Using knowledge graph embedding models (KGEMs) is a popular approach for predicting links in knowledge graphs (KGs). Traditionally, the performance of KGEMs for link prediction is assessed using rank-based metrics, which evaluate their ability to give high scores to ground-truth entities. However, the literature claims that the KGEM evaluation procedure would benefit from adding supplementary dimensions to assess. That is why, in this paper, we extend our previously introduced metric Sem@K that measures the capability of models to predict valid entities w.r.t. domain and range constraints. In particular, we consider a broad range of KGs and take their respective characteristics into account to propose different versions of Sem@K. We also perform an extensive study to qualify the abilities of KGEMs as measured by our metric. Our experiments show that Sem@K provides a new perspective on KGEM quality. Its joint analysis with rank-based metrics offers different conclusions on the predictive power of models. Regarding Sem@K, some KGEMs are inherently better than others, but this semantic superiority is not indicative of their performance w.r.t. rank-based metrics. In this work, we generalize conclusions about the relative performance of KGEMs w.r.t. rank-based and semantic-oriented metrics at the level of families of models. The joint analysis of the aforementioned metrics gives more insight into the peculiarities of each model. This work paves the way for a more comprehensive evaluation of KGEM adequacy for specific downstream tasks.
Unsupervised representation learning methods are widely used for gaining insight into high-dimensional, unstructured, or structured data. In some cases, users may have prior topological knowledge about the data, such as a known cluster structure or the fact that the data is known to lie along a tree- or graph-structured topology. However, generic methods to ensure such structure is salient in the low-dimensional representations are lacking. This negatively impacts the interpretability of low-dimensional embeddings, and plausibly downstream learning tasks. To address this issue, we introduce topological regularization: a generic approach based on algebraic topology to incorporate topological prior knowledge into low-dimensional embeddings. We introduce a class of topological loss functions, and show that jointly optimizing an embedding loss with such a topological loss function as a regularizer yields embeddings that reflect not only local proximities but also the desired topological structure. We include a self-contained overview of the required foundational concepts in algebraic topology, and provide intuitive guidance on how to design topological loss functions for a variety of shapes, such as clusters, cycles, and bifurcations. We empirically evaluate the proposed approach on computational efficiency, robustness, and versatility in combination with linear and non-linear dimensionality reduction and graph embedding methods.
Knowledge graph embedding (KGE), which maps entities and relations in a knowledge graph into continuous vector spaces, has achieved great success in predicting missing links in knowledge graphs. However, knowledge graphs often contain incomplete triples that are difficult to inductively infer by KGEs. To address this challenge, we resort to analogical inference and propose a novel and general self-supervised framework AnKGE to enhance KGE models with analogical inference capability. We propose an analogical object retriever that retrieves appropriate analogical objects from entity-level, relation-level, and triple-level. And in AnKGE, we train an analogy function for each level of analogical inference with the original element embedding from a well-trained KGE model as input, which outputs the analogical object embedding. In order to combine inductive inference capability from the original KGE model and analogical inference capability enhanced by AnKGE, we interpolate the analogy score with the base model score and introduce the adaptive weights in the score function for prediction. Through extensive experiments on FB15k-237 and WN18RR datasets, we show that AnKGE achieves competitive results on link prediction task and well performs analogical inference.
Software Defect Prediction aims at predicting which software modules are the most probable to contain defects. The idea behind this approach is to save time during the development process by helping find bugs early. Defect Prediction models are based on historical data. Specifically, one can use data collected from past software distributions, or Versions, of the same target application under analysis. Defect Prediction based on past versions is called Cross Version Defect Prediction (CVDP). Traditionally, Static Code Metrics are used to predict defects. In this work, we use the Class Dependency Network (CDN) as another predictor for defects, combined with static code metrics. CDN data contains structural information about the target application being analyzed. Usually, CDN data is analyzed using different handcrafted network measures, like Social Network metrics. Our approach uses network embedding techniques to leverage CDN information without having to build the metrics manually. In order to use the embeddings between versions, we incorporate different embedding alignment techniques. To evaluate our approach, we performed experiments on 24 software release pairs and compared it against several benchmark methods. In these experiments, we analyzed the performance of two different graph embedding techniques, three anchor selection approaches, and two alignment techniques. We also built a meta-model based on two different embeddings and achieved a statistically significant improvement in AUC of 4.7% (p < 0.002) over the baseline method.
Inferring knowledge from clinical trials using knowledge graph embedding is an emerging area. However, customizing graph embeddings for different use cases remains a significant challenge. We propose custom2vec, an algorithmic framework to customize graph embeddings by incorporating user preferences in training the embeddings. It captures user preferences by adding custom nodes and links derived from manually vetted results of a separate information retrieval method. We propose a joint learning objective to preserve the original network structure while incorporating the user's custom annotations. We hypothesize that the custom training improves user-expected predictions, for example, in link prediction tasks. We demonstrate the effectiveness of custom2vec for clinical trials related to non-small cell lung cancer (NSCLC) with two customization scenarios: recommending immuno-oncology trials evaluating PD-1 inhibitors and exploring similar trials that compare new therapies with a standard of care. The results show that custom2vec training achieves better performance than the conventional training methods. Our approach is a novel way to customize knowledge graph embeddings and enable more accurate recommendations and predictions.
Numerous Graph Neural Networks (GNNs) have been developed to tackle the challenge of Knowledge Graph Embedding (KGE). However, many of these approaches overlook the crucial role of relation information and inadequately integrate it with entity information, resulting in diminished expressive power. In this paper, we propose a novel knowledge graph encoder that incorporates tensor decomposition within the aggregation function of Relational Graph Convolutional Network (R-GCN). Our model enhances the representation of neighboring entities by employing projection matrices of a low-rank tensor defined by relation types. This approach facilitates multi-task learning, thereby generating relation-aware representations. Furthermore, we introduce a low-rank estimation technique for the core tensor through CP decomposition, which effectively compresses and regularizes our model. We adopt a training strategy inspired by contrastive learning, which relieves the training limitation of the 1-N method inherent in handling vast graphs. We outperformed all our competitors on two common benchmark datasets, FB15k-237 and WN18RR, while using low-dimensional embeddings for entities and relations.
Multi-view data containing complementary and consensus information can facilitate representation learning by exploiting the intact integration of multi-view features. Because most objects in real world often have underlying connections, organizing multi-view data as heterogeneous graphs is beneficial to extracting latent information among different objects. Due to the powerful capability to gather information of neighborhood nodes, in this paper, we apply Graph Convolutional Network (GCN) to cope with heterogeneous-graph data originating from multi-view data, which is still under-explored in the field of GCN. In order to improve the quality of network topology and alleviate the interference of noises yielded by graph fusion, some methods undertake sorting operations before the graph convolution procedure. These GCN-based methods generally sort and select the most confident neighborhood nodes for each vertex, such as picking the top-k nodes according to pre-defined confidence values. Nonetheless, this is problematic due to the non-differentiable sorting operators and inflexible graph embedding learning, which may result in blocked gradient computations and undesired performance. To cope with these issues, we propose a joint framework dubbed Multi-view Graph Convolutional Network with Differentiable Node Selection (MGCN-DNS), which is constituted of an adaptive graph fusion layer, a graph learning module and a differentiable node selection schema. MGCN-DNS accepts multi-channel graph-structural data as inputs and aims to learn more robust graph fusion through a differentiable neural network. The effectiveness of the proposed method is verified by rigorous comparisons with considerable state-of-the-art approaches in terms of multi-view semi-supervised classification tasks.
Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.
Knowledge graph (KG) is used to represent data in terms of entities and structural relations between the entities. This representation can be used to solve complex problems such as recommendation systems and question answering. In this study, a set of candidate drugs for COVID-19 are proposed by using Drug repurposing knowledge graph (DRKG). DRKG is a biological knowledge graph constructed using a vast amount of open source biomedical knowledge to understand the mechanism of compounds and the related biological functions. Node and relation embeddings are learned using knowledge graph embedding models and neural network and attention related models. Different models are used to get the node embedding by changing the objective of the model. These embeddings are later used to predict if a candidate drug is effective to treat a disease or how likely it is for a drug to bind to a protein associated to a disease which can be modelled as a link prediction task between two nodes. RESCAL performed the best on the test dataset in terms of MR, MRR and Hits@3.
In this paper we generalize single-relation pseudo-Riemannian graph embedding models to multi-relational networks, and show that the typical approach of encoding relations as manifold transformations translates from the Riemannian to the pseudo-Riemannian case. In addition we construct a view of relations as separate spacetime submanifolds of multi-time manifolds, and consider an interpolation between a pseudo-Riemannian embedding model and its Wick-rotated Riemannian counterpart. We validate these extensions in the task of link prediction, focusing on flat Lorentzian manifolds, and demonstrate their use in both knowledge graph completion and knowledge discovery in a biological domain.
We study the problem of explaining link predictions in the Knowledge Graph Embedding (KGE) models. We propose an example-based approach that exploits the latent space representation of nodes and edges in a knowledge graph to explain predictions. We evaluated the importance of identified triples by observing progressing degradation of model performance upon influential triples removal. Our experiments demonstrate that this approach to generate explanations outperforms baselines on KGE models for two publicly available datasets.
Training labels for graph embedding algorithms could be costly to obtain in many practical scenarios. Active learning (AL) algorithms are very helpful to obtain the most useful labels for training while keeping the total number of label queries under a certain budget. The existing Active Graph Embedding framework proposes to use centrality score, density score, and entropy score to evaluate the value of unlabeled nodes, and it has been shown to be capable of bringing some improvement to the node classification tasks of Graph Convolutional Networks. However, when evaluating the importance of unlabeled nodes, it fails to consider the influence of existing labeled nodes on the value of unlabeled nodes. In other words, given the same unlabeled node, the computed informative score is always the same and is agnostic to the labeled node set. With the aim to address this limitation, in this work, we introduce 3 dissimilarity-based information scores for active learning: feature dissimilarity score (FDS), structure dissimilarity score (SDS), and embedding dissimilarity score (EDS). We find out that those three scores are able to take the influence of the labeled set on the value of unlabeled candidates into consideration, boosting our AL performance. According to experiments, our newly proposed scores boost the classification accuracy by 2.1% on average and are capable of generalizing to different Graph Neural Network architectures.
Examining graphs for similarity is a well-known challenge, but one that is mandatory for grouping graphs together. We present a data-driven method to cluster traffic scenes that is self-supervised, i.e. without manual labelling. We leverage the semantic scene graph model to create a generic graph embedding of the traffic scene, which is then mapped to a low-dimensional embedding space using a Siamese network, in which clustering is performed. In the training process of our novel approach, we augment existing traffic scenes in the Cartesian space to generate positive similarity samples. This allows us to overcome the challenge of reconstructing a graph and at the same time obtain a representation to describe the similarity of traffic scenes. We could show, that the resulting clusters possess common semantic characteristics. The approach was evaluated on the INTERACTION dataset.
We present the award-winning submission to the WikiKG90Mv2 track of OGB-LSC@NeurIPS 2022. The task is link-prediction on the large-scale knowledge graph WikiKG90Mv2, consisting of 90M+ nodes and 600M+ edges. Our solution uses a diverse ensemble of $85$ Knowledge Graph Embedding models combining five different scoring functions (TransE, TransH, RotatE, DistMult, ComplEx) and two different loss functions (log-sigmoid, sampled softmax cross-entropy). Each individual model is trained in parallel on a Graphcore Bow Pod$_{16}$ using BESS (Balanced Entity Sampling and Sharing), a new distribution framework for KGE training and inference based on balanced collective communications between workers. Our final model achieves a validation MRR of 0.2922 and a test-challenge MRR of 0.2562, winning the first place in the competition. The code is publicly available at: https://github.com/graphcore/distributed-kge-poplar/tree/2022-ogb-submission.
Video understanding is an important task in short video business platforms and it has a wide application in video recommendation and classification. Most of the existing video understanding works only focus on the information that appeared within the video content, including the video frames, audio and text. However, introducing common sense knowledge from the external Knowledge Graph (KG) dataset is essential for video understanding when referring to the content which is less relevant to the video. Owing to the lack of video knowledge graph dataset, the work which integrates video understanding and KG is rare. In this paper, we propose a heterogeneous dataset that contains the multi-modal video entity and fruitful common sense relations. This dataset also provides multiple novel video inference tasks like the Video-Relation-Tag (VRT) and Video-Relation-Video (VRV) tasks. Furthermore, based on this dataset, we propose an end-to-end model that jointly optimizes the video understanding objective with knowledge graph embedding, which can not only better inject factual knowledge into video understanding but also generate effective multi-modal entity embedding for KG. Comprehensive experiments indicate that combining video understanding embedding with factual knowledge benefits the content-based video retrieval performance. Moreover, it also helps the model generate better knowledge graph embedding which outperforms traditional KGE-based methods on VRT and VRV tasks with at least 42.36% and 17.73% improvement in HITS@10.
Knowledge graph embedding techniques are widely used for knowledge graph refinement tasks such as graph completion and triple classification. These techniques aim at embedding the entities and relations of a Knowledge Graph (KG) in a low dimensional continuous feature space. This paper adopts a transformer-based triplet network creating an embedding space that clusters the information about an entity or relation in the KG. It creates textual sequences from facts and fine-tunes a triplet network of pre-trained transformer-based language models. It adheres to an evaluation paradigm that relies on an efficient spatial semantic search technique. We show that this evaluation protocol is more adapted to a few-shot setting for the relation prediction task. Our proposed GilBERT method is evaluated on triplet classification and relation prediction tasks on multiple well-known benchmark knowledge graphs such as FB13, WN11, and FB15K. We show that GilBERT achieves better or comparable results to the state-of-the-art performance on these two refinement tasks.
Knowledge graph embedding (KGE) aims at learning powerful representations to benefit various artificial intelligence applications. Meanwhile, contrastive learning has been widely leveraged in graph learning as an effective mechanism to enhance the discriminative capacity of the learned representations. However, the complex structures of KG make it hard to construct appropriate contrastive pairs. Only a few attempts have integrated contrastive learning strategies with KGE. But, most of them rely on language models ( e.g., Bert) for contrastive pair construction instead of fully mining information underlying the graph structure, hindering expressive ability. Surprisingly, we find that the entities within a relational symmetrical structure are usually similar and correlated. To this end, we propose a knowledge graph contrastive learning framework based on relation-symmetrical structure, KGE-SymCL, which mines symmetrical structure information in KGs to enhance the discriminative ability of KGE models. Concretely, a plug-and-play approach is proposed by taking entities in the relation-symmetrical positions as positive pairs. Besides, a self-supervised alignment loss is designed to pull together positive pairs. Experimental results on link prediction and entity classification datasets demonstrate that our KGE-SymCL can be easily adopted to various KGE models for performance improvements. Moreover, extensive experiments show that our model could outperform other state-of-the-art baselines.
Social networks (SNs) are increasingly important sources of news for many people. The online connections made by users allows information to spread more easily than traditional news media (e.g., newspaper, television). However, they also make the spread of fake news easier than in traditional media, especially through the users' social network connections. In this paper, we focus on investigating if the SNs' users connection structure can aid fake news detection on Twitter. In particular, we propose to embed users based on their follower or friendship networks on the Twitter platform, so as to identify the groups that users form. Indeed, by applying unsupervised graph embedding methods on the graphs from the Twitter users' social network connections, we observe that users engaged with fake news are more tightly clustered together than users only engaged in factual news. Thus, we hypothesise that the embedded user's network can help detect fake news effectively. Through extensive experiments using a publicly available Twitter dataset, our results show that applying graph embedding methods on SNs, using the user connections as network information, can indeed classify fake news more effectively than most language-based approaches. Specifically, we observe a significant improvement over using only the textual information (i.e., TF.IDF or a BERT language model), as well as over models that deploy both advanced textual features (i.e., stance detection) and complex network features (e.g., users network, publishers cross citations). We conclude that the Twitter users' friendship and followers network information can significantly outperform language-based approaches, as well as the existing state-of-the-art fake news detection models that use a more sophisticated network structure, in classifying fake news on Twitter.
Graph representation learning models have demonstrated great capability in many real-world applications. Nevertheless, prior research indicates that these models can learn biased representations leading to discriminatory outcomes. A few works have been proposed to mitigate the bias in graph representations. However, most existing works require exceptional time and computing resources for training and fine-tuning. To this end, we study the problem of efficient fair graph representation learning and propose a novel framework FairMILE. FairMILE is a multi-level paradigm that can efficiently learn graph representations while enforcing fairness and preserving utility. It can work in conjunction with any unsupervised embedding approach and accommodate various fairness constraints. Extensive experiments across different downstream tasks demonstrate that FairMILE significantly outperforms state-of-the-art baselines in terms of running time while achieving a superior trade-off between fairness and utility.
Entity alignment aims to find entities in different knowledge graphs that semantically represent the same real-world entity. Recently, embedding-based entity alignment methods, which represent knowledge graphs as low-dimensional embeddings and perform entity alignments by measuring the similarity between entity embeddings, have achieved promising results. Most of these methods mainly focus on improving the knowledge graph embedding model or leveraging attributes to obtain more semantic information. However, the structural similarity between the two relations (considering all entities attached on the two relations) in different KGs has not been utilized in the existing methods. In this paper, we propose a novel embedding-based entity alignment method that takes the advantages of relation structural similarity. Specifically, our method first jointly learns the embeddings of two knowledge graphs in a uniform vector space, using the entity pairs regarding to the seed alignments (the alignments already known) that each shares the same embedding. Then, it iteratively computes the structural similarity between the relations in different knowledge graphs according to the seed alignments and the alignments with high reliability generated during training, which makes the embeddings of relations with high similarity closer to each other. Experimental results on five widely used real-world datasets show that the proposed approach significantly outperforms the state-of-the-art embedding-based ones for entity alignment.