Despite being the go-to choice for link prediction on knowledge graphs, research on interpretability of knowledge graph embeddings (KGE) has been relatively unexplored. We present KGEx, a novel post-hoc method that explains individual link predictions by drawing inspiration from surrogate models research. Given a target triple to predict, KGEx trains surrogate KGE models that we use to identify important training triples. To gauge the impact of a training triple, we sample random portions of the target triple neighborhood and we train multiple surrogate KGE models on each of them. To ensure faithfulness, each surrogate is trained by distilling knowledge from the original KGE model. We then assess how well surrogates predict the target triple being explained, the intuition being that those leading to faithful predictions have been trained on impactful neighborhood samples. Under this assumption, we then harvest triples that appear frequently across impactful neighborhoods. We conduct extensive experiments on two publicly available datasets, to demonstrate that KGEx is capable of providing explanations faithful to the black-box model.
Designing a new clinical trial entails many decisions, such as defining a cohort and setting the study objectives to name a few, and therefore can benefit from recommendations based on exhaustive mining of past clinical trial records. Here, we propose a novel recommendation methodology, based on neural embeddings trained on a first-of-a-kind knowledge graph of clinical trials. We addressed several important research questions in this context, including designing a knowledge graph (KG) for clinical trial data, effectiveness of various KG embedding (KGE) methods for it, a novel inductive inference using KGE, and its use in generating recommendations for clinical trial design. We used publicly available data from clinicaltrials.gov for the study. Results show that our recommendations approach achieves relevance scores of 70%-83%, measured as the text similarity to actual clinical trial elements, and the most relevant recommendation can be found near the top of list. Our study also suggests potential improvement in training KGE using node semantics.
The way we analyse clinical texts has undergone major changes over the last years. The introduction of language models such as BERT led to adaptations for the (bio)medical domain like PubMedBERT and ClinicalBERT. These models rely on large databases of archived medical documents. While performing well in terms of accuracy, both the lack of interpretability and limitations to transfer across languages limit their use in clinical setting. We introduce a novel light-weight graph-based embedding method specifically catering radiology reports. It takes into account the structure and composition of the report, while also connecting medical terms in the report through the multi-lingual SNOMED Clinical Terms knowledge base. The resulting graph embedding uncovers the underlying relationships among clinical terms, achieving a representation that is better understandable for clinicians and clinically more accurate, without reliance on large pre-training datasets. We show the use of this embedding on two tasks namely disease classification of X-ray reports and image classification. For disease classification our model is competitive with its BERT-based counterparts, while being magnitudes smaller in size and training data requirements. For image classification, we show the effectiveness of the graph embedding leveraging cross-modal knowledge transfer and show how this method is usable across different languages.
Knowledge graph embeddings are dense numerical representations of entities in a knowledge graph (KG). While the majority of approaches concentrate only on relational information, i.e., relations between entities, fewer approaches exist which also take information about literal values (e.g., textual descriptions or numerical information) into account. Those which exist are typically tailored towards a particular modality of literal and a particular embedding method. In this paper, we propose a set of universal preprocessing operators which can be used to transform KGs with literals for numerical, temporal, textual, and image information, so that the transformed KGs can be embedded with any method. The results on the kgbench dataset with three different embedding methods show promising results.
Large language models show human-like performance in knowledge extraction, reasoning and dialogue, but it remains controversial whether this performance is best explained by memorization and pattern matching, or whether it reflects human-like inferential semantics and world knowledge. Knowledge bases such as WikiData provide large-scale, high-quality representations of inferential semantics and world knowledge. We show that large language models learn to organize concepts in ways that are strikingly similar to how concepts are organized in such knowledge bases. Knowledge bases model collective, institutional knowledge, and large language models seem to induce such knowledge from raw text. We show that bigger and better models exhibit more human-like concept organization, across four families of language models and three knowledge graph embeddings.
The Natural Language Processing(NLP) community has been using crowd sourcing techniques to create benchmark datasets such as General Language Understanding and Evaluation(GLUE) for training modern Language Models such as BERT. GLUE tasks measure the reliability scores using inter annotator metrics i.e. Cohens Kappa. However, the reliability aspect of LMs has often been overlooked. To counter this problem, we explore a knowledge-guided LM ensembling approach that leverages reinforcement learning to integrate knowledge from ConceptNet and Wikipedia as knowledge graph embeddings. This approach mimics human annotators resorting to external knowledge to compensate for information deficits in the datasets. Across nine GLUE datasets, our research shows that ensembling strengthens reliability and accuracy scores, outperforming state of the art.
Pain is a complex concept that can interconnect with other concepts such as a disorder that might cause pain, a medication that might relieve pain, and so on. To fully understand the context of pain experienced by either an individual or across a population, we may need to examine all concepts related to pain and the relationships between them. This is especially useful when modeling pain that has been recorded in electronic health records. Knowledge graphs represent concepts and their relations by an interlinked network, enabling semantic and context-based reasoning in a computationally tractable form. These graphs can, however, be too large for efficient computation. Knowledge graph embeddings help to resolve this by representing the graphs in a low-dimensional vector space. These embeddings can then be used in various downstream tasks such as classification and link prediction. The various relations associated with pain which are required to construct such a knowledge graph can be obtained from external medical knowledge bases such as SNOMED CT, a hierarchical systematic nomenclature of medical terms. A knowledge graph built in this way could be further enriched with real-world examples of pain and its relations extracted from electronic health records. This paper describes the construction of such knowledge graph embedding models of pain concepts, extracted from the unstructured text of mental health electronic health records, combined with external knowledge created from relations described in SNOMED CT, and their evaluation on a subject-object link prediction task. The performance of the models was compared with other baseline models.
Recent works in neural knowledge graph inference attempt to combine logic rules with knowledge graph embeddings to benefit from prior knowledge. However, they usually cannot avoid rule grounding, and injecting a diverse set of rules has still not been thoroughly explored. In this work, we propose InjEx, a mechanism to inject multiple types of rules through simple constraints, which capture definite Horn rules. To start, we theoretically prove that InjEx can inject such rules. Next, to demonstrate that InjEx infuses interpretable prior knowledge into the embedding space, we evaluate InjEx on both the knowledge graph completion (KGC) and few-shot knowledge graph completion (FKGC) settings. Our experimental results reveal that InjEx outperforms both baseline KGC models as well as specialized few-shot models while maintaining its scalability and efficiency.
A knowledge graph is a powerful representation of real-world entities and their relations. The vast majority of these relations are defined as positive statements, but the importance of negative statements is increasingly recognized, especially under an Open World Assumption. Explicitly considering negative statements has been shown to improve performance on tasks such as entity summarization and question answering or domain-specific tasks such as protein function prediction. However, no attention has been given to the exploration of negative statements by knowledge graph embedding approaches despite the potential of negative statements to produce more accurate representations of entities in a knowledge graph. We propose a novel approach, TrueWalks, to incorporate negative statements into the knowledge graph representation learning process. In particular, we present a novel walk-generation method that is able to not only differentiate between positive and negative statements but also take into account the semantic implications of negation in ontology-rich knowledge graphs. This is of particular importance for applications in the biomedical domain, where the inadequacy of embedding approaches regarding negative statements at the ontology level has been identified as a crucial limitation. We evaluate TrueWalks in ontology-rich biomedical knowledge graphs in two different predictive tasks based on KG embeddings: protein-protein interaction prediction and gene-disease association prediction. We conduct an extensive analysis over established benchmarks and demonstrate that our method is able to improve the performance of knowledge graph embeddings on all tasks.
As a crucial extension of entity alignment (EA), multi-modal entity alignment (MMEA) aims to identify identical entities across disparate knowledge graphs (KGs) by exploiting associated visual information. However, existing MMEA approaches primarily concentrate on the fusion paradigm of multi-modal entity features, while neglecting the challenges presented by the pervasive phenomenon of missing and intrinsic ambiguity of visual images. In this paper, we present a further analysis of visual modality incompleteness, benchmarking latest MMEA models on our proposed dataset MMEA-UMVM, where the types of alignment KGs covering bilingual and monolingual, with standard (non-iterative) and iterative training paradigms to evaluate the model performance. Our research indicates that, in the face of modality incompleteness, models succumb to overfitting the modality noise, and exhibit performance oscillations or declines at high rates of missing modality. This proves that the inclusion of additional multi-modal data can sometimes adversely affect EA. To address these challenges, we introduce UMAEA , a robust multi-modal entity alignment approach designed to tackle uncertainly missing and ambiguous visual modalities. It consistently achieves SOTA performance across all 97 benchmark splits, significantly surpassing existing baselines with limited parameters and time consumption, while effectively alleviating the identified limitations of other models. Our code and benchmark data are available at https://github.com/zjukg/UMAEA.
Knowledge graphs represent facts about real-world entities. Most of these facts are defined as positive statements. The negative statements are scarce but highly relevant under the open-world assumption. Furthermore, they have been demonstrated to improve the performance of several applications, namely in the biomedical domain. However, no benchmark dataset supports the evaluation of the methods that consider these negative statements. We present a collection of datasets for three relation prediction tasks - protein-protein interaction prediction, gene-disease association prediction and disease prediction - that aim at circumventing the difficulties in building benchmarks for knowledge graphs with negative statements. These datasets include data from two successful biomedical ontologies, Gene Ontology and Human Phenotype Ontology, enriched with negative statements. We also generate knowledge graph embeddings for each dataset with two popular path-based methods and evaluate the performance in each task. The results show that the negative statements can improve the performance of knowledge graph embeddings.
Knowledge graphs have proven to be effective for modeling entities and their relationships through the use of ontologies. The recent emergence in interest for using knowledge graphs as a form of information modeling has led to their increased adoption in recommender systems. By incorporating users and items into the knowledge graph, these systems can better capture the implicit connections between them and provide more accurate recommendations. In this paper, we investigate and propose the construction of a personalized recommender system via knowledge graphs embedding applied to the vehicle purchase/sale domain. The results of our experimentation demonstrate the efficacy of the proposed method in providing relevant recommendations that are consistent with individual users.
Knowledge graph embeddings (KGE) have been extensively studied to embed large-scale relational data for many real-world applications. Existing methods have long ignored the fact many KGs contain two fundamentally different views: high-level ontology-view concepts and fine-grained instance-view entities. They usually embed all nodes as vectors in one latent space. However, a single geometric representation fails to capture the structural differences between two views and lacks probabilistic semantics towards concepts' granularity. We propose Concept2Box, a novel approach that jointly embeds the two views of a KG using dual geometric representations. We model concepts with box embeddings, which learn the hierarchy structure and complex relations such as overlap and disjoint among them. Box volumes can be interpreted as concepts' granularity. Different from concepts, we model entities as vectors. To bridge the gap between concept box embeddings and entity vector embeddings, we propose a novel vector-to-box distance metric and learn both embeddings jointly. Experiments on both the public DBpedia KG and a newly-created industrial KG showed the effectiveness of Concept2Box.
Knowledge graphs represent real-world entities and their relations in a semantically-rich structure supported by ontologies. Exploring this data with machine learning methods often relies on knowledge graph embeddings, which produce latent representations of entities that preserve structural and local graph neighbourhood properties, but sacrifice explainability. However, in tasks such as link or relation prediction, understanding which specific features better explain a relation is crucial to support complex or critical applications. We propose SEEK, a novel approach for explainable representations to support relation prediction in knowledge graphs. It is based on identifying relevant shared semantic aspects (i.e., subgraphs) between entities and learning representations for each subgraph, producing a multi-faceted and explainable representation. We evaluate SEEK on two real-world highly complex relation prediction tasks: protein-protein interaction prediction and gene-disease association prediction. Our extensive analysis using established benchmarks demonstrates that SEEK achieves significantly better performance than standard learning representation methods while identifying both sufficient and necessary explanations based on shared semantic aspects.
Relation extraction task is a crucial and challenging aspect of Natural Language Processing. Several methods have surfaced as of late, exhibiting notable performance in addressing the task; however, most of these approaches rely on vast amounts of data from large-scale knowledge graphs or language models pretrained on voluminous corpora. In this paper, we hone in on the effective utilization of solely the knowledge supplied by a corpus to create a high-performing model. Our objective is to showcase that by leveraging the hierarchical structure and relational distribution of entities within a corpus without introducing external knowledge, a relation extraction model can achieve significantly enhanced performance. We therefore proposed a relation extraction approach based on the incorporation of pretrained knowledge graph embeddings at the corpus scale into the sentence-level contextual representation. We conducted a series of experiments which revealed promising and very interesting results for our proposed approach.The obtained results demonstrated an outperformance of our method compared to context-based relation extraction models.
Knowledge graph embedding models (KGEMs) have gained considerable traction in recent years. These models learn a vector representation of knowledge graph entities and relations, a.k.a. knowledge graph embeddings (KGEs). Learning versatile KGEs is desirable as it makes them useful for a broad range of tasks. However, KGEMs are usually trained for a specific task, which makes their embeddings task-dependent. In parallel, the widespread assumption that KGEMs actually create a semantic representation of the underlying entities and relations (e.g., project similar entities closer than dissimilar ones) has been challenged. In this work, we design heuristics for generating protographs -- small, modified versions of a KG that leverage RDF/S information. The learnt protograph-based embeddings are meant to encapsulate the semantics of a KG, and can be leveraged in learning KGEs that, in turn, also better capture semantics. Extensive experiments on various evaluation benchmarks demonstrate the soundness of this approach, which we call Modular and Agnostic SCHema-based Integration of protograph Embeddings (MASCHInE). In particular, MASCHInE helps produce more versatile KGEs that yield substantially better performance for entity clustering and node classification tasks. For link prediction, using MASCHinE substantially increases the number of semantically valid predictions with equivalent rank-based performance.
Joint representation learning over multi-sourced knowledge graphs (KGs) yields transferable and expressive embeddings that improve downstream tasks. Entity alignment (EA) is a critical step in this process. Despite recent considerable research progress in embedding-based EA, how it works remains to be explored. In this paper, we provide a similarity flooding perspective to explain existing translation-based and aggregation-based EA models. We prove that the embedding learning process of these models actually seeks a fixpoint of pairwise similarities between entities. We also provide experimental evidence to support our theoretical analysis. We propose two simple but effective methods inspired by the fixpoint computation in similarity flooding, and demonstrate their effectiveness on benchmark datasets. Our work bridges the gap between recent embedding-based models and the conventional similarity flooding algorithm. It would improve our understanding of and increase our faith in embedding-based EA.
Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.
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.
Heterogeneous graph neural networks (HGNNs) can learn from typed and relational graph data more effectively than conventional GNNs. With larger parameter spaces, HGNNs may require more training data, which is often scarce in real-world applications due to privacy regulations (e.g., GDPR). Federated graph learning (FGL) enables multiple clients to train a GNN collaboratively without sharing their local data. However, existing FGL methods mainly focus on homogeneous GNNs or knowledge graph embeddings; few have considered heterogeneous graphs and HGNNs. In federated heterogeneous graph learning, clients may have private graph schemas. Conventional FL/FGL methods attempting to define a global HGNN model would violate schema privacy. To address these challenges, we propose FedHGN, a novel and general FGL framework for HGNNs. FedHGN adopts schema-weight decoupling to enable schema-agnostic knowledge sharing and employs coefficients alignment to stabilize the training process and improve HGNN performance. With better privacy preservation, FedHGN consistently outperforms local training and conventional FL methods on three widely adopted heterogeneous graph datasets with varying client numbers. The code is available at https://github.com/cynricfu/FedHGN .