Knowledge graph completion (KGC) aims to solve the incompleteness of knowledge graphs (KGs) by predicting missing links from known triples, numbers of knowledge graph embedding (KGE) models have been proposed to perform KGC by learning embeddings. Nevertheless, most existing embedding models map each relation into a unique vector, overlooking the specific fine-grained semantics of them under different entities. Additionally, the few available fine-grained semantic models rely on clustering algorithms, resulting in limited performance and applicability due to the cumbersome two-stage training process. In this paper, we present a novel method utilizing contextual dictionary lookup, enabling conventional embedding models to learn fine-grained semantics of relations in an end-to-end manner. More specifically, we represent each relation using a dictionary that contains multiple latent semantics. The composition of a given entity and the dictionary's central semantics serves as the context for generating a lookup, thus determining the fine-grained semantics of the relation adaptively. The proposed loss function optimizes both the central and fine-grained semantics simultaneously to ensure their semantic consistency. Besides, we introduce two metrics to assess the validity and accuracy of the dictionary lookup operation. We extend several KGE models with the method, resulting in substantial performance improvements on widely-used benchmark datasets.
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.
Identifying and discovering drug-target interactions(DTIs) are vital steps in drug discovery and development. They play a crucial role in assisting scientists in finding new drugs and accelerating the drug development process. Recently, knowledge graph and knowledge graph embedding (KGE) models have made rapid advancements and demonstrated impressive performance in drug discovery. However, such models lack authenticity and accuracy in drug target identification, leading to an increased misjudgment rate and reduced drug development efficiency. To address these issues, we focus on the problem of drug-target interactions, with knowledge mapping as the core technology. Specifically, a causal intervention-based confidence measure is employed to assess the triplet score to improve the accuracy of the drug-target interaction prediction model. Experimental results demonstrate that the developed confidence measurement method based on causal intervention can significantly enhance the accuracy of DTI link prediction, particularly for high-precision models. The predicted results are more valuable in guiding the design and development of subsequent drug development experiments, thereby significantly improving the efficiency of drug development.
Due to the increasing adoption of electronic health records (EHR), large scale EHRs have become another rich data source for translational clinical research. Despite its potential, deriving generalizable knowledge from EHR data remains challenging. First, EHR data are generated as part of clinical care with data elements too detailed and fragmented for research. Despite recent progress in mapping EHR data to common ontology with hierarchical structures, much development is still needed to enable automatic grouping of local EHR codes to meaningful clinical concepts at a large scale. Second, the total number of unique EHR features is large, imposing methodological challenges to derive reproducible knowledge graph, especially when interest lies in conditional dependency structure. Third, the detailed EHR data on a very large patient cohort imposes additional computational challenge to deriving a knowledge network. To overcome these challenges, we propose to infer the conditional dependency structure among EHR features via a latent graphical block model (LGBM). The LGBM has a two layer structure with the first providing semantic embedding vector (SEV) representation for the EHR features and the second overlaying a graphical block model on the latent SEVs. The block structures on the graphical model also allows us to cluster synonymous features in EHR. We propose to learn the LGBM efficiently, in both statistical and computational sense, based on the empirical point mutual information matrix. We establish the statistical rates of the proposed estimators and show the perfect recovery of the block structure. Numerical results from simulation studies and real EHR data analyses suggest that the proposed LGBM estimator performs well in finite sample.
Inductive knowledge graph completion has been considered as the task of predicting missing triplets between new entities that are not observed during training. While most inductive knowledge graph completion methods assume that all entities can be new, they do not allow new relations to appear at inference time. This restriction prohibits the existing methods from appropriately handling real-world knowledge graphs where new entities accompany new relations. In this paper, we propose an INductive knowledge GRAph eMbedding method, InGram, that can generate embeddings of new relations as well as new entities at inference time. Given a knowledge graph, we define a relation graph as a weighted graph consisting of relations and the affinity weights between them. Based on the relation graph and the original knowledge graph, InGram learns how to aggregate neighboring embeddings to generate relation and entity embeddings using an attention mechanism. Experimental results show that InGram outperforms 14 different state-of-the-art methods on varied inductive learning scenarios.
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.
Recent studies on automatic note generation have shown that doctors can save significant amounts of time when using automatic clinical note generation (Knoll et al., 2022). Summarization models have been used for this task to generate clinical notes as summaries of doctor-patient conversations (Krishna et al., 2021; Cai et al., 2022). However, assessing which model would best serve clinicians in their daily practice is still a challenging task due to the large set of possible correct summaries, and the potential limitations of automatic evaluation metrics. In this paper, we study evaluation methods and metrics for the automatic generation of clinical notes from medical conversations. In particular, we propose new task-specific metrics and we compare them to SOTA evaluation metrics in text summarization and generation, including: (i) knowledge-graph embedding-based metrics, (ii) customized model-based metrics, (iii) domain-adapted/fine-tuned metrics, and (iv) ensemble metrics. To study the correlation between the automatic metrics and manual judgments, we evaluate automatic notes/summaries by comparing the system and reference facts and computing the factual correctness, and the hallucination and omission rates for critical medical facts. This study relied on seven datasets manually annotated by domain experts. Our experiments show that automatic evaluation metrics can have substantially different behaviors on different types of clinical notes datasets. However, the results highlight one stable subset of metrics as the most correlated with human judgments with a relevant aggregation of different evaluation criteria.
A hyper-relational knowledge graph has been recently studied where a triplet is associated with a set of qualifiers; a qualifier is composed of a relation and an entity, providing auxiliary information for a triplet. While existing hyper-relational knowledge graph embedding methods assume that the entities are discrete objects, some information should be represented using numeric values, e.g., (J.R.R., was born in, 1892). Also, a triplet (J.R.R., educated at, Oxford Univ.) can be associated with a qualifier such as (start time, 1911). In this paper, we propose a unified framework named HyNT that learns representations of a hyper-relational knowledge graph containing numeric literals in either triplets or qualifiers. We define a context transformer and a prediction transformer to learn the representations based not only on the correlations between a triplet and its qualifiers but also on the numeric information. By learning compact representations of triplets and qualifiers and feeding them into the transformers, we reduce the computation cost of using transformers. Using HyNT, we can predict missing numeric values in addition to missing entities or relations in a hyper-relational knowledge graph. Experimental results show that HyNT significantly outperforms state-of-the-art methods on real-world datasets.
The main objective of Knowledge Graph (KG) embeddings is to learn low-dimensional representations of entities and relations, enabling the prediction of missing facts. A significant challenge in achieving better KG embeddings lies in capturing relation patterns, including symmetry, antisymmetry, inversion, commutative composition, non-commutative composition, hierarchy, and multiplicity. This study introduces a novel model called 3H-TH (3D Rotation and Translation in Hyperbolic space) that captures these relation patterns simultaneously. In contrast, previous attempts have not achieved satisfactory performance across all the mentioned properties at the same time. The experimental results demonstrate that the new model outperforms existing state-of-the-art models in terms of accuracy, hierarchy property, and other relation patterns in low-dimensional space, meanwhile performing similarly in high-dimensional space.
We propose KGT5-context, a simple sequence-to-sequence model for link prediction (LP) in knowledge graphs (KG). Our work expands on KGT5, a recent LP model that exploits textual features of the KG, has small model size, and is scalable. To reach good predictive performance, however, KGT5 relies on an ensemble with a knowledge graph embedding model, which itself is excessively large and costly to use. In this short paper, we show empirically that adding contextual information - i.e., information about the direct neighborhood of the query entity - alleviates the need for a separate KGE model to obtain good performance. The resulting KGT5-context model is simple, reduces model size significantly, and obtains state-of-the-art performance in our experimental study.
Recent years have witnessed remarkable progress on knowledge graph embedding (KGE) methods to learn the representations of entities and relations in static knowledge graphs (SKGs). However, knowledge changes over time. In order to represent the facts happening in a specific time, temporal knowledge graph (TKG) embedding approaches are put forward. While most existing models ignore the independence of semantic and temporal information. We empirically find that current models have difficulty distinguishing representations of the same entity or relation at different timestamps. In this regard, we propose a TimeLine-Traced Knowledge Graph Embedding method (TLT-KGE) for temporal knowledge graph completion. TLT-KGE aims to embed the entities and relations with timestamps as a complex vector or a quaternion vector. Specifically, TLT-KGE models semantic information and temporal information as different axes of complex number space or quaternion space. Meanwhile, two specific components carving the relationship between semantic and temporal information are devised to buoy the modeling. In this way, the proposed method can not only distinguish the independence of the semantic and temporal information, but also establish a connection between them. Experimental results on the link prediction task demonstrate that TLT-KGE achieves substantial improvements over state-of-the-art competitors. The source code will be available on https://github.com/zhangfw123/TLT-KGE.
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.
Negative sampling (NS) is widely used in knowledge graph embedding (KGE), which aims to generate negative triples to make a positive-negative contrast during training. However, existing NS methods are unsuitable when multi-modal information is considered in KGE models. They are also inefficient due to their complex design. In this paper, we propose Modality-Aware Negative Sampling (MANS) for multi-modal knowledge graph embedding (MMKGE) to address the mentioned problems. MANS could align structural and visual embeddings for entities in KGs and learn meaningful embeddings to perform better in multi-modal KGE while keeping lightweight and efficient. Empirical results on two benchmarks demonstrate that MANS outperforms existing NS methods. Meanwhile, we make further explorations about MANS to confirm its effectiveness.
Knowledge Graph Embedding (KGE) is a fundamental technique that extracts expressive representation from knowledge graph (KG) to facilitate diverse downstream tasks. The emerging federated KGE (FKGE) collaboratively trains from distributed KGs held among clients while avoiding exchanging clients' sensitive raw KGs, which can still suffer from privacy threats as evidenced in other federated model trainings (e.g., neural networks). However, quantifying and defending against such privacy threats remain unexplored for FKGE which possesses unique properties not shared by previously studied models. In this paper, we conduct the first holistic study of the privacy threat on FKGE from both attack and defense perspectives. For the attack, we quantify the privacy threat by proposing three new inference attacks, which reveal substantial privacy risk by successfully inferring the existence of the KG triple from victim clients. For the defense, we propose DP-Flames, a novel differentially private FKGE with private selection, which offers a better privacy-utility tradeoff by exploiting the entity-binding sparse gradient property of FKGE and comes with a tight privacy accountant by incorporating the state-of-the-art private selection technique. We further propose an adaptive privacy budget allocation policy to dynamically adjust defense magnitude across the training procedure. Comprehensive evaluations demonstrate that the proposed defense can successfully mitigate the privacy threat by effectively reducing the success rate of inference attacks from $83.1\%$ to $59.4\%$ on average with only a modest utility decrease.
The cascade of 2D geometric transformations were exploited to model relations between entities in a knowledge graph (KG), leading to an effective KG embedding (KGE) model, CompoundE. Furthermore, the rotation in the 3D space was proposed as a new KGE model, Rotate3D, by leveraging its non-commutative property. Inspired by CompoundE and Rotate3D, we leverage 3D compound geometric transformations, including translation, rotation, scaling, reflection, and shear and propose a family of KGE models, named CompoundE3D, in this work. CompoundE3D allows multiple design variants to match rich underlying characteristics of a KG. Since each variant has its own advantages on a subset of relations, an ensemble of multiple variants can yield superior performance. The effectiveness and flexibility of CompoundE3D are experimentally verified on four popular link prediction datasets.
The link prediction task aims to predict missing entities or relations in the knowledge graph and is essential for the downstream application. Existing well-known models deal with this task by mainly focusing on representing knowledge graph triplets in the distance space or semantic space. However, they can not fully capture the information of head and tail entities, nor even make good use of hierarchical level information. Thus, in this paper, we propose a novel knowledge graph embedding model for the link prediction task, namely, HIE, which models each triplet (\textit{h}, \textit{r}, \textit{t}) into distance measurement space and semantic measurement space, simultaneously. Moreover, HIE is introduced into hierarchical-aware space to leverage rich hierarchical information of entities and relations for better representation learning. Specifically, we apply distance transformation operation on the head entity in distance space to obtain the tail entity instead of translation-based or rotation-based approaches. Experimental results of HIE on four real-world datasets show that HIE outperforms several existing state-of-the-art knowledge graph embedding methods on the link prediction task and deals with complex relations accurately.
Link prediction with knowledge graph embedding (KGE) is a popular method for knowledge graph completion. Furthermore, training KGEs on non-English knowledge graph promote knowledge extraction and knowledge graph reasoning in the context of these languages. However, many challenges in non-English KGEs pose to learning a low-dimensional representation of a knowledge graph's entities and relations. This paper proposes "Farspredict" a Persian knowledge graph based on Farsbase (the most comprehensive knowledge graph in Persian). It also explains how the knowledge graph structure affects link prediction accuracy in KGE. To evaluate Farspredict, we implemented the popular models of KGE on it and compared the results with Freebase. Given the analysis results, some optimizations on the knowledge graph are carried out to improve its functionality in the KGE. As a result, a new Persian knowledge graph is achieved. Implementation results in the KGE models on Farspredict outperforming Freebases in many cases. At last, we discuss what improvements could be effective in enhancing the quality of Farspredict and how much it improves.
Knowledge graph embedding (KGE) that maps entities and relations into vector representations is essential for downstream applications. Conventional KGE methods require high-dimensional representations to learn the complex structure of knowledge graph, but lead to oversized model parameters. Recent advances reduce parameters by low-dimensional entity representations, while developing techniques (e.g., knowledge distillation or reinvented representation forms) to compensate for reduced dimension. However, such operations introduce complicated computations and model designs that may not benefit large knowledge graphs. To seek a simple strategy to improve the parameter efficiency of conventional KGE models, we take inspiration from that deeper neural networks require exponentially fewer parameters to achieve expressiveness comparable to wider networks for compositional structures. We view all entity representations as a single-layer embedding network, and conventional KGE methods that adopt high-dimensional entity representations equal widening the embedding network to gain expressiveness. To achieve parameter efficiency, we instead propose a deeper embedding network for entity representations, i.e., a narrow entity embedding layer plus a multi-layer dimension lifting network (LiftNet). Experiments on three public datasets show that by integrating LiftNet, four conventional KGE methods with 16-dimensional representations achieve comparable link prediction accuracy as original models that adopt 512-dimensional representations, saving 68.4% to 96.9% parameters.
Knowledge graph embedding models (KGEMs) are used for various tasks related to knowledge graphs (KGs), including link prediction. They are trained with loss functions that consider batches of true and false triples. However, different kinds of false triples exist and recent works suggest that they should not be valued equally, leading to specific negative sampling procedures. In line with this recent assumption, we posit that negative triples that are semantically valid w.r.t. signatures of relations (domain and range) are high-quality negatives. Hence, we enrich the three main loss functions for link prediction such that all kinds of negatives are sampled but treated differently based on their semantic validity. In an extensive and controlled experimental setting, we show that the proposed loss functions systematically provide satisfying results which demonstrates both the generality and superiority of our proposed approach. In fact, the proposed loss functions (1) lead to better MRR and Hits@10 values, and (2) drive KGEMs towards better semantic correctness as measured by the Sem@K metric. This highlights that relation signatures globally improve KGEMs, and thus should be incorporated into loss functions. Domains and ranges of relations being largely available in schema-defined KGs, this makes our approach both beneficial and widely usable in practice.
With the widespread use of knowledge graphs (KG) in various automated AI systems and applications, it is very important to ensure that information retrieval algorithms leveraging them are free from societal biases. Previous works have depicted biases that persist in KGs, as well as employed several metrics for measuring the biases. However, such studies lack the systematic exploration of the sensitivity of the bias measurements, through varying sources of data, or the embedding algorithms used. To address this research gap, in this work, we present a holistic analysis of bias measurement on the knowledge graph. First, we attempt to reveal data biases that surface in Wikidata for thirteen different demographics selected from seven continents. Next, we attempt to unfold the variance in the detection of biases by two different knowledge graph embedding algorithms - TransE and ComplEx. We conduct our extensive experiments on a large number of occupations sampled from the thirteen demographics with respect to the sensitive attribute, i.e., gender. Our results show that the inherent data bias that persists in KG can be altered by specific algorithm bias as incorporated by KG embedding learning algorithms. Further, we show that the choice of the state-of-the-art KG embedding algorithm has a strong impact on the ranking of biased occupations irrespective of gender. We observe that the similarity of the biased occupations across demographics is minimal which reflects the socio-cultural differences around the globe. We believe that this full-scale audit of the bias measurement pipeline will raise awareness among the community while deriving insights related to design choices of data and algorithms both and refrain from the popular dogma of ``one-size-fits-all''.