The objective of Entity Alignment (EA) is to identify equivalent entity pairs from multiple Knowledge Graphs (KGs) and create a more comprehensive and unified KG. The majority of EA methods have primarily focused on the structural modality of KGs, lacking exploration of multi-modal information. A few multi-modal EA methods have made good attempts in this field. Still, they have two shortcomings: (1) inconsistent and inefficient modality modeling that designs complex and distinct models for each modality; (2) ineffective modality fusion due to the heterogeneous nature of modalities in EA. To tackle these challenges, we propose PathFusion, consisting of two main components: (1) MSP, a unified modeling approach that simplifies the alignment process by constructing paths connecting entities and modality nodes to represent multiple modalities; (2) IRF, an iterative fusion method that effectively combines information from different modalities using the path as an information carrier. Experimental results on real-world datasets demonstrate the superiority of PathFusion over state-of-the-art methods, with 22.4%-28.9% absolute improvement on Hits@1, and 0.194-0.245 absolute improvement on MRR.
Ontology matching (OM) entails the identification of semantic relationships between concepts within two or more knowledge graphs (KGs) and serves as a critical step in integrating KGs from various sources. Recent advancements in deep OM models have harnessed the power of transformer-based language models and the advantages of knowledge graph embedding. Nevertheless, these OM models still face persistent challenges, such as a lack of reference alignments, runtime latency, and unexplored different graph structures within an end-to-end framework. In this study, we introduce a novel self-supervised learning OM framework with input ontologies, called LaKERMap. This framework capitalizes on the contextual and structural information of concepts by integrating implicit knowledge into transformers. Specifically, we aim to capture multiple structural contexts, encompassing both local and global interactions, by employing distinct training objectives. To assess our methods, we utilize the Bio-ML datasets and tasks. The findings from our innovative approach reveal that LaKERMap surpasses state-of-the-art systems in terms of alignment quality and inference time. Our models and codes are available here: https://github.com/ellenzhuwang/lakermap.
Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs.
Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.
Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose \textbf{One for All (OFA)}, the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.
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) 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.
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.
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.
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.
Cross-lingual entity alignment is the task of finding the same semantic entities from different language knowledge graphs. In this paper, we propose a simple and novel unsupervised method for cross-language entity alignment. We utilize the deep learning multi-language encoder combined with a machine translator to encode knowledge graph text, which reduces the reliance on label data. Unlike traditional methods that only emphasize global or local alignment, our method simultaneously considers both alignment strategies. We first view the alignment task as a bipartite matching problem and then adopt the re-exchanging idea to accomplish alignment. Compared with the traditional bipartite matching algorithm that only gives one optimal solution, our algorithm generates ranked matching results which enabled many potentials downstream tasks. Additionally, our method can adapt two different types of optimization (minimal and maximal) in the bipartite matching process, which provides more flexibility. Our evaluation shows, we each scored 0.966, 0.990, and 0.996 Hits@1 rates on the DBP15K dataset in Chinese, Japanese, and French to English alignment tasks. We outperformed the state-of-the-art method in unsupervised and semi-supervised categories. Compared with the state-of-the-art supervised method, our method outperforms 2.6% and 0.4% in Ja-En and Fr-En alignment tasks while marginally lower by 0.2% in the Zh-En alignment task.
Large language models (LLMs) acquire extensive knowledge during pre-training, known as their parametric knowledge. However, in order to remain up-to-date and align with human instructions, LLMs inevitably require external knowledge during their interactions with users. This raises a crucial question: How will LLMs respond when external knowledge interferes with their parametric knowledge? To investigate this question, we propose a framework that systematically elicits LLM parametric knowledge and introduces external knowledge. Specifically, we uncover the impacts by constructing a parametric knowledge graph to reveal the different knowledge structures of LLMs, and introduce external knowledge through distractors of varying degrees, methods, positions, and formats. Our experiments on both black-box and open-source models demonstrate that LLMs tend to produce responses that deviate from their parametric knowledge, particularly when they encounter direct conflicts or confounding changes of information within detailed contexts. We also find that while LLMs are sensitive to the veracity of external knowledge, they can still be distracted by unrelated information. These findings highlight the risk of hallucination when integrating external knowledge, even indirectly, during interactions with current LLMs. All the data and results are publicly available.
Irregular data in real-world are usually organized as heterogeneous graphs (HGs) consisting of multiple types of nodes and edges. To explore useful knowledge from real-world data, both the large-scale encyclopedic HG datasets and corresponding effective learning methods are crucial, but haven't been well investigated. In this paper, we construct a large-scale HG benchmark dataset named UniKG from Wikidata to facilitate knowledge mining and heterogeneous graph representation learning. Overall, UniKG contains more than 77 million multi-attribute entities and 2000 diverse association types, which significantly surpasses the scale of existing HG datasets. To perform effective learning on the large-scale UniKG, two key measures are taken, including (i) the semantic alignment strategy for multi-attribute entities, which projects the feature description of multi-attribute nodes into a common embedding space to facilitate node aggregation in a large receptive field; (ii) proposing a novel plug-and-play anisotropy propagation module (APM) to learn effective multi-hop anisotropy propagation kernels, which extends methods of large-scale homogeneous graphs to heterogeneous graphs. These two strategies enable efficient information propagation among a tremendous number of multi-attribute entities and meantimes adaptively mine multi-attribute association through the multi-hop aggregation in large-scale HGs. We set up a node classification task on our UniKG dataset, and evaluate multiple baseline methods which are constructed by embedding our APM into large-scale homogenous graph learning methods. Our UniKG dataset and the baseline codes have been released at https://github.com/Yide-Qiu/UniKG.
Extensive studies have been devoted to privatizing general-domain Large Language Models (LLMs) as Domain-Specific LLMs via feeding specific-domain data. However, these privatization efforts often ignored a critical aspect: Dual Logic Ability, which is a core reasoning ability for LLMs. The dual logic ability of LLMs ensures that they can maintain a consistent stance when confronted with both positive and negative statements about the same fact. Our study focuses on how the dual logic ability of LLMs is affected during the privatization process in the medical domain. We conduct several experiments to analyze the dual logic ability of LLMs by examining the consistency of the stance in responses to paired questions about the same fact. In our experiments, interestingly, we observed a significant decrease in the dual logic ability of existing LLMs after privatization. Besides, our results indicate that incorporating general domain dual logic data into LLMs not only enhances LLMs' dual logic ability but also further improves their accuracy. These findings underscore the importance of prioritizing LLMs' dual logic ability during the privatization process. Our study establishes a benchmark for future research aimed at exploring LLMs' dual logic ability during the privatization process and offers valuable guidance for privatization efforts in real-world applications.
Knowledge graphs enable data scientists to learn end-to-end on heterogeneous knowledge. However, most end-to-end models solely learn from the relational information encoded in graphs' structure: raw values, encoded as literal nodes, are either omitted completely or treated as regular nodes without consideration for their values. In either case we lose potentially relevant information which could have otherwise been exploited by our learning methods. We propose a multimodal message passing network which not only learns end-to-end from the structure of graphs, but also from their possibly divers set of multimodal node features. Our model uses dedicated (neural) encoders to naturally learn embeddings for node features belonging to five different types of modalities, including numbers, texts, dates, images and geometries, which are projected into a joint representation space together with their relational information. We implement and demonstrate our model on node classification and link prediction for artificial and real-worlds datasets, and evaluate the effect that each modality has on the overall performance in an inverse ablation study. Our results indicate that end-to-end multimodal learning from any arbitrary knowledge graph is indeed possible, and that including multimodal information can significantly affect performance, but that much depends on the characteristics of the data.