Recent work on knowledge graph completion (KGC) focused on learning embeddings of entities and relations in knowledge graphs. These embedding methods require that all test entities are observed at training time, resulting in a time-consuming retraining process for out-of-knowledge-graph (OOKG) entities. To address this issue, current inductive knowledge embedding methods employ graph neural networks (GNNs) to represent unseen entities by aggregating information of known neighbors. They face three important challenges: (i) data sparsity, (ii) the presence of complex patterns in knowledge graphs (e.g., inter-rule correlations), and (iii) the presence of interactions among rule mining, rule inference, and embedding. In this paper, we propose a virtual neighbor network with inter-rule correlations (VNC) that consists of three stages: (i) rule mining, (ii) rule inference, and (iii) embedding. In the rule mining process, to identify complex patterns in knowledge graphs, both logic rules and inter-rule correlations are extracted from knowledge graphs based on operations over relation embeddings. To reduce data sparsity, virtual neighbors for OOKG entities are predicted and assigned soft labels by optimizing a rule-constrained problem. We also devise an iterative framework to capture the underlying relations between rule learning and embedding learning. In our experiments, results on both link prediction and triple classification tasks show that the proposed VNC framework achieves state-of-the-art performance on four widely-used knowledge graphs. Further analysis reveals that VNC is robust to the proportion of unseen entities and effectively mitigates data sparsity.
We consider a contrastive learning approach to knowledge graph embedding (KGE) via InfoNCE. For KGE, efficient learning relies on augmenting the training data with negative triples. However, most KGE works overlook the bias from generating the negative triples-false negative triples (factual triples missing from the knowledge graph). We argue that the generation of high-quality (i.e., hard) negative triples might lead to an increase in false negative triples. To mitigate the impact of false negative triples during the generation of hard negative triples, we propose the Hardness and Structure-aware (\textbf{HaSa}) contrastive KGE method, which alleviates the effect of false negative triples while generating the hard negative triples. Experiments show that HaSa improves the performance of InfoNCE-based KGE approaches and achieves state-of-the-art results in several metrics for WN18RR datasets and competitive results for FB15k-237 datasets compared to both classic and pre-trained LM-based KGE methods.
Temporal Knowledge graph completion (TKGC) is a crucial task that involves reasoning at known timestamps to complete the missing part of facts and has attracted more and more attention in recent years. Most existing methods focus on learning representations based on graph neural networks while inaccurately extracting information from timestamps and insufficiently utilizing the implied information in relations. To address these problems, we propose a novel TKGC model, namely Pre-trained Language Model with Prompts for TKGC (PPT). We convert a series of sampled quadruples into pre-trained language model inputs and convert intervals between timestamps into different prompts to make coherent sentences with implicit semantic information. We train our model with a masking strategy to convert TKGC task into a masked token prediction task, which can leverage the semantic information in pre-trained language models. Experiments on three benchmark datasets and extensive analysis demonstrate that our model has great competitiveness compared to other models with four metrics. Our model can effectively incorporate information from temporal knowledge graphs into the language models.
Self-supervised knowledge-graph completion (KGC) relies on estimating a scoring model over (entity, relation, entity)-tuples, for example, by embedding an initial knowledge graph. Prediction quality can be improved by calibrating the scoring model, typically by adjusting the prediction thresholds using manually annotated examples. In this paper, we attempt for the first time cold-start calibration for KGC, where no annotated examples exist initially for calibration, and only a limited number of tuples can be selected for annotation. Our new method ACTC finds good per-relation thresholds efficiently based on a limited set of annotated tuples. Additionally to a few annotated tuples, ACTC also leverages unlabeled tuples by estimating their correctness with Logistic Regression or Gaussian Process classifiers. We also experiment with different methods for selecting candidate tuples for annotation: density-based and random selection. Experiments with five scoring models and an oracle annotator show an improvement of 7% points when using ACTC in the challenging setting with an annotation budget of only 10 tuples, and an average improvement of 4% points over different budgets.
Knowledge graphs (KGs), as a structured form of knowledge representation, have been widely applied in the real world. Recently, few-shot knowledge graph completion (FKGC), which aims to predict missing facts for unseen relations with few-shot associated facts, has attracted increasing attention from practitioners and researchers. However, existing FKGC methods are based on metric learning or meta-learning, which often suffer from the out-of-distribution and overfitting problems. Meanwhile, they are incompetent at estimating uncertainties in predictions, which is critically important as model predictions could be very unreliable in few-shot settings. Furthermore, most of them cannot handle complex relations and ignore path information in KGs, which largely limits their performance. In this paper, we propose a normalizing flow-based neural process for few-shot knowledge graph completion (NP-FKGC). Specifically, we unify normalizing flows and neural processes to model a complex distribution of KG completion functions. This offers a novel way to predict facts for few-shot relations while estimating the uncertainty. Then, we propose a stochastic ManifoldE decoder to incorporate the neural process and handle complex relations in few-shot settings. To further improve performance, we introduce an attentive relation path-based graph neural network to capture path information in KGs. Extensive experiments on three public datasets demonstrate that our method significantly outperforms the existing FKGC methods and achieves state-of-the-art performance. Code is available at https://github.com/RManLuo/NP-FKGC.git.
Temporal knowledge graph completion (TKGC) aims to predict the missing links among the entities in a temporal knwoledge graph (TKG). Most previous TKGC methods only consider predicting the missing links among the entities seen in the training set, while they are unable to achieve great performance in link prediction concerning newly-emerged unseen entities. Recently, a new task, i.e., TKG few-shot out-of-graph (OOG) link prediction, is proposed, where TKGC models are required to achieve great link prediction performance concerning newly-emerged entities that only have few-shot observed examples. In this work, we propose a TKGC method FITCARL that combines few-shot learning with reinforcement learning to solve this task. In FITCARL, an agent traverses through the whole TKG to search for the prediction answer. A policy network is designed to guide the search process based on the traversed path. To better address the data scarcity problem in the few-shot setting, we introduce a module that computes the confidence of each candidate action and integrate it into the policy for action selection. We also exploit the entity concept information with a novel concept regularizer to boost model performance. Experimental results show that FITCARL achieves stat-of-the-art performance on TKG few-shot OOG link prediction.
Learning logical rules is critical to improving reasoning in KGs. This is due to their ability to provide logical and interpretable explanations when used for predictions, as well as their ability to generalize to other tasks, domains, and data. While recent methods have been proposed to learn logical rules, the majority of these methods are either restricted by their computational complexity and can not handle the large search space of large-scale KGs, or show poor generalization when exposed to data outside the training set. In this paper, we propose an end-to-end neural model for learning compositional logical rules called NCRL. NCRL detects the best compositional structure of a rule body, and breaks it into small compositions in order to infer the rule head. By recurrently merging compositions in the rule body with a recurrent attention unit, NCRL finally predicts a single rule head. Experimental results show that NCRL learns high-quality rules, as well as being generalizable. Specifically, we show that NCRL is scalable, efficient, and yields state-of-the-art results for knowledge graph completion on large-scale KGs. Moreover, we test NCRL for systematic generalization by learning to reason on small-scale observed graphs and evaluating on larger unseen ones.
Accurate identification of disease genes has consistently been one of the keys to decoding a disease's molecular mechanism. Most current approaches focus on constructing biological networks and utilizing machine learning, especially, deep learning to identify disease genes, but ignore the complex relations between entities in the biological knowledge graph. In this paper, we construct a biological knowledge graph centered on diseases and genes, and develop an end-to-end Knowledge graph completion model for Disease Gene Prediction using interactional tensor decomposition (called KDGene). KDGene introduces an interaction module between the embeddings of entities and relations to tensor decomposition, which can effectively enhance the information interaction in biological knowledge. Experimental results show that KDGene significantly outperforms state-of-the-art algorithms. Furthermore, the comprehensive biological analysis of the case of diabetes mellitus confirms KDGene's ability for identifying new and accurate candidate genes. This work proposes a scalable knowledge graph completion framework to identify disease candidate genes, from which the results are promising to provide valuable references for further wet experiments.
Knowledge graph completion (KGC) aims to discover missing relations of query entities. Current text-based models utilize the entity name and description to infer the tail entity given the head entity and a certain relation. Existing approaches also consider the neighborhood of the head entity. However, these methods tend to model the neighborhood using a flat structure and are only restricted to 1-hop neighbors. In this work, we propose a node neighborhood-enhanced framework for knowledge graph completion. It models the head entity neighborhood from multiple hops using graph neural networks to enrich the head node information. Moreover, we introduce an additional edge link prediction task to improve KGC. Evaluation on two public datasets shows that this framework is simple yet effective. The case study also shows that the model is able to predict explainable predictions.
A fundamental task for knowledge graphs (KGs) is knowledge graph completion (KGC). It aims to predict unseen edges by learning representations for all the entities and relations in a KG. A common concern when learning representations on traditional graphs is degree bias. It can affect graph algorithms by learning poor representations for lower-degree nodes, often leading to low performance on such nodes. However, there has been limited research on whether there exists degree bias for embedding-based KGC and how such bias affects the performance of KGC. In this paper, we validate the existence of degree bias in embedding-based KGC and identify the key factor to degree bias. We then introduce a novel data augmentation method, KG-Mixup, to generate synthetic triples to mitigate such bias. Extensive experiments have demonstrated that our method can improve various embedding-based KGC methods and outperform other methods tackling the bias problem on multiple benchmark datasets.
The task of fully inductive link prediction in knowledge graphs has gained significant attention, with various graph neural networks being proposed to address it. This task presents greater challenges than traditional inductive link prediction tasks with only new nodes, as models must be capable of zero-shot generalization to both unseen nodes and unseen relation types in the inference graph. Despite the development of novel models, a unifying theoretical understanding of their success remains elusive, and the limitations of these methods are not well-studied. In this work, we introduce the concept of double permutation-equivariant representations and demonstrate its necessity for effective performance in this task. We show that many existing models, despite their diverse architectural designs, conform to this framework. However, we also identify inherent limitations in double permutation-equivariant representations, which restrict these models's ability to learn effectively on datasets with varying characteristics. Our findings suggest that while double equivariance is necessary for meta-learning across knowledge graphs from different domains, it is not sufficient. There remains a fundamental gap between double permutation-equivariant models and the concept of foundation models designed to learn patterns across all domains.
In this paper we present a novel method, $\textit{Knowledge Persistence}$ ($\mathcal{KP}$), for faster evaluation of Knowledge Graph (KG) completion approaches. Current ranking-based evaluation is quadratic in the size of the KG, leading to long evaluation times and consequently a high carbon footprint. $\mathcal{KP}$ addresses this by representing the topology of the KG completion methods through the lens of topological data analysis, concretely using persistent homology. The characteristics of persistent homology allow $\mathcal{KP}$ to evaluate the quality of the KG completion looking only at a fraction of the data. Experimental results on standard datasets show that the proposed metric is highly correlated with ranking metrics (Hits@N, MR, MRR). Performance evaluation shows that $\mathcal{KP}$ is computationally efficient: In some cases, the evaluation time (validation+test) of a KG completion method has been reduced from 18 hours (using Hits@10) to 27 seconds (using $\mathcal{KP}$), and on average (across methods & data) reduces the evaluation time (validation+test) by $\approx$ $\textbf{99.96}\%$.
Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.
Numerous Graph Neural Networks (GNNs) have been developed to tackle the challenge of Knowledge Graph Embedding (KGE). However, many of these approaches overlook the crucial role of relation information and inadequately integrate it with entity information, resulting in diminished expressive power. In this paper, we propose a novel knowledge graph encoder that incorporates tensor decomposition within the aggregation function of Relational Graph Convolutional Network (R-GCN). Our model enhances the representation of neighboring entities by employing projection matrices of a low-rank tensor defined by relation types. This approach facilitates multi-task learning, thereby generating relation-aware representations. Furthermore, we introduce a low-rank estimation technique for the core tensor through CP decomposition, which effectively compresses and regularizes our model. We adopt a training strategy inspired by contrastive learning, which relieves the training limitation of the 1-N method inherent in handling vast graphs. We outperformed all our competitors on two common benchmark datasets, FB15k-237 and WN18RR, while using low-dimensional embeddings for entities and relations.
A temporal knowledge graph (TKG) stores the events derived from the data involving time. Predicting events is extremely challenging due to the time-sensitive property of events. Besides, the previous TKG completion (TKGC) approaches cannot represent both the timeliness and the causality properties of events, simultaneously. To address these challenges, we propose a Logic and Commonsense-Guided Embedding model (LCGE) to jointly learn the time-sensitive representation involving timeliness and causality of events, together with the time-independent representation of events from the perspective of commonsense. Specifically, we design a temporal rule learning algorithm to construct a rule-guided predicate embedding regularization strategy for learning the causality among events. Furthermore, we could accurately evaluate the plausibility of events via auxiliary commonsense knowledge. The experimental results of TKGC task illustrate the significant performance improvements of our model compared with the existing approaches. More interestingly, our model is able to provide the explainability of the predicted results in the view of causal inference. The source code and datasets of this paper are available at https://github.com/ngl567/LCGE.
We present the award-winning submission to the WikiKG90Mv2 track of OGB-LSC@NeurIPS 2022. The task is link-prediction on the large-scale knowledge graph WikiKG90Mv2, consisting of 90M+ nodes and 600M+ edges. Our solution uses a diverse ensemble of $85$ Knowledge Graph Embedding models combining five different scoring functions (TransE, TransH, RotatE, DistMult, ComplEx) and two different loss functions (log-sigmoid, sampled softmax cross-entropy). Each individual model is trained in parallel on a Graphcore Bow Pod$_{16}$ using BESS (Balanced Entity Sampling and Sharing), a new distribution framework for KGE training and inference based on balanced collective communications between workers. Our final model achieves a validation MRR of 0.2922 and a test-challenge MRR of 0.2562, winning the first place in the competition. The code is publicly available at: https://github.com/graphcore/distributed-kge-poplar/tree/2022-ogb-submission.
The ability of knowledge graphs to represent complex relationships at scale has led to their adoption for various needs including knowledge representation, question-answering, and recommendation systems. Knowledge graphs are often incomplete in the information they represent, necessitating the need for knowledge graph completion tasks. Pre-trained and fine-tuned language models have shown promise in these tasks although these models ignore the intrinsic information encoded in the knowledge graph, namely the entity and relation types. In this work, we propose the Knowledge Graph Language Model (KGLM) architecture, where we introduce a new entity/relation embedding layer that learns to differentiate distinctive entity and relation types, therefore allowing the model to learn the structure of the knowledge graph. In this work, we show that further pre-training the language models with this additional embedding layer using the triples extracted from the knowledge graph, followed by the standard fine-tuning phase sets a new state-of-the-art performance for the link prediction task on the benchmark datasets.
Completing missing facts is a fundamental task for temporal knowledge graphs (TKGs). Recently, graph neural network (GNN) based methods, which can simultaneously explore topological and temporal information, have become the state-of-the-art (SOTA) to complete TKGs. However, these studies are based on hand-designed architectures and fail to explore the diverse topological and temporal properties of TKG. To address this issue, we propose to use neural architecture search (NAS) to design data-specific message passing architecture for TKG completion. In particular, we develop a generalized framework to explore topological and temporal information in TKGs. Based on this framework, we design an expressive search space to fully capture various properties of different TKGs. Meanwhile, we adopt a search algorithm, which trains a supernet structure by sampling single path for efficient search with less cost. We further conduct extensive experiments on three benchmark datasets. The results show that the searched architectures by our method achieve the SOTA performances. Besides, the searched models can also implicitly reveal diverse properties in different TKGs. Our code is released in https://github.com/striderdu/SPA.
This paper presents a parameter-lite transfer learning approach of pretrained language models (LM) for knowledge graph (KG) completion. Instead of finetuning, which modifies all LM parameters, we only tune a few new parameters while keeping the original LM parameters fixed. We establish this via reformulating KG completion as a "fill-in-the-blank" task, and introducing a parameter-lite encoder on top of the original LMs. We show that, by tuning far fewer parameters than finetuning, LMs transfer non-trivially to most tasks and reach competitiveness with prior state-of-the-art approaches. For instance, we outperform the fully finetuning approaches on a KG completion benchmark by tuning only 1% of the parameters. The code and datasets are available at \url{https://github.com/yuanyehome/PALT}.
Large language models appear to learn facts from the large text corpora they are trained on. Such facts are encoded implicitly within their many parameters, making it difficult to verify or manipulate what knowledge has been learned. Language models have recently been extended to multilingual language models (MLLMs), enabling knowledge to be learned across hundreds of languages. Meanwhile, knowledge graphs contain facts in an explicit triple format, which require careful and costly curation and are only available in a few high-resource languages, restricting their research and application. To address these issues, we propose to enhance MLLMs with knowledge from multilingual knowledge graphs (MLKGs) so as to tackle language and knowledge graph tasks across many languages, including low-resource ones. Specifically, we introduce a lightweight adapter set to enhance MLLMs with cross-lingual entity alignment and facts from MLKGs for many languages. Experiments on common benchmarks show that such enhancement benefits both MLLMs and MLKGs, achieving: (1) comparable or improved performance for knowledge graph completion and entity alignment relative to baselines, especially for low-resource languages (for which knowledge graphs are unavailable); and (2) improved MLLM performance on language understanding tasks that require multilingual factual knowledge; all while maintaining performance on other general language tasks.