Knowledge graph completion (KGC) has become a focus of attention across deep learning community owing to its excellent contribution to numerous downstream tasks. Although recently have witnessed a surge of work on KGC, they are still insufficient to accurately capture complex relations, since they adopt the single and static representations. In this work, we propose a novel Disentangled Knowledge Graph Attention Network (DisenKGAT) for KGC, which leverages both micro-disentanglement and macro-disentanglement to exploit representations behind Knowledge graphs (KGs). To achieve micro-disentanglement, we put forward a novel relation-aware aggregation to learn diverse component representation. For macro-disentanglement, we leverage mutual information as a regularization to enhance independence. With the assistance of disentanglement, our model is able to generate adaptive representations in terms of the given scenario. Besides, our work has strong robustness and flexibility to adapt to various score functions. Extensive experiments on public benchmark datasets have been conducted to validate the superiority of DisenKGAT over existing methods in terms of both accuracy and explainability.
Social media platforms provide convenient means for users to participate in multiple online activities on various contents and create fast widespread interactions. However, this rapidly growing access has also increased the diverse information, and characterizing user types to understand people's lifestyle decisions shared in social media is challenging. In this paper, we propose a weakly supervised graph embedding based framework for understanding user types. We evaluate the user embedding learned using weak supervision over well-being related tweets from Twitter, focusing on 'Yoga', 'Keto diet'. Experiments on real-world datasets demonstrate that the proposed framework outperforms the baselines for detecting user types. Finally, we illustrate data analysis on different types of users (e.g., practitioner vs. promotional) from our dataset. While we focus on lifestyle-related tweets (i.e., yoga, keto), our method for constructing user representation readily generalizes to other domains.
Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe-drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe-drug associations. In this paper, we proposed a novel method, Graph2MDA, to predict microbe-drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences, and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe-drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaningness of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75\%-95\% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method.\
Recently, several Knowledge Graph Embedding (KGE) approaches have been devised to represent entities and relations in dense vector space and employed in downstream tasks such as link prediction. A few KGE techniques address interpretability, i.e., mapping the connectivity patterns of the relations (i.e., symmetric/asymmetric, inverse, and composition) to a geometric interpretation such as rotations. Other approaches model the representations in higher dimensional space such as four-dimensional space (4D) to enhance the ability to infer the connectivity patterns (i.e., expressiveness). However, modeling relation and entity in a 4D space often comes at the cost of interpretability. This paper proposes HopfE, a novel KGE approach aiming to achieve the interpretability of inferred relations in the four-dimensional space. We first model the structural embeddings in 3D Euclidean space and view the relation operator as an SO(3) rotation. Next, we map the entity embedding vector from a 3D space to a 4D hypersphere using the inverse Hopf Fibration, in which we embed the semantic information from the KG ontology. Thus, HopfE considers the structural and semantic properties of the entities without losing expressivity and interpretability. Our empirical results on four well-known benchmarks achieve state-of-the-art performance for the KG completion task.
Collaborative Metric Learning (CML) recently emerged as a powerful paradigm for recommendation based on implicit feedback collaborative filtering. However, standard CML methods learn fixed user and item representations, which fails to capture the complex interests of users. Existing extensions of CML also either ignore the heterogeneity of user-item relations, i.e. that a user can simultaneously like very different items, or the latent item-item relations, i.e. that a user's preference for an item depends, not only on its intrinsic characteristics, but also on items they previously interacted with. In this paper, we present a hierarchical CML model that jointly captures latent user-item and item-item relations from implicit data. Our approach is inspired by translation mechanisms from knowledge graph embedding and leverages memory-based attention networks. We empirically show the relevance of this joint relational modeling, by outperforming existing CML models on recommendation tasks on several real-world datasets. Our experiments also emphasize the limits of current CML relational models on very sparse datasets.
Graphs can be used to describe complex systems. Recently, whole graph embedding (graph representation learning) can compress a graph into a compact lower-dimension vector while preserving intrinsic properties, earning much attention. However, most graph embedding methods have problems such as tedious parameter tuning or poor explanation. This paper presents a simple and hyperparameter-free whole graph embedding method based on the DHC (Degree, H-index, and Coreness) theorem and Shannon Entropy (E), abbreviated as DHC-E. The DHC-E can provide a trade-off between simplicity and quality for supervised classification learning tasks involving molecular, social, and brain networks. Moreover, it performs well in lower-dimensional graph visualization. Overall, the DHC-E is simple, hyperparameter-free, and explainable for whole graph embedding with promising potential for exploring graph classification and lower-dimensional graph visualization.
Deep extreme classification (XC) seeks to train deep architectures that can tag a data point with its most relevant subset of labels from an extremely large label set. The core utility of XC comes from predicting labels that are rarely seen during training. Such rare labels hold the key to personalized recommendations that can delight and surprise a user. However, the large number of rare labels and small amount of training data per rare label offer significant statistical and computational challenges. State-of-the-art deep XC methods attempt to remedy this by incorporating textual descriptions of labels but do not adequately address the problem. This paper presents ECLARE, a scalable deep learning architecture that incorporates not only label text, but also label correlations, to offer accurate real-time predictions within a few milliseconds. Core contributions of ECLARE include a frugal architecture and scalable techniques to train deep models along with label correlation graphs at the scale of millions of labels. In particular, ECLARE offers predictions that are 2 to 14% more accurate on both publicly available benchmark datasets as well as proprietary datasets for a related products recommendation task sourced from the Bing search engine. Code for ECLARE is available at https://github.com/Extreme-classification/ECLARE.
Healthcare representation learning on the Electronic Health Records is crucial for downstream medical prediction tasks in health informatics. Many NLP techniques, such as RNN and self-attention, have been adapted to learn medical representations from hierarchical and time-stamped EHRs data, but fail when they lack either general or task-specific data. Hence, some recent works train healthcare representations by incorporating medical ontology, by self-supervised tasks like diagnosis prediction, but (1) the small-scale, monotonous ontology is insufficient for robust learning, and (2) critical contexts or dependencies underlying patient journeys are barely exploited to enhance ontology learning. To address the challenges, we propose a Transformer-based representation learning approach: Mutual Integration of Patient journey and medical Ontology (MIPO), which is a robust end-to-end framework. Specifically, the proposed method focuses on task-specific representation learning by a sequential diagnoses predictive task, which is also beneficial to the ontology-based disease typing task. To integrate information in the patient's visiting records, we further introduce a graph-embedding module, which can mitigate the challenge of data insufficiency in healthcare. In this way, MIPO creates a mutual integration to benefit both healthcare representation learning and medical ontology embedding. Such an effective integration is guaranteed by joint training over fused embeddings of the two modules, targeting both task-specific prediction and ontology-based disease typing tasks simultaneously. Extensive experiments conducted on two real-world benchmark datasets have shown MIPO consistently achieves better performance than state-of-the-art methods no matter whether the training data is sufficient or not. Also, MIPO derives more interpretable diagnose embedding results compared to its counterparts.
Representation learning over temporal networks has drawn considerable attention in recent years. Efforts are mainly focused on modeling structural dependencies and temporal evolving regularities in Euclidean space which, however, underestimates the inherent complex and hierarchical properties in many real-world temporal networks, leading to sub-optimal embeddings. To explore these properties of a complex temporal network, we propose a hyperbolic temporal graph network (HTGN) that fully takes advantage of the exponential capacity and hierarchical awareness of hyperbolic geometry. More specially, HTGN maps the temporal graph into hyperbolic space, and incorporates hyperbolic graph neural network and hyperbolic gated recurrent neural network, to capture the evolving behaviors and implicitly preserve hierarchical information simultaneously. Furthermore, in the hyperbolic space, we propose two important modules that enable HTGN to successfully model temporal networks: (1) hyperbolic temporal contextual self-attention (HTA) module to attend to historical states and (2) hyperbolic temporal consistency (HTC) module to ensure stability and generalization. Experimental results on multiple real-world datasets demonstrate the superiority of HTGN for temporal graph embedding, as it consistently outperforms competing methods by significant margins in various temporal link prediction tasks. Specifically, HTGN achieves AUC improvement up to 9.98% for link prediction and 11.4% for new link prediction. Moreover, the ablation study further validates the representational ability of hyperbolic geometry and the effectiveness of the proposed HTA and HTC modules.
Entity alignment (EA) plays an important role in automatically integrating knowledge graphs (KGs) from multiple sources. Recent approaches based on Graph Neural Network (GNN) obtain entity representation from relation information and have achieved promising results. Besides, more and more methods introduce semi-supervision to ask for more labeled training data. However, two challenges still exist in GNN-based EA methods: (1) Deeper GNN Encoder: The GNN encoder of current methods has limited depth (usually 2-layers). (2) Low-quality Bootstrapping: The generated semi-supervised data is of low quality. In this paper, we propose a novel framework, Echo Entity Alignment (EchoEA), which leverages 4-levels self-attention mechanism to spread entity information to relations and echo back to entities. Furthermore, we propose attribute-combined bi-directional global-filtered strategy (ABGS) to improve bootstrapping, reduce false samples and generate high-quality training data. The experimental results on three real-world cross-lingual datasets are stable at around 96\% at hits@1 on average, showing that our approach not only significantly outperforms the state-of-the-art GNN-based methods, but also is universal and transferable for existing EA methods.
Learning embeddings for entities and relations in knowledge graph (KG) have benefited many downstream tasks. In recent years, scoring functions, the crux of KG learning, have been human-designed to measure the plausibility of triples and capture different kinds of relations in KGs. However, as relations exhibit intricate patterns that are hard to infer before training, none of them consistently perform the best on benchmark tasks. In this paper, inspired by the recent success of automated machine learning (AutoML), we search bilinear scoring functions for different KG tasks through the AutoML techniques. However, it is non-trivial to explore domain-specific information here. We first set up a search space for AutoBLM by analyzing existing scoring functions. Then, we propose a progressive algorithm (AutoBLM) and an evolutionary algorithm (AutoBLM+), which are further accelerated by filter and predictor to deal with the domain-specific properties for KG learning. Finally, we perform extensive experiments on benchmarks in KG completion, multi-hop query, and entity classification tasks. Empirical results show that the searched scoring functions are KG dependent, new to the literature, and outperform the existing scoring functions. AutoBLM+ is better than AutoBLM as the evolutionary algorithm can flexibly explore better structures in the same budget.
Knowledge graph embedding research has mainly focused on the two smallest normed division algebras, $\mathbb{R}$ and $\mathbb{C}$. Recent results suggest that trilinear products of quaternion-valued embeddings can be a more effective means to tackle link prediction. In addition, models based on convolutions on real-valued embeddings often yield state-of-the-art results for link prediction. In this paper, we investigate a composition of convolution operations with hypercomplex multiplications. We propose the four approaches QMult, OMult, ConvQ and ConvO to tackle the link prediction problem. QMult and OMult can be considered as quaternion and octonion extensions of previous state-of-the-art approaches, including DistMult and ComplEx. ConvQ and ConvO build upon QMult and OMult by including convolution operations in a way inspired by the residual learning framework. We evaluated our approaches on seven link prediction datasets including WN18RR, FB15K-237 and YAGO3-10. Experimental results suggest that the benefits of learning hypercomplex-valued vector representations become more apparent as the size and complexity of the knowledge graph grows. ConvO outperforms state-of-the-art approaches on FB15K-237 in MRR, Hit@1 and Hit@3, while QMult, OMult, ConvQ and ConvO outperform state-of-the-approaches on YAGO3-10 in all metrics. Results also suggest that link prediction performances can be further improved via prediction averaging. To foster reproducible research, we provide an open-source implementation of approaches, including training and evaluation scripts as well as pretrained models.
While representation learning has yielded a great success on many graph learning tasks, there is little understanding behind the structures that are being captured by these embeddings. For example, we wonder if the topological features, such as the Triangle Count, the Degree of the node and other centrality measures are concretely encoded in the embeddings. Furthermore, we ask if the presence of these structures in the embeddings is necessary for a better performance on the downstream tasks, such as clustering and classification. To address these questions, we conduct an extensive empirical study over three classes of unsupervised graph embedding models and seven different variants of Graph Autoencoders. Our results show that five topological features: the Degree, the Local Clustering Score, the Betweenness Centrality, the Eigenvector Centrality, and Triangle Count are concretely preserved in the first layer of the graph autoencoder that employs the SUM aggregation rule, under the condition that the model preserves the second-order proximity. We supplement further evidence for the presence of these features by revealing a hierarchy in the distribution of the topological features in the embeddings of the aforementioned model. We also show that a model with such properties can outperform other models on certain downstream tasks, especially when the preserved features are relevant to the task at hand. Finally, we evaluate the suitability of our findings through a test case study related to social influence prediction.
In knowledge graph embedding, the theoretical relationship between the softmax cross-entropy and negative sampling loss functions has not been investigated. This makes it difficult to fairly compare the results of the two different loss functions. We attempted to solve this problem by using the Bregman divergence to provide a unified interpretation of the softmax cross-entropy and negative sampling loss functions. Under this interpretation, we can derive theoretical findings for fair comparison. Experimental results on the FB15k-237 and WN18RR datasets show that the theoretical findings are valid in practical settings.
The high cost of data labeling often results in node label shortage in real applications. To improve node classification accuracy, graph-based semi-supervised learning leverages the ample unlabeled nodes to train together with the scarce available labeled nodes. However, most existing methods require the information of all nodes, including those to be predicted, during model training, which is not practical for dynamic graphs with newly added nodes. To address this issue, an adversarially regularized graph attention model is proposed to classify newly added nodes in a partially labeled graph. An attention-based aggregator is designed to generate the representation of a node by aggregating information from its neighboring nodes, thus naturally generalizing to previously unseen nodes. In addition, adversarial training is employed to improve the model's robustness and generalization ability by enforcing node representations to match a prior distribution. Experiments on real-world datasets demonstrate the effectiveness of the proposed method in comparison with the state-of-the-art methods. The code is available at https://github.com/JiarenX/AGAIN.
Knowledge graph embedding techniques are key to making knowledge graphs amenable to the plethora of machine learning approaches based on vector representations. Link prediction is often used as a proxy to evaluate the quality of these embeddings. Given that the creation of benchmarks for link prediction is a time-consuming endeavor, most work on the subject matter uses only a few benchmarks. As benchmarks are crucial for the fair comparison of algorithms, ensuring their quality is tantamount to providing a solid ground for developing better solutions to link prediction and ipso facto embedding knowledge graphs. First studies of benchmarks pointed to limitations pertaining to information leaking from the development to the test fragments of some benchmark datasets. We spotted a further common limitation of three of the benchmarks commonly used for evaluating link prediction approaches: out-of-vocabulary entities in the test and validation sets. We provide an implementation of an approach for spotting and removing such entities and provide corrected versions of the datasets WN18RR, FB15K-237, and YAGO3-10. Our experiments on the corrected versions of WN18RR, FB15K-237, and YAGO3-10 suggest that the measured performance of state-of-the-art approaches is altered significantly with p-values <1%, <1.4%, and <1%, respectively. Overall, state-of-the-art approaches gain on average absolute $3.29 \pm 0.24\%$ in all metrics on WN18RR. This means that some of the conclusions achieved in previous works might need to be revisited. We provide an open-source implementation of our experiments and corrected datasets at at https://github.com/dice-group/OOV-In-Link-Prediction.
Graph embedding is essential for graph mining tasks. With the prevalence of graph data in real-world applications, many methods have been proposed in recent years to learn high-quality graph embedding vectors various types of graphs. However, most existing methods usually randomly select the negative samples from the original graph to enhance the training data without considering the noise. In addition, most of these methods only focus on the explicit graph structures and cannot fully capture complex semantics of edges such as various relationships or asymmetry. In order to address these issues, we propose a robust and generalized framework for adversarial graph embedding based on generative adversarial networks. Inspired by generative adversarial network, we propose a robust and generalized framework for adversarial graph embedding, named AGE. AGE generates the fake neighbor nodes as the enhanced negative samples from the implicit distribution, and enables the discriminator and generator to jointly learn each node's robust and generalized representation. Based on this framework, we propose three models to handle three types of graph data and derive the corresponding optimization algorithms, i.e., UG-AGE and DG-AGE for undirected and directed homogeneous graphs, respectively, and HIN-AGE for heterogeneous information networks. Extensive experiments show that our methods consistently and significantly outperform existing state-of-the-art methods across multiple graph mining tasks, including link prediction, node classification, and graph reconstruction.
Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug discovery domain, KGs can be employed as part of a process which can result in lab-based experiments being performed, or impact on other decisions, incurring significant time and financial costs and most importantly, ultimately influencing patient healthcare. For KGE models to have impact in this domain, a better understanding of not only of performance, but also the various factors which determine it, is required. In this study we investigate, over the course of many thousands of experiments, the predictive performance of five KGE models on two public drug discovery-oriented KGs. Our goal is not to focus on the best overall model or configuration, instead we take a deeper look at how performance can be affected by changes in the training setup, choice of hyperparameters, model parameter initialisation seed and different splits of the datasets. Our results highlight that these factors have significant impact on performance and can even affect the ranking of models. Indeed these factors should be reported along with model architectures to ensure complete reproducibility and fair comparisons of future work, and we argue this is critical for the acceptance of use, and impact of KGEs in a biomedical setting.
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.
Numeric values associated to edges of a knowledge graph have been used to represent uncertainty, edge importance, and even out-of-band knowledge in a growing number of scenarios, ranging from genetic data to social networks. Nevertheless, traditional knowledge graph embedding models are not designed to capture such information, to the detriment of predictive power. We propose a novel method that injects numeric edge attributes into the scoring layer of a traditional knowledge graph embedding architecture. Experiments with publicly available numeric-enriched knowledge graphs show that our method outperforms traditional numeric-unaware baselines as well as the recent UKGE model.