not produce calibrated classification probabilities. In this paper, we propose a training procedure that obviates the need for negative sampling by adding a novel regularization term to the loss function. Our results for two relational embedding models (DistMult and SimplE) show the merit of our proposal both in terms of performance and speed.
We present an effective graph neural network (GNN)-based knowledge graph embedding model, which we name WGE, to capture entity- and relation-focused graph structures. Given a knowledge graph, WGE builds a single undirected entity-focused graph that views entities as nodes. WGE also constructs another single undirected graph from relation-focused constraints, which views entities and relations as nodes. WGE then proposes a GNN-based architecture to better learn vector representations of entities and relations from these two single entity- and relation-focused graphs. WGE feeds the learned entity and relation representations into a weighted score function to return the triple scores for knowledge graph completion. Experimental results show that WGE outperforms strong baselines on seven benchmark datasets for knowledge graph completion.
A few models have tried to tackle the link prediction problem, also known as knowledge graph completion, by embedding knowledge graphs in comparably lower dimensions. However, the state-of-the-art results are attained at the cost of considerably increasing the dimensionality of embeddings which causes scalability issues in the case of huge knowledge bases. Transformers have been successfully used recently as powerful encoders for knowledge graphs, but available models still have scalability issues. To address this limitation, we introduce a Transformer-based model to gain expressive low-dimensional embeddings. We utilize a large number of self-attention heads as the key to applying query-dependent projections to capture mutual information between entities and relations. Empirical results on WN18RR and FB15k-237 as standard link prediction benchmarks demonstrate that our model has favorably comparable performance with the current state-of-the-art models. Notably, we yield our promising results with a significant reduction of 66.9% in the dimensionality of embeddings compared to the five best recent state-of-the-art competitors on average.
Adoption of recently developed methods from machine learning has given rise to creation of drug-discovery knowledge graphs (KG) that utilize the interconnected nature of the domain. Graph-based modelling of the data, combined with KG embedding (KGE) methods, are promising as they provide a more intuitive representation and are suitable for inference tasks such as predicting missing links. One common application is to produce ranked lists of genes for a given disease, where the rank is based on the perceived likelihood of association between the gene and the disease. It is thus critical that these predictions are not only pertinent but also biologically meaningful. However, KGs can be biased either directly due to the underlying data sources that are integrated or due to modeling choices in the construction of the graph, one consequence of which is that certain entities can get topologically overrepresented. We demonstrate the effect of these inherent structural imbalances, resulting in densely-connected entities being highly ranked no matter the context. We provide support for this observation across different datasets, models as well as predictive tasks. Further, we present various graph perturbation experiments which yield more support to the observation that KGE models can be more influenced by the frequency of entities rather than any biological information encoded within the relations. Our results highlight the importance of data modeling choices, and emphasizes the need for practitioners to be mindful of these issues when interpreting model outputs and during KG composition.
Learning the embeddings of knowledge graphs (KG) is vital in artificial intelligence, and can benefit various downstream applications, such as recommendation and question answering. In recent years, many research efforts have been proposed for knowledge graph embedding (KGE). However, most previous KGE methods ignore the semantic similarity between the related entities and entity-relation couples in different triples since they separately optimize each triple with the scoring function. To address this problem, we propose a simple yet efficient contrastive learning framework for tensor decomposition based (TDB) KGE, which can shorten the semantic distance of the related entities and entity-relation couples in different triples and thus improve the performance of KGE. We evaluate our proposed method on three standard KGE datasets: WN18RR, FB15k-237 and YAGO3-10. Our method can yield some new state-of-the-art results, achieving 51.2% MRR, 46.8% Hits@1 on the WN18RR dataset, 37.8% MRR, 28.6% Hits@1 on FB15k-237 dataset, and 59.1% MRR, 51.8% Hits@1 on the YAGO3-10 dataset.