Knowledge graphs offer a structured representation of real-world entities and their relationships, enabling a wide range of applications from information retrieval to automated reasoning. In this paper, we conduct a systematic comparison between traditional rule-based approaches and modern deep learning methods for link prediction. We focus on KBGAT, a graph neural network model that leverages multi-head attention to jointly encode both entity and relation features within local neighborhood structures. To advance this line of research, we introduce \textbf{GCAT} (Graph Collaborative Attention Network), a refined model that enhances context aggregation and interaction between heterogeneous nodes. Experimental results on four widely-used benchmark datasets demonstrate that GCAT not only consistently outperforms rule-based methods but also achieves competitive or superior performance compared to existing neural embedding models. Our findings highlight the advantages of attention-based architectures in capturing complex relational patterns for knowledge graph completion tasks.
Ontology embeddings map classes, relations, and individuals in ontologies into $\mathbb{R}^n$, and within $\mathbb{R}^n$ similarity between entities can be computed or new axioms inferred. For ontologies in the Description Logic $\mathcal{EL}^{++}$, several embedding methods have been developed that explicitly generate models of an ontology. However, these methods suffer from some limitations; they do not distinguish between statements that are unprovable and provably false, and therefore they may use entailed statements as negatives. Furthermore, they do not utilize the deductive closure of an ontology to identify statements that are inferred but not asserted. We evaluated a set of embedding methods for $\mathcal{EL}^{++}$ ontologies, incorporating several modifications that aim to make use of the ontology deductive closure. In particular, we designed novel negative losses that account both for the deductive closure and different types of negatives and formulated evaluation methods for knowledge base completion. We demonstrate that our embedding methods improve over the baseline ontology embedding in the task of knowledge base or ontology completion.
Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.
In this work, we introduce and analyze an approach to knowledge transfer from one collection of facts to another without the need for entity or relation matching. The method works for both canonicalized knowledge bases and uncanonicalized or open knowledge bases, i.e., knowledge bases where more than one copy of a real-world entity or relation may exist. The main contribution is a method that can make use of large-scale pre-training on facts, which were collected from unstructured text, to improve predictions on structured data from a specific domain. The introduced method is most impactful on small datasets such as ReVerb20k, where a 6% absolute increase of mean reciprocal rank and 65% relative decrease of mean rank over the previously best method was achieved, despite not relying on large pre-trained models like Bert. To understand the obtained pre-trained models better, we then introduce a novel dataset for the analysis of pre-trained models for Open Knowledge Base Completion, called Doge (Diagnostics of Open knowledge Graph Embeddings). It consists of 6 subsets and is designed to measure multiple properties of a pre-trained model: robustness against synonyms, ability to perform deductive reasoning, presence of gender stereotypes, consistency with reverse relations, and coverage of different areas of general knowledge. Using the introduced dataset, we show that the existing OKBC models lack consistency in the presence of synonyms and inverse relations and are unable to perform deductive reasoning. Moreover, their predictions often align with gender stereotypes, which persist even when presented with counterevidence. We additionally investigate the role of pre-trained word embeddings and demonstrate that avoiding biased word embeddings is not a sufficient measure to prevent biased behavior of OKBC models.
Despite their impressive scale, knowledge bases (KBs), such as Wikidata, still contain significant gaps. Language models (LMs) have been proposed as a source for filling these gaps. However, prior works have focused on prominent entities with rich coverage by LMs, neglecting the crucial case of long-tail entities. In this paper, we present a novel method for LM-based-KB completion that is specifically geared for facts about long-tail entities. The method leverages two different LMs in two stages: for candidate retrieval and for candidate verification and disambiguation. To evaluate our method and various baselines, we introduce a novel dataset, called MALT, rooted in Wikidata. Our method outperforms all baselines in F1, with major gains especially in recall.
Generating vector representations (embeddings) of OWL ontologies is a growing task due to its applications in predicting missing facts and knowledge-enhanced learning in fields such as bioinformatics. The underlying semantics of OWL ontologies are expressed using Description Logics (DLs). Initial approaches to generate embeddings relied on constructing a graph out of ontologies, neglecting the semantics of the logic therein. Recent semantic-preserving embedding methods often target lightweight DL languages like $\mathcal{EL}^{++}$, ignoring more expressive information in ontologies. Although some approaches aim to embed more descriptive DLs like $\mathcal{ALC}$, those methods require the existence of individuals, while many real-world ontologies are devoid of them. We propose an ontology embedding method for the $\mathcal{ALC}$ DL language that considers the lattice structure of concept descriptions. We use connections between DL and Category Theory to materialize the lattice structure and embed it using an order-preserving embedding method. We show that our method outperforms state-of-the-art methods in several knowledge base completion tasks. Furthermore, we incoporate saturation procedures that increase the information within the constructed lattices. We make our code and data available at \url{https://github.com/bio-ontology-research-group/catE}.
Structured knowledge bases (KBs) are a foundation of many intelligent applications, yet are notoriously incomplete. Language models (LMs) have recently been proposed for unsupervised knowledge base completion (KBC), yet, despite encouraging initial results, questions regarding their suitability remain open. Existing evaluations often fall short because they only evaluate on popular subjects, or sample already existing facts from KBs. In this work, we introduce a novel, more challenging benchmark dataset, and a methodology tailored for a realistic assessment of the KBC potential of LMs. For automated assessment, we curate a dataset called WD-KNOWN, which provides an unbiased random sample of Wikidata, containing over 3.9 million facts. In a second step, we perform a human evaluation on predictions that are not yet in the KB, as only this provides real insights into the added value over existing KBs. Our key finding is that biases in dataset conception of previous benchmarks lead to a systematic overestimate of LM performance for KBC. However, our results also reveal strong areas of LMs. We could, for example, perform a significant completion of Wikidata on the relations nativeLanguage, by a factor of ~21 (from 260k to 5.8M) at 82% precision, usedLanguage, by a factor of ~2.1 (from 2.1M to 6.6M) at 82% precision, and citizenOf by a factor of ~0.3 (from 4.2M to 5.3M) at 90% precision. Moreover, we find that LMs possess surprisingly strong generalization capabilities: even on relations where most facts were not directly observed in LM training, prediction quality can be high.
Knowledge base completion (KBC) aims to predict the missing links in knowledge graphs. Previous KBC tasks and approaches mainly focus on the setting where all test entities and relations have appeared in the training set. However, there has been limited research on the zero-shot KBC settings, where we need to deal with unseen entities and relations that emerge in a constantly growing knowledge base. In this work, we systematically examine different possible scenarios of zero-shot KBC and develop a comprehensive benchmark, ZeroKBC, that covers these scenarios with diverse types of knowledge sources. Our systematic analysis reveals several missing yet important zero-shot KBC settings. Experimental results show that canonical and state-of-the-art KBC systems cannot achieve satisfactory performance on this challenging benchmark. By analyzing the strength and weaknesses of these systems on solving ZeroKBC, we further present several important observations and promising future directions.
Automated completion of open knowledge bases (Open KBs), which are constructed from triples of the form (subject phrase, relation phrase, object phrase), obtained via open information extraction (Open IE) system, are useful for discovering novel facts that may not be directly present in the text. However, research in Open KB completion (Open KBC) has so far been limited to resource-rich languages like English. Using the latest advances in multilingual Open IE, we construct the first multilingual Open KBC dataset, called mOKB6, containing facts from Wikipedia in six languages (including English). Improving the previous Open KB construction pipeline by doing multilingual coreference resolution and keeping only entity-linked triples, we create a dense Open KB. We experiment with several models for the task and observe a consistent benefit of combining languages with the help of shared embedding space as well as translations of facts. We also observe that current multilingual models struggle to remember facts seen in languages of different scripts.
In this paper, we propose a new method for knowledge base completion (KBC): instance-based learning (IBL). For example, to answer (Jill Biden, lived city,? ), instead of going directly to Washington D.C., our goal is to find Joe Biden, who has the same lived city as Jill Biden. Through prototype entities, IBL provides interpretability. We develop theories for modeling prototypes and combining IBL with translational models. Experiments on various tasks confirmed the IBL model's effectiveness and interpretability. In addition, IBL shed light on the mechanism of rule-based KBC models. Previous research has generally agreed that rule-based models provide rules with semantically compatible premises and hypotheses. We challenge this view. We begin by demonstrating that some logical rules represent {\it instance-based equivalence} (i.e. prototypes) rather than semantic compatibility. These are denoted as {\it IBL rules}. Surprisingly, despite occupying only a small portion of the rule space, IBL rules outperform non-IBL rules in all four benchmarks. We use a variety of experiments to demonstrate that rule-based models work because they have the ability to represent instance-based equivalence via IBL rules. The findings provide new insights of how rule-based models work and how to interpret their rules.
Learning from positive and unlabeled (PU) data is a setting where the learner only has access to positive and unlabeled samples while having no information on negative examples. Such PU setting is of great importance in various tasks such as medical diagnosis, social network analysis, financial markets analysis, and knowledge base completion, which also tend to be intrinsically imbalanced, i.e., where most examples are actually negatives. Most existing approaches for PU learning, however, only consider artificially balanced datasets and it is unclear how well they perform in the realistic scenario of imbalanced and long-tail data distribution. This paper proposes to tackle this challenge via robust and efficient self-supervised pretraining. However, training conventional self-supervised learning methods when applied with highly imbalanced PU distribution needs better reformulation. In this paper, we present \textit{ImPULSeS}, a unified representation learning framework for \underline{Im}balanced \underline{P}ositive \underline{U}nlabeled \underline{L}earning leveraging \underline{Se}lf-\underline{S}upervised debiase pre-training. ImPULSeS uses a generic combination of large-scale unsupervised learning with debiased contrastive loss and additional reweighted PU loss. We performed different experiments across multiple datasets to show that ImPULSeS is able to halve the error rate of the previous state-of-the-art, even compared with previous methods that are given the true prior. Moreover, our method showed increased robustness to prior misspecification and superior performance even when pretraining was performed on an unrelated dataset. We anticipate such robustness and efficiency will make it much easier for practitioners to obtain excellent results on other PU datasets of interest. The source code is available at \url{https://github.com/JSchweisthal/ImPULSeS}
Ontologies are one of the richest sources of knowledge. Real-world ontologies often contain thousands of axioms and are often human-made. Hence, they may contain inconsistency and incomplete information which may impair classical reasoners to compute entailments that are considered as useful. To overcome these two challenges, we propose FALCON, a Fuzzy Ontology Neural reasoner to approximate reasoning over ALC ontologies. We provide an approximate technique for the model generation step in classical ALC reasoners. Our approximation is not guaranteed to construct exact logical models, but can approximate arbitrary models, which is notably faster for some large ontologies. Moreover, by sampling multiple approximate logical models, our technique supports approximate entailment also over inconsistent ontologies. Theoretical results show that more models generated lead to closer, i.e., faithful approximation of entailment over ALC entailments. Experimental results show that FALCON enables approximate reasoning and reasoning in the presence of inconsistency. Our experiments further demonstrate how ontologies can improve knowledge base completion in biomedicine by incorporating knowledge expressed in ALC.
Entity linking aims to link ambiguous mentions to their corresponding entities in a knowledge base, which is significant and fundamental for various downstream applications, e.g., knowledge base completion, question answering, and information extraction. While great efforts have been devoted to this task, most of these studies follow the assumption that large-scale labeled data is available. However, when the labeled data is insufficient for specific domains due to labor-intensive annotation work, the performance of existing algorithms will suffer an intolerable decline. In this paper, we endeavor to solve the problem of few-shot entity linking, which only requires a minimal amount of in-domain labeled data and is more practical in real situations. Specifically, we firstly propose a novel weak supervision strategy to generate non-trivial synthetic entity-mention pairs based on mention rewriting. Since the quality of the synthetic data has a critical impact on effective model training, we further design a meta-learning mechanism to assign different weights to each synthetic entity-mention pair automatically. Through this way, we can profoundly exploit rich and precious semantic information to derive a well-trained entity linking model under the few-shot setting. The experiments on real-world datasets show that the proposed method can extensively improve the state-of-the-art few-shot entity linking model and achieve impressive performance when only a small amount of labeled data is available. Moreover, we also demonstrate the outstanding ability of the model's transferability.
Almost all statements in knowledge bases have a temporal scope during which they are valid. Hence, knowledge base completion (KBC) on temporal knowledge bases (TKB), where each statement \textit{may} be associated with a temporal scope, has attracted growing attention. Prior works assume that each statement in a TKB \textit{must} be associated with a temporal scope. This ignores the fact that the scoping information is commonly missing in a KB. Thus prior work is typically incapable of handling generic use cases where a TKB is composed of temporal statements with/without a known temporal scope. In order to address this issue, we establish a new knowledge base embedding framework, called TIME2BOX, that can deal with atemporal and temporal statements of different types simultaneously. Our main insight is that answers to a temporal query always belong to a subset of answers to a time-agnostic counterpart. Put differently, time is a filter that helps pick out answers to be correct during certain periods. We introduce boxes to represent a set of answer entities to a time-agnostic query. The filtering functionality of time is modeled by intersections over these boxes. In addition, we generalize current evaluation protocols on time interval prediction. We describe experiments on two datasets and show that the proposed method outperforms state-of-the-art (SOTA) methods on both link prediction and time prediction.
We present Harmonic Memory Networks (HMem), a neural architecture for knowledge base completion that models entities as weighted sums of pairwise bindings between an entity's neighbors and corresponding relations. Since entities are modeled as aggregated neighborhoods, representations of unseen entities can be generated on the fly. We demonstrate this with two new datasets: WNGen and FBGen. Experiments show that the model is SOTA on benchmarks, and flexible enough to evolve without retraining as the knowledge graph grows.
Learning good representations on multi-relational graphs is essential to knowledge base completion (KBC). In this paper, we propose a new self-supervised training objective for multi-relational graph representation learning, via simply incorporating relation prediction into the commonly used 1vsAll objective. The new training objective contains not only terms for predicting the subject and object of a given triple, but also a term for predicting the relation type. We analyse how this new objective impacts multi-relational learning in KBC: experiments on a variety of datasets and models show that relation prediction can significantly improve entity ranking, the most widely used evaluation task for KBC, yielding a 6.1% increase in MRR and 9.9% increase in Hits@1 on FB15k-237 as well as a 3.1% increase in MRR and 3.4% in Hits@1 on Aristo-v4. Moreover, we observe that the proposed objective is especially effective on highly multi-relational datasets, i.e. datasets with a large number of predicates, and generates better representations when larger embedding sizes are used.
The aim of knowledge base completion is to predict unseen facts from existing facts in knowledge bases. In this work, we introduce the first approach for transfer of knowledge from one collection of facts to another without the need for entity or relation matching. The method works for both canonicalized knowledge bases and uncanonicalized or open knowledge bases, i.e., knowledge bases where more than one copy of a real-world entity or relation may exist. Such knowledge bases are a natural output of automated information extraction tools that extract structured data from unstructured text. Our main contribution is a method that can make use of a large-scale pre-training on facts, collected from unstructured text, to improve predictions on structured data from a specific domain. The introduced method is the most impactful on small datasets such as ReVerb20K, where we obtained 6% absolute increase of mean reciprocal rank and 65% relative decrease of mean rank over the previously best method, despite not relying on large pre-trained models like BERT.
Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes. Predicting missing links in these graphs can boost many important applications, such as drug design and repurposing. Recent work has shown that general-domain language models (LMs) can serve as "soft" KGs, and that they can be fine-tuned for the task of KG completion. In this work, we study scientific LMs for KG completion, exploring whether we can tap into their latent knowledge to enhance biomedical link prediction. We evaluate several domain-specific LMs, fine-tuning them on datasets centered on drugs and diseases that we represent as KGs and enrich with textual entity descriptions. We integrate the LM-based models with KG embedding models, using a router method that learns to assign each input example to either type of model and provides a substantial boost in performance. Finally, we demonstrate the advantage of LM models in the inductive setting with novel scientific entities. Our datasets and code are made publicly available.
Probing complex language models has recently revealed several insights into linguistic and semantic patterns found in the learned representations. In this article, we probe BERT specifically to understand and measure the relational knowledge it captures in its parametric memory. While probing for linguistic understanding is commonly applied to all layers of BERT as well as fine-tuned models, this has not been done for factual knowledge. We utilize existing knowledge base completion tasks (LAMA) to probe every layer of pre-trained as well as fine-tuned BERT models(ranking, question answering, NER). Our findings show that knowledge is not just contained in BERT's final layers. Intermediate layers contribute a significant amount (17-60%) to the total knowledge found. Probing intermediate layers also reveals how different types of knowledge emerge at varying rates. When BERT is fine-tuned, relational knowledge is forgotten. The extent of forgetting is impacted by the fine-tuning objective and the training data. We found that ranking models forget the least and retain more knowledge in their final layer compared to masked language modeling and question-answering. However, masked language modeling performed the best at acquiring new knowledge from the training data. When it comes to learning facts, we found that capacity and fact density are key factors. We hope this initial work will spur further research into understanding the parametric memory of language models and the effect of training objectives on factual knowledge. The code to repeat the experiments is publicly available on GitHub.
Knowledge graph embedding has been an active research topic for knowledge base completion (KGC), with progressive improvement from the initial TransE, TransH, RotatE et al to the current state-of-the-art QuatE. However, QuatE ignores the multi-faceted nature of the entity and the complexity of the relation, only using rigorous operation on quaternion space to capture the interaction between entitiy pair and relation, leaving opportunities for better knowledge representation which will finally help KGC. In this paper, we propose a novel model, QuatDE, with a dynamic mapping strategy to explicitly capture the variety of relational patterns and separate different semantic information of the entity, using transition vectors to adjust the point position of the entity embedding vectors in the quaternion space via Hamilton product, enhancing the feature interaction capability between elements of the triplet. Experiment results show QuatDE achieves state-of-the-art performance on three well-established knowledge graph completion benchmarks. In particular, the MR evaluation has relatively increased by 26% on WN18 and 15% on WN18RR, which proves the generalization of QuatDE.