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.
Contextualized entity representations learned by state-of-the-art transformer-based language models (TLMs) like BERT, GPT, T5, etc., leverage the attention mechanism to learn the data context from training data corpus. However, these models do not use the knowledge context. Knowledge context can be understood as semantics about entities and their relationship with neighboring entities in knowledge graphs. We propose a novel and effective technique to infuse knowledge context from multiple knowledge graphs for conceptual and ambiguous entities into TLMs during fine-tuning. It projects knowledge graph embeddings in the homogeneous vector-space, introduces new token-types for entities, aligns entity position ids, and a selective attention mechanism. We take BERT as a baseline model and implement the "Knowledge-Infused BERT" by infusing knowledge context from ConceptNet and WordNet, which significantly outperforms BERT and other recent knowledge-aware BERT variants like ERNIE, SenseBERT, and BERT_CS over eight different subtasks of GLUE benchmark. The KI-BERT-base model even significantly outperforms BERT-large for domain-specific tasks like SciTail and academic subsets of QQP, QNLI, and MNLI.
Content-based histopathological image retrieval (CBHIR) has become popular in recent years in the domain of histopathological image analysis. CBHIR systems provide auxiliary diagnosis information for pathologists by searching for and returning regions that are contently similar to the region of interest (ROI) from a pre-established database. While, it is challenging and yet significant in clinical applications to retrieve diagnostically relevant regions from a database that consists of histopathological whole slide images (WSIs) for a query ROI. In this paper, we propose a novel framework for regions retrieval from WSI-database based on hierarchical graph convolutional networks (GCNs) and Hash technique. Compared to the present CBHIR framework, the structural information of WSI is preserved through graph embedding of GCNs, which makes the retrieval framework more sensitive to regions that are similar in tissue distribution. Moreover, benefited from the hierarchical GCN structures, the proposed framework has good scalability for both the size and shape variation of ROIs. It allows the pathologist defining query regions using free curves according to the appearance of tissue. Thirdly, the retrieval is achieved based on Hash technique, which ensures the framework is efficient and thereby adequate for practical large-scale WSI-database. The proposed method was validated on two public datasets for histopathological WSI analysis and compared to the state-of-the-art methods. The proposed method achieved mean average precision above 0.857 on the ACDC-LungHP dataset and above 0.864 on the Camelyon16 dataset in the irregular region retrieval tasks, which are superior to the state-of-the-art methods. The average retrieval time from a database within 120 WSIs is 0.802 ms.
Membership inference attacks (MIAs) infer whether a specific data record is used for target model training. MIAs have provoked many discussions in the information security community since they give rise to severe data privacy issues, especially for private and sensitive datasets. Knowledge Graphs (KGs), which describe domain-specific subjects and relationships among them, are valuable and sensitive, such as medical KGs constructed from electronic health records. However, the privacy threat to knowledge graphs is critical but rarely explored. In this paper, we conduct the first empirical evaluation of privacy threats to knowledge graphs triggered by knowledge graph embedding methods (KGEs). We propose three types of membership inference attacks: transfer attacks (TAs), prediction loss-based attacks (PLAs), and prediction correctness-based attacks (PCAs), according to attack difficulty levels. In the experiments, we conduct three inference attacks against four standard KGE methods over three benchmark datasets. In addition, we also propose the attacks against medical KG and financial KG. The results demonstrate that the proposed attack methods can easily explore the privacy leakage of knowledge graphs.
Several methods have been developed to extract information from electroencephalograms (EEG). One of them is Phase-Amplitude Coupling (PAC) which is a type of Cross-Frequency Coupling (CFC) method, consisting in measure the synchronization of phase and amplitude for the different EEG bands and electrodes. This provides information regarding brain areas that are synchronously activated, and eventually, a marker of functional connectivity between these areas. In this work, intra and inter electrode PAC is computed obtaining the relationship among different electrodes used in EEG. The connectivity information is then treated as a graph in which the different nodes are the electrodes and the edges PAC values between them. These structures are embedded to create a feature vector that can be further used to classify multichannel EEG samples. The proposed method has been applied to classified EEG samples acquired using specific auditory stimuli in a task designed for dyslexia disorder diagnosis in seven years old children EEG's. The proposed method provides AUC values up to 0.73 and allows selecting the most discriminant electrodes and EEG bands.
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.
Among the top approaches of recent years, link prediction using knowledge graph embedding (KGE) models has gained significant attention for knowledge graph completion. Various embedding models have been proposed so far, among which, some recent KGE models obtain state-of-the-art performance on link prediction tasks by using embeddings with a high dimension (e.g. 1000) which accelerate the costs of training and evaluation considering the large scale of KGs. In this paper, we propose a simple but effective performance boosting strategy for KGE models by using multiple low dimensions in different repetition rounds of the same model. For example, instead of training a model one time with a large embedding size of 1200, we repeat the training of the model 6 times in parallel with an embedding size of 200 and then combine the 6 separate models for testing while the overall numbers of adjustable parameters are same (6*200=1200) and the total memory footprint remains the same. We show that our approach enables different models to better cope with their expressiveness issues on modeling various graph patterns such as symmetric, 1-n, n-1 and n-n. In order to justify our findings, we conduct experiments on various KGE models. Experimental results on standard benchmark datasets, namely FB15K, FB15K-237 and WN18RR, show that multiple low-dimensional models of the same kind outperform the corresponding single high-dimensional models on link prediction in a certain range and have advantages in training efficiency by using parallel training while the overall numbers of adjustable parameters are same.
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.
Given one or more query vertices, Community Search (CS) aims to find densely intra-connected and loosely inter-connected structures containing query vertices. Attributed Community Search (ACS), a related problem, is more challenging since it finds communities with both cohesive structures and homogeneous vertex attributes. However, most methods for the CS task rely on inflexible pre-defined structures and studies for ACS treat each attribute independently. Moreover, the most popular ACS strategies decompose ACS into two separate sub-problems, i.e., the CS task and subsequent attribute filtering task. However, in real-world graphs, the community structure and the vertex attributes are closely correlated to each other. This correlation is vital for the ACS problem. In this paper, we propose Graph Neural Network models for both CS and ACS problems, i.e., Query Driven-GNN and Attributed Query Driven-GNN. In QD-GNN, we combine the local query-dependent structure and global graph embedding. In order to extend QD-GNN to handle attributes, we model vertex attributes as a bipartite graph and capture the relation between attributes by constructing GNNs on this bipartite graph. With a Feature Fusion operator, AQD-GNN processes the structure and attribute simultaneously and predicts communities according to each attributed query. Experiments on real-world graphs with ground-truth communities demonstrate that the proposed models outperform existing CS and ACS algorithms in terms of both efficiency and effectiveness. More recently, an interactive setting for CS is proposed that allows users to adjust the predicted communities. We further verify our approaches under the interactive setting and extend to the attributed context. Our method achieves 2.37% and 6.29% improvements in F1-score than the state-of-the-art model without attributes and with attributes respectively.
Graph embedding, aiming to learn low-dimensional representations (aka. embeddings) of nodes, has received significant attention recently. Recent years have witnessed a surge of efforts made on static graphs, among which Graph Convolutional Network (GCN) has emerged as an effective class of models. However, these methods mainly focus on the static graph embedding. In this work, we propose an efficient dynamic graph embedding approach, Dynamic Graph Convolutional Network (DyGCN), which is an extension of GCN-based methods. We naturally generalizes the embedding propagation scheme of GCN to dynamic setting in an efficient manner, which is to propagate the change along the graph to update node embeddings. The most affected nodes are first updated, and then their changes are propagated to the further nodes and leads to their update. Extensive experiments conducted on various dynamic graphs demonstrate that our model can update the node embeddings in a time-saving and performance-preserving way.
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.
Conventional network data has largely focused on pairwise interactions between two entities, yet multi-way interactions among multiple entities have been frequently observed in real-life hypergraph networks. In this article, we propose a novel method for detecting community structure in general hypergraph networks, uniform or non-uniform. The proposed method introduces a null vertex to augment a non-uniform hypergraph into a uniform multi-hypergraph, and then embeds the multi-hypergraph in a low-dimensional vector space such that vertices within the same community are close to each other. The resultant optimization task can be efficiently tackled by an alternative updating scheme. The asymptotic consistencies of the proposed method are established in terms of both community detection and hypergraph estimation, which are also supported by numerical experiments on some synthetic and real-life hypergraph networks.
Recent knowledge graph embedding (KGE) models based on hyperbolic geometry have shown great potential in a low-dimensional embedding space. However, the necessity of hyperbolic space in KGE is still questionable, because the calculation based on hyperbolic geometry is much more complicated than Euclidean operations. In this paper, based on the state-of-the-art hyperbolic-based model RotH, we develop two lightweight Euclidean-based models, called RotL and Rot2L. The RotL model simplifies the hyperbolic operations while keeping the flexible normalization effect. Utilizing a novel two-layer stacked transformation and based on RotL, the Rot2L model obtains an improved representation capability, yet costs fewer parameters and calculations than RotH. The experiments on link prediction show that Rot2L achieves the state-of-the-art performance on two widely-used datasets in low-dimensional knowledge graph embeddings. Furthermore, RotL achieves similar performance as RotH but only requires half of the training time.
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.
Zero-shot graph embedding is a major challenge for supervised graph learning. Although a recent method RECT has shown promising performance, its working mechanisms are not clear and still needs lots of training data. In this paper, we give deep insights into RECT, and address its fundamental limits. We show that its core part is a GNN prototypical model in which a class prototype is described by its mean feature vector. As such, RECT maps nodes from the raw-input feature space into an intermediate-level semantic space that connects the raw-input features to both seen and unseen classes. This mechanism makes RECT work well on both seen and unseen classes, which however also reduces the discrimination. To realize its full potentials, we propose two label expansion strategies. Specifically, besides expanding the labeled node set of seen classes, we can also expand that of unseen classes. Experiments on real-world datasets validate the superiority of our methods.
Despite the importance and abundance of temporal knowledge graphs, most of the current research has been focused on reasoning on static graphs. In this paper, we study the challenging problem of inference over temporal knowledge graphs. In particular, the task of temporal link prediction. In general, this is a difficult task due to data non-stationarity, data heterogeneity, and its complex temporal dependencies. We propose Chronological Rotation embedding (ChronoR), a novel model for learning representations for entities, relations, and time. Learning dense representations is frequently used as an efficient and versatile method to perform reasoning on knowledge graphs. The proposed model learns a k-dimensional rotation transformation parametrized by relation and time, such that after each fact's head entity is transformed using the rotation, it falls near its corresponding tail entity. By using high dimensional rotation as its transformation operator, ChronoR captures rich interaction between the temporal and multi-relational characteristics of a Temporal Knowledge Graph. Experimentally, we show that ChronoR is able to outperform many of the state-of-the-art methods on the benchmark datasets for temporal knowledge graph link prediction.
Many problems such as node classification and link prediction in network data can be solved using graph embeddings. However, it is difficult to use graphs to capture non-binary relations such as communities of nodes. These kinds of complex relations are expressed more naturally as hypergraphs. While hypergraphs are a generalization of graphs, state-of-the-art graph embedding techniques are not adequate for solving prediction and classification tasks on large hypergraphs accurately in reasonable time. In this paper, we introduce HyperNetVec, a novel hierarchical framework for scalable unsupervised hypergraph embedding. HyperNetVec exploits shared-memory parallelism and is capable of generating high quality embeddings for real-world hypergraphs with millions of nodes and hyperedges in only a couple of minutes while existing hypergraph systems either fail for such large hypergraphs or may take days to produce the embeddings.
Most real-world datasets are inherently heterogeneous graphs, which involve a diversity of node and relation types. Heterogeneous graph embedding is to learn the structure and semantic information from the graph, and then embed it into the low-dimensional node representation. Existing methods usually capture the composite relation of a heterogeneous graph by defining metapath, which represent a semantic of the graph. However, these methods either ignore node attributes, or discard the local and global information of the graph, or only consider one metapath. To address these limitations, we propose a Metapaths-guided Neighbors-aggregated Heterogeneous Graph Neural Network(MHN) to improve performance. Specially, MHN employs node base embedding to encapsulate node attributes, BFS and DFS neighbors aggregation within a metapath to capture local and global information, and metapaths aggregation to combine different semantics of the heterogeneous graph. We conduct extensive experiments for the proposed MHN on three real-world heterogeneous graph datasets, including node classification, link prediction and online A/B test on Alibaba mobile application. Results demonstrate that MHN performs better than other state-of-the-art baselines.