Graph embedding is becoming an important method with applications in various areas, including social networks and knowledge graph completion. In particular, Poincar\'e embedding has been proposed to capture the hierarchical structure of graphs, and its effectiveness has been reported. However, most of the existing methods have isometric mappings in the embedding space, and the choice of the origin point can be arbitrary. This fact is not desirable when the distance from the origin is used as an indicator of hierarchy, as in the case of Poincar\'e embedding. In this paper, we propose cone embedding, embedding method in a metric cone, which solve these problems, and we gain further benefits: 1) we provide an indicator of hierarchical information that is both geometrically and intuitively natural to interpret, and 2) we can extract the hierarchical structure from a graph embedding output of other methods by learning additional one-dimensional parameters.
Zero-shot Learning (ZSL), which aims to predict for those classes that have never appeared in the training data, has arisen hot research interests. The key of implementing ZSL is to leverage the prior knowledge of classes which builds the semantic relationship between classes and enables the transfer of the learned models (e.g., features) from training classes (i.e., seen classes) to unseen classes. However, the priors adopted by the existing methods are relatively limited with incomplete semantics. In this paper, we explore richer and more competitive prior knowledge to model the inter-class relationship for ZSL via ontology-based knowledge representation and semantic embedding. Meanwhile, to address the data imbalance between seen classes and unseen classes, we developed a generative ZSL framework with Generative Adversarial Networks (GANs). Our main findings include: (i) an ontology-enhanced ZSL framework that can be applied to different domains, such as image classification (IMGC) and knowledge graph completion (KGC); (ii) a comprehensive evaluation with multiple zero-shot datasets from different domains, where our method often achieves better performance than the state-of-the-art models. In particular, on four representative ZSL baselines of IMGC, the ontology-based class semantics outperform the previous priors e.g., the word embeddings of classes by an average of 12.4 accuracy points in the standard ZSL across two example datasets (see Figure 4).
Knowledge graph completion refers to predicting missing triples. Most approaches achieve this goal by predicting entities, given an entity and a relation. We predict missing triples via the relation prediction. To this end, we frame the relation prediction problem as a multi-label classification problem and propose a shallow neural model (SHALLOM) that accurately infers missing relations from entities. SHALLOM is analogous to C-BOW as both approaches predict a central token (p) given surrounding tokens ((s,o)). Our experiments indicate that SHALLOM outperforms state-of-the-art approaches on the FB15K-237 and WN18RR with margins of up to $3\%$ and $8\%$ (absolute), respectively, while requiring a maximum training time of 8 minutes on these datasets. We ensure the reproducibility of our results by providing an open-source implementation including training and evaluation scripts at {\url{https://github.com/dice-group/Shallom}.}
Knowledge Graph Completion is a task of expanding the knowledge graph/base through estimating possible entities, or proper nouns, that can be connected using a set of predefined relations, or verb/predicates describing interconnections of two things. Generally, we describe this problem as adding new edges to a current network of vertices and edges. Traditional approaches mainly focus on using the existing graphical information that is intrinsic of the graph and train the corresponding embeddings to describe the information; however, we think that the corpus that are related to the entities should also contain information that can positively influence the embeddings to better make predictions. In our project, we try numerous ways of using extracted or raw textual information to help existing KG embedding frameworks reach better prediction results, in the means of adding a similarity function to the regularization part in the loss function. Results have shown that we have made decent improvements over baseline KG embedding methods.
Temporal knowledge graphs (TKGs) inherently reflect the transient nature of real-world knowledge, as opposed to static knowledge graphs. Naturally, automatic TKG completion has drawn much research interests for a more realistic modeling of relational reasoning. However, most of the existing mod-els for TKG completion extend static KG embeddings that donot fully exploit TKG structure, thus lacking in 1) account-ing for temporally relevant events already residing in the lo-cal neighborhood of a query, and 2) path-based inference that facilitates multi-hop reasoning and better interpretability. In this paper, we propose T-GAP, a novel model for TKG completion that maximally utilizes both temporal information and graph structure in its encoder and decoder. T-GAP encodes query-specific substructure of TKG by focusing on the temporal displacement between each event and the query times-tamp, and performs path-based inference by propagating attention through the graph. Our empirical experiments demonstrate that T-GAP not only achieves superior performance against state-of-the-art baselines, but also competently generalizes to queries with unseen timestamps. Through extensive qualitative analyses, we also show that T-GAP enjoys from transparent interpretability, and follows human intuition in its reasoning process.
Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug discovery rely on incorporating information from different biomedical databases. These databases contain various biological entities and relations such as proteins (PDB), genes (Gene Ontology), drugs (DrugBank), diseases (DDB), and protein-protein interactions (BioGRID). The process of semantically integrating heterogeneous biomedical databases is often riddled with imperfections. The quality of data-driven drug discovery relies on the accuracy of the mining methods used and the data's quality as well. Thus, having complete and refined biomedical knowledge graphs is central to achieving more accurate drug discovery outcomes. Here we propose using the latest graph representation learning and embedding models to refine and complete biomedical knowledge graphs. This preliminary work demonstrates learning discrete representations of the integrated biomedical knowledge graph Chem2Bio2RD [3]. We perform a knowledge graph completion and refinement task using a simple top-K cosine similarity measure between the learned embedding vectors to predict missing links between drugs and targets present in the data. We show that this simple procedure can be used alternatively to binary classifiers in link prediction.
Large knowledge graphs often grow to store temporal facts that model the dynamic relations or interactions of entities along the timeline. Since such temporal knowledge graphs often suffer from incompleteness, it is important to develop time-aware representation learning models that help to infer the missing temporal facts. While the temporal facts are typically evolving, it is observed that many facts often show a repeated pattern along the timeline, such as economic crises and diplomatic activities. This observation indicates that a model could potentially learn much from the known facts appeared in history. To this end, we propose a new representation learning model for temporal knowledge graphs, namely CyGNet, based on a novel timeaware copy-generation mechanism. CyGNet is not only able to predict future facts from the whole entity vocabulary, but also capable of identifying facts with repetition and accordingly predicting such future facts with reference to the known facts in the past. We evaluate the proposed method on the knowledge graph completion task using five benchmark datasets. Extensive experiments demonstrate the effectiveness of CyGNet for predicting future facts with repetition as well as de novo fact prediction.
Most researches for knowledge graph completion learn representations of entities and relations to predict missing links in incomplete knowledge graphs. However, these methods fail to take full advantage of both the contextual information of entity and relation. Here, we extract contexts of entities and relations from the triplets which they compose. We propose a model named AggrE, which conducts efficient aggregations respectively on entity context and relation context in multi-hops, and learns context-enhanced entity and relation embeddings for knowledge graph completion. The experiment results show that AggrE is competitive to existing models.
Relation and event extraction is an important task in natural language processing. We introduce a system which uses contextualized knowledge graph completion to classify relations and events between known entities in a noisy text environment. We report results which show that our system is able to effectively extract relations and events from a dataset of wet lab protocols.
Most existing knowledge graphs suffer from incompleteness. Embedding knowledge graphs into continuous vector spaces has recently attracted increasing interest in knowledge base completion. However, in most existing embedding methods, only fact triplets are utilized, and logical rules have not been thoroughly studied for the knowledge base completion task. To overcome the problem, we propose an association rules enhanced knowledge graph attention network (AR-KGAT). The AR-KGAT captures both entity and relation features for high-order neighborhoods of any given entity in an end-to-end manner under the graph attention network framework. The major component of AR-KGAT is an encoder of an effective neighborhood aggregator, which addresses the problems by aggregating neighbors with both association-rules-based and graph-based attention weights. Additionally, the proposed model also encapsulates the representations from multi-hop neighbors of nodes to refine their embeddings. The decoder enables AR-KGAT to be translational between entities and relations while keeping the superior link prediction performance. A logic-like inference pattern is utilized as constraints for knowledge graph embedding. Then, the global loss is minimized over both atomic and complex formulas to achieve the embedding task. In this manner, we learn embeddings compatible with triplets and rules, which are certainly more predictive for knowledge acquisition and inference. We conduct extensive experiments on two benchmark datasets: WN18RR and FB15k-237, for two knowledge graph completion tasks: the link prediction and triplet classification to evaluate the proposed AR-KGAT model. The results show that the proposed AR-KGAT model achieves significant and consistent improvements over state-of-the-art methods.
Knowledge graphs have been demonstrated to be an effective tool for numerous intelligent applications. However, a large amount of valuable knowledge still exists implicitly in the knowledge graphs. To enrich the existing knowledge graphs, recent years witness that many algorithms for link prediction and knowledge graphs embedding have been designed to infer new facts. But most of these studies focus on the static knowledge graphs and ignore the temporal information that reflects the validity of knowledge. Developing the model for temporal knowledge graphs completion is an increasingly important task. In this paper, we build a new tensor decomposition model for temporal knowledge graphs completion inspired by the Tucker decomposition of order 4 tensor. We demonstrate that the proposed model is fully expressive and report state-of-the-art results for several public benchmarks. Additionally, we present several regularization schemes to improve the strategy and study their impact on the proposed model. Experimental studies on three temporal datasets (i.e. ICEWS2014, ICEWS2005-15, GDELT) justify our design and demonstrate that our model outperforms baselines with an explicit margin on link prediction task.
Discovering precise and interpretable rules from knowledge graphs is regarded as an essential challenge, which can improve the performances of many downstream tasks and even provide new ways to approach some Natural Language Processing research topics. In this paper, we present a fundamental theory for rule-based knowledge graph reasoning, based on which the connectivity dependencies in the graph are captured via multiple rule types. It is the first time for some of these rule types in a knowledge graph to be considered. Based on these rule types, our theory can provide precise interpretations to unknown triples. Then, we implement our theory by what we call the RuleDict model. Results show that our RuleDict model not only provides precise rules to interpret new triples, but also achieves state-of-the-art performances on one benchmark knowledge graph completion task, and is competitive on other tasks.
Tensor factorization based models have shown great power in knowledge graph completion (KGC). However, their performance usually suffers from the overfitting problem seriously. This motivates various regularizers -- such as the squared Frobenius norm and tensor nuclear norm regularizers -- while the limited applicability significantly limits their practical usage. To address this challenge, we propose a novel regularizer -- namely, DUality-induced RegulArizer (DURA) -- which is not only effective in improving the performance of existing models but widely applicable to various methods. The major novelty of DURA is based on the observation that, for an existing tensor factorization based KGC model (primal), there is often another distance based KGC model (dual) closely associated with it. Experiments show that DURA yields consistent and significant improvements on benchmarks.
The existing literature on knowledge graph completion mostly focuses on the link prediction task. However, knowledge graphs have an additional incompleteness problem: their nodes possess numerical attributes, whose values are often missing. Our approach, denoted as MrAP, imputes the values of missing attributes by propagating information across the multi-relational structure of a knowledge graph. It employs regression functions for predicting one node attribute from another depending on the relationship between the nodes and the type of the attributes. The propagation mechanism operates iteratively in a message passing scheme that collects the predictions at every iteration and updates the value of the node attributes. Experiments over two benchmark datasets show the effectiveness of our approach.
There has recently been increasing interest in learning representations of temporal knowledge graphs (KGs), which record the dynamic relationships between entities over time. Temporal KGs often exhibit multiple simultaneous non-Euclidean structures, such as hierarchical and cyclic structures. However, existing embedding approaches for temporal KGs typically learn entity representations and their dynamic evolution in the Euclidean space, which might not capture such intrinsic structures very well. To this end, we propose Dy- ERNIE, a non-Euclidean embedding approach that learns evolving entity representations in a product of Riemannian manifolds, where the composed spaces are estimated from the sectional curvatures of underlying data. Product manifolds enable our approach to better reflect a wide variety of geometric structures on temporal KGs. Besides, to capture the evolutionary dynamics of temporal KGs, we let the entity representations evolve according to a velocity vector defined in the tangent space at each timestamp. We analyze in detail the contribution of geometric spaces to representation learning of temporal KGs and evaluate our model on temporal knowledge graph completion tasks. Extensive experiments on three real-world datasets demonstrate significantly improved performance, indicating that the dynamics of multi-relational graph data can be more properly modeled by the evolution of embeddings on Riemannian manifolds.
Knowledge graphs (KGs) consisting of triples are always incomplete, so it's important to do Knowledge Graph Completion (KGC) by predicting missing triples. Multi-Source KG is a common situation in real KG applications which can be viewed as a set of related individual KGs where different KGs contains relations of different aspects of entities. It's intuitive that, for each individual KG, its completion could be greatly contributed by the triples defined and labeled in other ones. However, because of the data privacy and sensitivity, a set of relevant knowledge graphs cannot complement each other's KGC by just collecting data from different knowledge graphs together. Therefore, in this paper, we introduce federated setting to keep their privacy without triple transferring between KGs and apply it in embedding knowledge graph, a typical method which have proven effective for KGC in the past decade. We propose a Federated Knowledge Graph Embedding framework FedE, focusing on learning knowledge graph embeddings by aggregating locally-computed updates. Finally, we conduct extensive experiments on datasets derived from KGE benchmark datasets and results show the effectiveness of our proposed FedE.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
Objective: To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. Methods: We propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from both PubMed and COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant, and used this subset to construct a knowledge graph. Five SOTA, neural knowledge graph completion algorithms were used to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach. Results: Accuracy classifier based on PubMedBERT achieved the best performance (F1= 0.854) in classifying semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1=0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as some candidate drugs that have not yet been studied. Discovery patterns enabled generation of plausible hypotheses regarding the relationships between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (paclitaxel, SB 203580, alpha 2-antiplasmin, pyrrolidine dithiocarbamate, and butylated hydroxytoluene) with their mechanistic explanations were further discussed. Conclusion: We show that an LBD approach can be feasible for discovering drug candidates for COVID-19, and for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions.
Link prediction based on knowledge graph embeddings (KGE) aims to predict new triples to automatically construct knowledge graphs (KGs). However, recent KGE models achieve performance improvements by excessively increasing the embedding dimensions, which may cause enormous training costs and require more storage space. In this paper, instead of training high-dimensional models, we propose MulDE, a novel knowledge distillation framework, which includes multiple low-dimensional hyperbolic KGE models as teachers and two student components, namely Junior and Senior. Under a novel iterative distillation strategy, the Junior component, a low-dimensional KGE model, asks teachers actively based on its preliminary prediction results, and the Senior component integrates teachers' knowledge adaptively to train the Junior component based on two mechanisms: relation-specific scaling and contrast attention. The experimental results show that MulDE can effectively improve the performance and training speed of low-dimensional KGE models. The distilled 32-dimensional model is competitive compared to the state-of-the-art high-dimensional methods on several widely-used datasets.
Many graph embedding approaches have been proposed for knowledge graph completion via link prediction. Among those, translating embedding approaches enjoy the advantages of light-weight structure, high efficiency and great interpretability. Especially when extended to complex vector space, they show the capability in handling various relation patterns including symmetry, antisymmetry, inversion and composition. However, previous translating embedding approaches defined in complex vector space suffer from two main issues: 1) representing and modeling capacities of the model are limited by the translation function with rigorous multiplication of two complex numbers; and 2) embedding ambiguity caused by one-to-many relations is not explicitly alleviated. In this paper, we propose a relation-adaptive translation function built upon a novel weighted product in complex space, where the weights are learnable, relation-specific and independent to embedding size. The translation function only requires eight more scalar parameters each relation, but improves expressive power and alleviates embedding ambiguity problem. Based on the function, we then present our Relation-adaptive translating Embedding (RatE) approach to score each graph triple. Moreover, a novel negative sampling method is proposed to utilize both prior knowledge and self-adversarial learning for effective optimization. Experiments verify RatE achieves state-of-the-art performance on four link prediction benchmarks.