Many applications need access to background knowledge about how different concepts and entities are related. Although Knowledge Graphs (KG) and Large Language Models (LLM) can address this need to some extent, KGs are inevitably incomplete and their relational schema is often too coarse-grained, while LLMs are inefficient and difficult to control. As an alternative, we propose to extract relation embeddings from relatively small language models. In particular, we show that masked language models such as RoBERTa can be straightforwardly fine-tuned for this purpose, using only a small amount of training data. The resulting model, which we call RelBERT, captures relational similarity in a surprisingly fine-grained way, allowing us to set a new state-of-the-art in analogy benchmarks. Crucially, RelBERT is capable of modelling relations that go well beyond what the model has seen during training. For instance, we obtained strong results on relations between named entities with a model that was only trained on lexical relations between concepts, and we observed that RelBERT can recognise morphological analogies despite not being trained on such examples. Overall, we find that RelBERT significantly outperforms strategies based on prompting language models that are several orders of magnitude larger, including recent GPT-based models and open source models.
Large language models (LLMs) have demonstrated impressive reasoning abilities in complex tasks. However, they lack up-to-date knowledge and experience hallucinations during reasoning, which can lead to incorrect reasoning processes and diminish their performance and trustworthiness. Knowledge graphs (KGs), which capture vast amounts of facts in a structured format, offer a reliable source of knowledge for reasoning. Nevertheless, existing KG-based LLM reasoning methods only treat KGs as factual knowledge bases and overlook the importance of their structural information for reasoning. In this paper, we propose a novel method called reasoning on graphs (RoG) that synergizes LLMs with KGs to enable faithful and interpretable reasoning. Specifically, we present a planning-retrieval-reasoning framework, where RoG first generates relation paths grounded by KGs as faithful plans. These plans are then used to retrieve valid reasoning paths from the KGs for LLMs to conduct faithful reasoning. Furthermore, RoG not only distills knowledge from KGs to improve the reasoning ability of LLMs through training but also allows seamless integration with any arbitrary LLMs during inference. Extensive experiments on two benchmark KGQA datasets demonstrate that RoG achieves state-of-the-art performance on KG reasoning tasks and generates faithful and interpretable reasoning results.
knowledge graph-based recommendation methods have achieved great success in the field of recommender systems. However, over-reliance on high-quality knowledge graphs is a bottleneck for such methods. Specifically, the long-tailed distribution of entities of KG and noise issues in the real world will make item-entity dependent relations deviate from reflecting true characteristics and significantly harm the performance of modeling user preference. Contrastive learning, as a novel method that is employed for data augmentation and denoising, provides inspiration to fill this research gap. However, the mainstream work only focuses on the long-tail properties of the number of items clicked, while ignoring that the long-tail properties of total number of clicks per user may also affect the performance of the recommendation model. Therefore, to tackle these problems, motivated by the Debiased Contrastive Learning of Unsupervised Sentence Representations (DCLR), we propose Two-Level Debiased Contrastive Graph Learning (TDCGL) model. Specifically, we design the Two-Level Debiased Contrastive Learning (TDCL) and deploy it in the KG, which is conducted not only on User-Item pairs but also on User-User pairs for modeling higher-order relations. Also, to reduce the bias caused by random sampling in contrastive learning, with the exception of the negative samples obtained by random sampling, we add a noise-based generation of negation to ensure spatial uniformity. Considerable experiments on open-source datasets demonstrate that our method has excellent anti-noise capability and significantly outperforms state-of-the-art baselines. In addition, ablation studies about the necessity for each level of TDCL are conducted.
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.
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Large Language Models (LLMs) are advancing at a rapid pace, with significant improvements at natural language processing and coding tasks. Yet, their ability to work with formal languages representing data, specifically within the realm of knowledge graph engineering, remains under-investigated. To evaluate the proficiency of various LLMs, we created a set of five tasks that probe their ability to parse, understand, analyze, and create knowledge graphs serialized in Turtle syntax. These tasks, each embodying distinct degrees of complexity and being able to scale with the size of the problem, have been integrated into our automated evaluation system, the LLM-KG-Bench. The evaluation encompassed four commercially available LLMs - GPT-3.5, GPT-4, Claude 1.3, and Claude 2.0, as well as two freely accessible offline models, GPT4All Vicuna and GPT4All Falcon 13B. This analysis offers an in-depth understanding of the strengths and shortcomings of LLMs in relation to their application within RDF knowledge graph engineering workflows utilizing Turtle representation. While our findings show that the latest commercial models outperform their forerunners in terms of proficiency with the Turtle language, they also reveal an apparent weakness. These models fall short when it comes to adhering strictly to the output formatting constraints, a crucial requirement in this context.
Existing multi-relational graph neural networks use one of two strategies for identifying informative relations: either they reduce this problem to low-level weight learning, or they rely on handcrafted chains of relational dependencies, called meta-paths. However, the former approach faces challenges in the presence of many relations (e.g., knowledge graphs), while the latter requires substantial domain expertise to identify relevant meta-paths. In this work we propose a novel approach to learn meta-paths and meta-path GNNs that are highly accurate based on a small number of informative meta-paths. Key element of our approach is a scoring function for measuring the potential informativeness of a relation in the incremental construction of the meta-path. Our experimental evaluation shows that the approach manages to correctly identify relevant meta-paths even with a large number of relations, and substantially outperforms existing multi-relational GNNs on synthetic and real-world experiments.
With the recent spike in the number and availability of Large Language Models (LLMs), it has become increasingly important to provide large and realistic benchmarks for evaluating Knowledge Graph Question Answering (KGQA) systems. So far the majority of benchmarks rely on pattern-based SPARQL query generation approaches. The subsequent natural language (NL) question generation is conducted through crowdsourcing or other automated methods, such as rule-based paraphrasing or NL question templates. Although some of these datasets are of considerable size, their pitfall lies in their pattern-based generation approaches, which do not always generalize well to the vague and linguistically diverse questions asked by humans in real-world contexts. In this paper, we introduce Spider4SPARQL - a new SPARQL benchmark dataset featuring 9,693 previously existing manually generated NL questions and 4,721 unique, novel, and complex SPARQL queries of varying complexity. In addition to the NL/SPARQL pairs, we also provide their corresponding 166 knowledge graphs and ontologies, which cover 138 different domains. Our complex benchmark enables novel ways of evaluating the strengths and weaknesses of modern KGQA systems. We evaluate the system with state-of-the-art KGQA systems as well as LLMs, which achieve only up to 45\% execution accuracy, demonstrating that Spider4SPARQL is a challenging benchmark for future research.
Most knowledge graph completion (KGC) methods learn latent representations of entities and relations of a given graph by mapping them into a vector space. Although the majority of these methods focus on static knowledge graphs, a large number of publicly available KGs contain temporal information stating the time instant/period over which a certain fact has been true. Such graphs are often known as temporal knowledge graphs. Furthermore, knowledge graphs may also contain textual descriptions of entities and relations. Both temporal information and textual descriptions are not taken into account during representation learning by static KGC methods, and only structural information of the graph is leveraged. Recently, some studies have used temporal information to improve link prediction, yet they do not exploit textual descriptions and do not support inductive inference (prediction on entities that have not been seen in training). We propose a novel framework called TEMT that exploits the power of pre-trained language models (PLMs) for text-enhanced temporal knowledge graph completion. The knowledge stored in the parameters of a PLM allows TEMT to produce rich semantic representations of facts and to generalize on previously unseen entities. TEMT leverages textual and temporal information available in a KG, treats them separately, and fuses them to get plausibility scores of facts. Unlike previous approaches, TEMT effectively captures dependencies across different time points and enables predictions on unseen entities. To assess the performance of TEMT, we carried out several experiments including time interval prediction, both in transductive and inductive settings, and triple classification. The experimental results show that TEMT is competitive with the state-of-the-art.
Knowledge graphs (KGs) are gaining prominence in Healthcare AI, especially in drug discovery and pharmaceutical research as they provide a structured way to integrate diverse information sources, enhancing AI system interpretability. This interpretability is crucial in healthcare, where trust and transparency matter, and eXplainable AI (XAI) supports decision making for healthcare professionals. This overview summarizes recent literature on the impact of KGs in healthcare and their role in developing explainable AI models. We cover KG workflow, including construction, relationship extraction, reasoning, and their applications in areas like Drug-Drug Interactions (DDI), Drug Target Interactions (DTI), Drug Development (DD), Adverse Drug Reactions (ADR), and bioinformatics. We emphasize the importance of making KGs more interpretable through knowledge-infused learning in healthcare. Finally, we highlight research challenges and provide insights for future directions.
Large language models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs (KGs) to enhance language modeling via joint training and customized model architectures, applying this to LLMs is problematic owing to their large number of parameters and high computational cost. Therefore, how to enhance pre-trained LLMs using grounded knowledge, e.g., retrieval-augmented generation, remains an open question. In this work, we propose Graph Neural Prompting (GNP), a novel plug-and-play method to assist pre-trained LLMs in learning beneficial knowledge from KGs. GNP encompasses various designs, including a standard graph neural network encoder, a cross-modality pooling module, a domain projector, and a self-supervised link prediction objective. Extensive experiments on multiple datasets demonstrate the superiority of GNP on both commonsense and biomedical reasoning tasks across different LLM sizes and settings. Code is available at https://github.com/meettyj/GNP.
Knowledge graph completion (KGC) revolves around populating missing triples in a knowledge graph using available information. Text-based methods, which depend on textual descriptions of triples, often encounter difficulties when these descriptions lack sufficient information for accurate prediction-an issue inherent to the datasets and not easily resolved through modeling alone. To address this and ensure data consistency, we first use large language models (LLMs) to generate coherent descriptions, bridging the semantic gap between queries and answers. Secondly, we utilize inverse relations to create a symmetric graph, thereby providing augmented training samples for KGC. Additionally, we employ the label information inherent in knowledge graphs (KGs) to enhance the existing contrastive framework, making it fully supervised. These efforts have led to significant performance improvements on the WN18RR and FB15k-237 datasets. According to standard evaluation metrics, our approach achieves a 4.2% improvement in Hit@1 on WN18RR and a 3.4% improvement in Hit@3 on FB15k-237, demonstrating superior performance.
Published biomedical information has and continues to rapidly increase. The recent advancements in Natural Language Processing (NLP), have generated considerable interest in automating the extraction, normalization, and representation of biomedical knowledge about entities such as genes and diseases. Our study analyzes germline abstracts in the construction of knowledge graphs of the of the immense work that has been done in this area for genes and diseases. This paper presents SimpleGermKG, an automatic knowledge graph construction approach that connects germline genes and diseases. For the extraction of genes and diseases, we employ BioBERT, a pre-trained BERT model on biomedical corpora. We propose an ontology-based and rule-based algorithm to standardize and disambiguate medical terms. For semantic relationships between articles, genes, and diseases, we implemented a part-whole relation approach to connect each entity with its data source and visualize them in a graph-based knowledge representation. Lastly, we discuss the knowledge graph applications, limitations, and challenges to inspire the future research of germline corpora. Our knowledge graph contains 297 genes, 130 diseases, and 46,747 triples. Graph-based visualizations are used to show the results.
The availability of vast amounts of visual data with heterogeneous features is a key factor for developing, testing, and benchmarking of new computer vision (CV) algorithms and architectures. Most visual datasets are created and curated for specific tasks or with limited image data distribution for very specific situations, and there is no unified approach to manage and access them across diverse sources, tasks, and taxonomies. This not only creates unnecessary overheads when building robust visual recognition systems, but also introduces biases into learning systems and limits the capabilities of data-centric AI. To address these problems, we propose the Vision Knowledge Graph (VisionKG), a novel resource that interlinks, organizes and manages visual datasets via knowledge graphs and Semantic Web technologies. It can serve as a unified framework facilitating simple access and querying of state-of-the-art visual datasets, regardless of their heterogeneous formats and taxonomies. One of the key differences between our approach and existing methods is that ours is knowledge-based rather than metadatabased. It enhances the enrichment of the semantics at both image and instance levels and offers various data retrieval and exploratory services via SPARQL. VisionKG currently contains 519 million RDF triples that describe approximately 40 million entities, and are accessible at https://vision.semkg.org and through APIs. With the integration of 30 datasets and four popular CV tasks, we demonstrate its usefulness across various scenarios when working with CV pipelines.
Bilinear based models are powerful and widely used approaches for Knowledge Graphs Completion (KGC). Although bilinear based models have achieved significant advances, these studies mainly concentrate on posterior properties (based on evidence, e.g. symmetry pattern) while neglecting the prior properties. In this paper, we find a prior property named "the law of identity" that cannot be captured by bilinear based models, which hinders them from comprehensively modeling the characteristics of KGs. To address this issue, we introduce a solution called Unit Ball Bilinear Model (UniBi). This model not only achieves theoretical superiority but also offers enhanced interpretability and performance by minimizing ineffective learning through minimal constraints. Experiments demonstrate that UniBi models the prior property and verify its interpretability and performance.
Nowadays, increasingly more data are available as knowledge graphs (KGs). While this data model supports advanced reasoning and querying, they remain difficult to mine due to their size and complexity. Graph mining approaches can be used to extract patterns from KGs. However this presents two main issues. First, graph mining approaches tend to extract too many patterns for a human analyst to interpret (pattern explosion). Second, real-life KGs tend to differ from the graphs usually treated in graph mining: they are multigraphs, their vertex degrees tend to follow a power-law, and the way in which they model knowledge can produce spurious patterns. Recently, a graph mining approach named GraphMDL+ has been proposed to tackle the problem of pattern explosion, using the Minimum Description Length (MDL) principle. However, GraphMDL+, like other graph mining approaches, is not suited for KGs without adaptations. In this paper we propose KG-MDL, a graph pattern mining approach based on the MDL principle that, given a KG, generates a human-sized and descriptive set of graph patterns, and so in a parameter-less and anytime way. We report on experiments on medium-sized KGs showing that our approach generates sets of patterns that are both small enough to be interpreted by humans and descriptive of the KG. We show that the extracted patterns highlight relevant characteristics of the data: both of the schema used to create the data, and of the concrete facts it contains. We also discuss the issues related to mining graph patterns on knowledge graphs, as opposed to other types of graph data.
Human knowledge is subject to uncertainties, imprecision, incompleteness and inconsistencies. Moreover, the meaning of many everyday terms is dependent on the context. That poses a huge challenge for the Semantic Web. This paper introduces work on an intuitive notation and model for defeasible reasoning with imperfect knowledge, and relates it to previous work on argumentation theory. PKN is to N3 as defeasible reasoning is to deductive logic. Further work is needed on an intuitive syntax for describing reasoning strategies and tactics in declarative terms, drawing upon the AIF ontology for inspiration. The paper closes with observations on symbolic approaches in the era of large language models.
Applying link prediction (LP) methods over knowledge graphs (KG) for tasks such as causal event prediction presents an exciting opportunity. However, typical LP models are ill-suited for this task as they are incapable of performing inductive link prediction for new, unseen event entities and they require retraining as knowledge is added or changed in the underlying KG. We introduce a case-based reasoning model, EvCBR, to predict properties about new consequent events based on similar cause-effect events present in the KG. EvCBR uses statistical measures to identify similar events and performs path-based predictions, requiring no training step. To generalize our methods beyond the domain of event prediction, we frame our task as a 2-hop LP task, where the first hop is a causal relation connecting a cause event to a new effect event and the second hop is a property about the new event which we wish to predict. The effectiveness of our method is demonstrated using a novel dataset of newsworthy events with causal relations curated from Wikidata, where EvCBR outperforms baselines including translational-distance-based, GNN-based, and rule-based LP models.
Wikipedia articles are hierarchically organized through categories and lists, providing one of the most comprehensive and universal taxonomy, but its open creation is causing redundancies and inconsistencies. Assigning DBPedia classes to Wikipedia categories and lists can alleviate the problem, realizing a large knowledge graph which is essential for categorizing digital contents through entity linking and typing. However, the existing approach of CaLiGraph is producing incomplete and non-fine grained mappings. In this paper, we tackle the problem as ontology alignment, where structural information of knowledge graphs and lexical and semantic features of ontology class names are utilized to discover confident mappings, which are in turn utilized for finetuing pretrained language models in a distant supervision fashion. Our method SLHCat consists of two main parts: 1) Automatically generating training data by leveraging knowledge graph structure, semantic similarities, and named entity typing. 2) Finetuning and prompt-tuning of the pre-trained language model BERT are carried out over the training data, to capture semantic and syntactic properties of class names. Our model SLHCat is evaluated over a benchmark dataset constructed by annotating 3000 fine-grained CaLiGraph-DBpedia mapping pairs. SLHCat is outperforming the baseline model by a large margin of 25% in accuracy, offering a practical solution for large-scale ontology mapping.
Datasets that pair Knowledge Graphs (KG) and text together (KG-T) can be used to train forward and reverse neural models that generate text from KG and vice versa. However models trained on datasets where KG and text pairs are not equivalent can suffer from more hallucination and poorer recall. In this paper, we verify this empirically by generating datasets with different levels of noise and find that noisier datasets do indeed lead to more hallucination. We argue that the ability of forward and reverse models trained on a dataset to cyclically regenerate source KG or text is a proxy for the equivalence between the KG and the text in the dataset. Using cyclic evaluation we find that manually created WebNLG is much better than automatically created TeKGen and T-REx. Guided by these observations, we construct a new, improved dataset called LAGRANGE using heuristics meant to improve equivalence between KG and text and show the impact of each of the heuristics on cyclic evaluation. We also construct two synthetic datasets using large language models (LLMs), and observe that these are conducive to models that perform significantly well on cyclic generation of text, but less so on cyclic generation of KGs, probably because of a lack of a consistent underlying ontology.