Knowledge graph embedding plays an important role in knowledge representation, reasoning, and data mining applications. However, for multiple cross-domain knowledge graphs, state-of-the-art embedding models cannot make full use of the data from different knowledge domains while preserving the privacy of exchanged data. In addition, the centralized embedding model may not scale to the extensive real-world knowledge graphs. Therefore, we propose a novel decentralized scalable learning framework, \emph{Federated Knowledge Graphs Embedding} (FKGE), where embeddings from different knowledge graphs can be learnt in an asynchronous and peer-to-peer manner while being privacy-preserving. FKGE exploits adversarial generation between pairs of knowledge graphs to translate identical entities and relations of different domains into near embedding spaces. In order to protect the privacy of the training data, FKGE further implements a privacy-preserving neural network structure to guarantee no raw data leakage. We conduct extensive experiments to evaluate FKGE on 11 knowledge graphs, demonstrating a significant and consistent improvement in model quality with at most 17.85\% and 7.90\% increases in performance on triple classification and link prediction tasks.
Semantic embedding has been widely investigated for aligning knowledge graph (KG) entities. Current methods have explored and utilized the graph structure, the entity names and attributes, but ignore the ontology (or ontological schema) which contains critical meta information such as classes and their membership relationships with entities. In this paper, we propose an ontology-guided entity alignment method named OntoEA, where both KGs and their ontologies are jointly embedded, and the class hierarchy and the class disjointness are utilized to avoid false mappings. Extensive experiments on seven public and industrial benchmarks have demonstrated the state-of-the-art performance of OntoEA and the effectiveness of the ontologies.
Brain image analysis has advanced substantially in recent years with the proliferation of neuroimaging datasets acquired at different resolutions. While research on brain image super-resolution has undergone a rapid development in the recent years, brain graph super-resolution is still poorly investigated because of the complex nature of non-Euclidean graph data. In this paper, we propose the first-ever deep graph super-resolution (GSR) framework that attempts to automatically generate high-resolution (HR) brain graphs with N' nodes (i.e., anatomical regions of interest (ROIs)) from low-resolution (LR) graphs with N nodes where N < N'. First, we formalize our GSR problem as a node feature embedding learning task. Once the HR nodes' embeddings are learned, the pairwise connectivity strength between brain ROIs can be derived through an aggregation rule based on a novel Graph U-Net architecture. While typically the Graph U-Net is a node-focused architecture where graph embedding depends mainly on node attributes, we propose a graph-focused architecture where the node feature embedding is based on the graph topology. Second, inspired by graph spectral theory, we break the symmetry of the U-Net architecture by super-resolving the low-resolution brain graph structure and node content with a GSR layer and two graph convolutional network layers to further learn the node embeddings in the HR graph. Third, to handle the domain shift between the ground-truth and the predicted HR brain graphs, we incorporate adversarial regularization to align their respective distributions. Our proposed AGSR-Net framework outperformed its variants for predicting high-resolution functional brain graphs from low-resolution ones. Our AGSR-Net code is available on GitHub at https://github.com/basiralab/AGSR-Net.
Knowledge representation learning has received a lot of attention in the past few years. The success of existing methods heavily relies on the quality of knowledge graphs. The entities with few triplets tend to be learned with less expressive power. Fortunately, there are many knowledge graphs constructed from various sources, the representations of which could contain much information. We propose an adversarial embedding transfer network ATransN, which transfers knowledge from one or more teacher knowledge graphs to a target one through an aligned entity set without explicit data leakage. Specifically, we add soft constraints on aligned entity pairs and neighbours to the existing knowledge representation learning methods. To handle the problem of possible distribution differences between teacher and target knowledge graphs, we introduce an adversarial adaption module. The discriminator of this module evaluates the degree of consistency between the embeddings of an aligned entity pair. The consistency score is then used as the weights of soft constraints. It is not necessary to acquire the relations and triplets in teacher knowledge graphs because we only utilize the entity representations. Knowledge graph completion results show that ATransN achieves better performance against baselines without transfer on three datasets, CN3l, WK3l, and DWY100k. The ablation study demonstrates that ATransN can bring steady and consistent improvement in different settings. The extension of combining other knowledge graph embedding algorithms and the extension with three teacher graphs display the promising generalization of the adversarial transfer network.
In this paper, we propose a novel subspace learning framework for one-class classification. The proposed framework presents the problem in the form of graph embedding. It includes the previously proposed subspace one-class techniques as its special cases and provides further insight on what these techniques actually optimize. The framework allows to incorporate other meaningful optimization goals via the graph preserving criterion and reveals a spectral solution and a spectral regression-based solution as alternatives to the previously used gradient-based technique. We combine the subspace learning framework iteratively with Support Vector Data Description applied in the subspace to formulate Graph-Embedded Subspace Support Vector Data Description. We experimentally analyzed the performance of newly proposed different variants. We demonstrate improved performance against the baselines and the recently proposed subspace learning methods for one-class classification.
Despite the recent success of reconciling spike-based coding with the error backpropagation algorithm, spiking neural networks are still mostly applied to tasks stemming from sensory processing, operating on traditional data structures like visual or auditory data. A rich data representation that finds wide application in industry and research is the so-called knowledge graph - a graph-based structure where entities are depicted as nodes and relations between them as edges. Complex systems like molecules, social networks and industrial factory systems can be described using the common language of knowledge graphs, allowing the usage of graph embedding algorithms to make context-aware predictions in these information-packed environments. We propose a spike-based algorithm where nodes in a graph are represented by single spike times of neuron populations and relations as spike time differences between populations. Learning such spike-based embeddings only requires knowledge about spike times and spike time differences, compatible with recently proposed frameworks for training spiking neural networks. The presented model is easily mapped to current neuromorphic hardware systems and thereby moves inference on knowledge graphs into a domain where these architectures thrive, unlocking a promising industrial application area for this technology.
Unsupervised attributed graph representation learning is challenging since both structural and feature information are required to be represented in the latent space. Existing methods concentrate on learning latent representation via reconstruction tasks, but cannot directly optimize representation and are prone to oversmoothing, thus limiting the applications on downstream tasks. To alleviate these issues, we propose a novel graph embedding framework named Deep Manifold Attributed Graph Embedding (DMAGE). A node-to-node geodesic similarity is proposed to compute the inter-node similarity between the data space and the latent space and then use Bergman divergence as loss function to minimize the difference between them. We then design a new network structure with fewer aggregation to alleviate the oversmoothing problem and incorporate graph structure augmentation to improve the representation's stability. Our proposed DMAGE surpasses state-of-the-art methods by a significant margin on three downstream tasks: unsupervised visualization, node clustering, and link prediction across four popular datasets.
The scoring function, which measures the plausibility of triplets in knowledge graphs (KGs), is the key to ensure the excellent performance of KG embedding, and its design is also an important problem in the literature. Automated machine learning (AutoML) techniques have recently been introduced into KG to design task-aware scoring functions, which achieve state-of-the-art performance in KG embedding. However, the effectiveness of searched scoring functions is still not as good as desired. In this paper, observing that existing scoring functions can exhibit distinct performance on different semantic patterns, we are motivated to explore such semantics by searching relation-aware scoring functions. But the relation-aware search requires a much larger search space than the previous one. Hence, we propose to encode the space as a supernet and propose an efficient alternative minimization algorithm to search through the supernet in a one-shot manner. Finally, experimental results on benchmark datasets demonstrate that the proposed method can efficiently search relation-aware scoring functions, and achieve better embedding performance than state-of-the-art methods.
Knowledge Graph (KG) is a flexible structure that is able to describe the complex relationship between data entities. Currently, most KG embedding models are trained based on negative sampling, i.e., the model aims to maximize some similarity of the connected entities in the KG, while minimizing the similarity of the sampled disconnected entities. Negative sampling helps to reduce the time complexity of model learning by only considering a subset of negative instances, which may fail to deliver stable model performance due to the uncertainty in the sampling procedure. To avoid such deficiency, we propose a new framework for KG embedding -- Efficient Non-Sampling Knowledge Graph Embedding (NS-KGE). The basic idea is to consider all of the negative instances in the KG for model learning, and thus to avoid negative sampling. The framework can be applied to square-loss based knowledge graph embedding models or models whose loss can be converted to a square loss. A natural side-effect of this non-sampling strategy is the increased computational complexity of model learning. To solve the problem, we leverage mathematical derivations to reduce the complexity of non-sampling loss function, which eventually provides us both better efficiency and better accuracy in KG embedding compared with existing models. Experiments on benchmark datasets show that our NS-KGE framework can achieve a better performance on efficiency and accuracy over traditional negative sampling based models, and that the framework is applicable to a large class of knowledge graph embedding models.
We propose a deep Graph Neural Network (GNN) model that alternates two types of layers. The first type is inspired by Reservoir Computing (RC) and generates new vertex features by iterating a non-linear map until it converges to a fixed point. The second type of layer implements graph pooling operations, that gradually reduce the support graph and the vertex features, and further improve the computational efficiency of the RC-based GNN. The architecture is, therefore, pyramidal. In the last layer, the features of the remaining vertices are combined into a single vector, which represents the graph embedding. Through a mathematical derivation introduced in this paper, we show formally how graph pooling can reduce the computational complexity of the model and speed-up the convergence of the dynamical updates of the vertex features. Our proposed approach to the design of RC-based GNNs offers an advantageous and principled trade-off between accuracy and complexity, which we extensively demonstrate in experiments on a large set of graph datasets.
Knowledge bases often consist of facts which are harvested from a variety of sources, many of which are noisy and some of which conflict, resulting in a level of uncertainty for each triple. Knowledge bases are also often incomplete, prompting the use of embedding methods to generalize from known facts, however, existing embedding methods only model triple-level uncertainty, and reasoning results lack global consistency. To address these shortcomings, we propose BEUrRE, a novel uncertain knowledge graph embedding method with calibrated probabilistic semantics. BEUrRE models each entity as a box (i.e. axis-aligned hyperrectangle) and relations between two entities as affine transforms on the head and tail entity boxes. The geometry of the boxes allows for efficient calculation of intersections and volumes, endowing the model with calibrated probabilistic semantics and facilitating the incorporation of relational constraints. Extensive experiments on two benchmark datasets show that BEUrRE consistently outperforms baselines on confidence prediction and fact ranking due to its probabilistic calibration and ability to capture high-order dependencies among facts.
Fake tweets are observed to be ever-increasing, demanding immediate countermeasures to combat their spread. During COVID-19, tweets with misinformation should be flagged and neutralized in their early stages to mitigate the damages. Most of the existing methods for early detection of fake news assume to have enough propagation information for large labeled tweets -- which may not be an ideal setting for cases like COVID-19 where both aspects are largely absent. In this work, we present ENDEMIC, a novel early detection model which leverages exogenous and endogenous signals related to tweets, while learning on limited labeled data. We first develop a novel dataset, called CTF for early COVID-19 Twitter fake news, with additional behavioral test sets to validate early detection. We build a heterogeneous graph with follower-followee, user-tweet, and tweet-retweet connections and train a graph embedding model to aggregate propagation information. Graph embeddings and contextual features constitute endogenous, while time-relative web-scraped information constitutes exogenous signals. ENDEMIC is trained in a semi-supervised fashion, overcoming the challenge of limited labeled data. We propose a co-attention mechanism to fuse signal representations optimally. Experimental results on ECTF, PolitiFact, and GossipCop show that ENDEMIC is highly reliable in detecting early fake tweets, outperforming nine state-of-the-art methods significantly.
Knowledge Graph Embeddings (KGEs) have been intensively explored in recent years due to their promise for a wide range of applications. However, existing studies focus on improving the final model performance without acknowledging the computational cost of the proposed approaches, in terms of execution time and environmental impact. This paper proposes a simple yet effective KGE framework which can reduce the training time and carbon footprint by orders of magnitudes compared with state-of-the-art approaches, while producing competitive performance. We highlight three technical innovations: full batch learning via relational matrices, closed-form Orthogonal Procrustes Analysis for KGEs, and non-negative-sampling training. In addition, as the first KGE method whose entity embeddings also store full relation information, our trained models encode rich semantics and are highly interpretable. Comprehensive experiments and ablation studies involving 13 strong baselines and two standard datasets verify the effectiveness and efficiency of our algorithm.
The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, Enzymatic Link Prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions catalogued in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity. We explore both transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding for predicting enzymatic links improves link prediction by 24% over fingerprint-similarity-based approaches. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can also guide visualization. The code and datasets are available through https://github.com/HassounLab/ELP.
The problem of code generation from textual program descriptions has long been viewed as a grand challenge in software engineering. In recent years, many deep learning based approaches have been proposed, which can generate a sequence of code from a sequence of textual program description. However, the existing approaches ignore the global relationships among API methods, which are important for understanding the usage of APIs. In this paper, we propose to model the dependencies among API methods as an API dependency graph (ADG) and incorporate the graph embedding into a sequence-to-sequence (Seq2Seq) model. In addition to the existing encoder-decoder structure, a new module named ``embedder" is introduced. In this way, the decoder can utilize both global structural dependencies and textual program description to predict the target code. We conduct extensive code generation experiments on three public datasets and in two programming languages (Python and Java). Our proposed approach, called ADG-Seq2Seq, yields significant improvements over existing state-of-the-art methods and maintains its performance as the length of the target code increases. Extensive ablation tests show that the proposed ADG embedding is effective and outperforms the baselines.
Learning and reasoning over graphs is increasingly done by means of probabilistic models, e.g. exponential random graph models, graph embedding models, and graph neural networks. When graphs are modeling relations between people, however, they will inevitably reflect biases, prejudices, and other forms of inequity and inequality. An important challenge is thus to design accurate graph modeling approaches while guaranteeing fairness according to the specific notion of fairness that the problem requires. Yet, past work on the topic remains scarce, is limited to debiasing specific graph modeling methods, and often aims to ensure fairness in an indirect manner. We propose a generic approach applicable to most probabilistic graph modeling approaches. Specifically, we first define the class of fair graph models corresponding to a chosen set of fairness criteria. Given this, we propose a fairness regularizer defined as the KL-divergence between the graph model and its I-projection onto the set of fair models. We demonstrate that using this fairness regularizer in combination with existing graph modeling approaches efficiently trades-off fairness with accuracy, whereas the state-of-the-art models can only make this trade-off for the fairness criterion that they were specifically designed for.
Dynamic graphs arise in a plethora of practical scenarios such as social networks, communication networks, and financial transaction networks. Given a dynamic graph, it is fundamental and essential to learn a graph representation that is expected not only to preserve structural proximity but also jointly capture the time-evolving patterns. Recently, graph convolutional network (GCN) has been widely explored and used in non-Euclidean application domains. The main success of GCN, especially in handling dependencies and passing messages within nodes, lies in its approximation to Laplacian smoothing. As a matter of fact, this smoothing technique can not only encourage must-link node pairs to get closer but also push cannot-link pairs to shrink together, which potentially cause serious feature shrink or oversmoothing problem, especially when stacking graph convolution in multiple layers or steps. For learning time-evolving patterns, a natural solution is to preserve historical state and combine it with the current interactions to obtain the most recent representation. Then the serious feature shrink or oversmoothing problem could happen when stacking graph convolution explicitly or implicitly according to current prevalent methods, which would make nodes too similar to distinguish each other. To solve this problem in dynamic graph embedding, we analyze the shrinking properties in the node embedding space at first, and then design a simple yet versatile method, which exploits L2 feature normalization constraint to rescale all nodes to hypersphere of a unit ball so that nodes would not shrink together, and yet similar nodes can still get closer. Extensive experiments on four real-world dynamic graph datasets compared with competitive baseline models demonstrate the effectiveness of the proposed method.
Graph neural networks (GNNs) have attracted tremendous attention from the graph learning community in recent years. It has been widely adopted in various real-world applications from diverse domains, such as social networks and biological graphs. The research and applications of graph deep learning present new challenges, including the sparse nature of graph data, complicated training of GNNs, and non-standard evaluation of graph tasks. To tackle the issues, we present CogDL, a comprehensive library for graph deep learning that allows researchers and practitioners to conduct experiments, compare methods, and build applications with ease and efficiency. In CogDL, we propose a unified design for the training and evaluation of GNN models for various graph tasks, making it unique among existing graph learning libraries. By utilizing this unified trainer, CogDL can optimize the GNN training loop with several training techniques, such as mixed precision training. Moreover, we develop efficient sparse operators for CogDL, enabling it to become the most competitive graph library for efficiency. Another important CogDL feature is its focus on ease of use with the aim of facilitating open and reproducible research of graph learning. We leverage CogDL to report and maintain benchmark results on fundamental graph tasks, which can be reproduced and directly used by the community.
While most network embedding techniques model the relative positions of nodes in a network, recently there has been significant interest in structural embeddings that model node role equivalences, irrespective of their distances to any specific nodes. We present PhUSION, a proximity-based unified framework for computing structural and positional node embeddings, which leverages well-established methods for calculating node proximity scores. Clarifying a point of contention in the literature, we show which step of PhUSION produces the different kinds of embeddings and what steps can be used by both. Moreover, by aggregating the PhUSION node embeddings, we obtain graph-level features that model information lost by previous graph feature learning and kernel methods. In a comprehensive empirical study with over 10 datasets, 4 tasks, and 35 methods, we systematically reveal successful design choices for node and graph-level machine learning with embeddings.
Semi-supervised learning (SSL) has tremendous value in practice due to its ability to utilize both labeled data and unlabelled data. An important class of SSL methods is to naturally represent data as graphs such that the label information of unlabelled samples can be inferred from the graphs, which corresponds to graph-based semi-supervised learning (GSSL) methods. GSSL methods have demonstrated their advantages in various domains due to their uniqueness of structure, the universality of applications, and their scalability to large scale data. Focusing on this class of methods, this work aims to provide both researchers and practitioners with a solid and systematic understanding of relevant advances as well as the underlying connections among them. This makes our paper distinct from recent surveys that cover an overall picture of SSL methods while neglecting fundamental understanding of GSSL methods. In particular, a major contribution of this paper lies in a new generalized taxonomy for GSSL, including graph regularization and graph embedding methods, with the most up-to-date references and useful resources such as codes, datasets, and applications. Furthermore, we present several potential research directions as future work with insights into this rapidly growing field.