Graph Neural Networks (GNNs) have shown remarkable merit in performing various learning-based tasks in complex networks. The superior performance of GNNs often correlates with the availability and quality of node-level features in the input networks. However, for many network applications, such node-level information may be missing or unreliable, thereby limiting the applicability and efficacy of GNNs. To address this limitation, we present a novel approach denoted as Ego-centric Spectral subGraph Embedding Augmentation (ESGEA), which aims to enhance and design node features, particularly in scenarios where information is lacking. Our method leverages the topological structure of the local subgraph to create topology-aware node features. The subgraph features are generated using an efficient spectral graph embedding technique, and they serve as node features that capture the local topological organization of the network. The explicit node features, if present, are then enhanced with the subgraph embeddings in order to improve the overall performance. ESGEA is compatible with any GNN-based architecture and is effective even in the absence of node features. We evaluate the proposed method in a social network graph classification task where node attributes are unavailable, as well as in a node classification task where node features are corrupted or even absent. The evaluation results on seven datasets and eight baseline models indicate up to a 10% improvement in AUC and a 7% improvement in accuracy for graph and node classification tasks, respectively.
In recent years, Massive Open Online Courses (MOOCs) have gained significant traction as a rapidly growing phenomenon in online learning. Unlike traditional classrooms, MOOCs offer a unique opportunity to cater to a diverse audience from different backgrounds and geographical locations. Renowned universities and MOOC-specific providers, such as Coursera, offer MOOC courses on various subjects. Automated assessment tasks like grade and early dropout predictions are necessary due to the high enrollment and limited direct interaction between teachers and learners. However, current automated assessment approaches overlook the structural links between different entities involved in the downstream tasks, such as the students and courses. Our hypothesis suggests that these structural relationships, manifested through an interaction graph, contain valuable information that can enhance the performance of the task at hand. To validate this, we construct a unique knowledge graph for a large MOOC dataset, which will be publicly available to the research community. Furthermore, we utilize graph embedding techniques to extract latent structural information encoded in the interactions between entities in the dataset. These techniques do not require ground truth labels and can be utilized for various tasks. Finally, by combining entity-specific features, behavioral features, and extracted structural features, we enhance the performance of predictive machine learning models in student assignment grade prediction. Our experiments demonstrate that structural features can significantly improve the predictive performance of downstream assessment tasks. The code and data are available in \url{https://github.com/DSAatUSU/MOOPer_grade_prediction}
Graph embedding has become a powerful tool for learning latent representations of nodes in a graph. Despite its superior performance in various graph-based machine learning tasks, serious privacy concerns arise when the graph data contains personal or sensitive information. To address this issue, we investigate and develop graph embedding algorithms that satisfy local differential privacy (LDP). We introduce a novel privacy-preserving graph embedding framework, named PrivGE, to protect node data privacy. Specifically, we propose an LDP mechanism to obfuscate node data and utilize personalized PageRank as the proximity measure to learn node representations. Furthermore, we provide a theoretical analysis of the privacy guarantees and utility offered by the PrivGE framework. Extensive experiments on several real-world graph datasets demonstrate that PrivGE achieves an optimal balance between privacy and utility, and significantly outperforms existing methods in node classification and link prediction tasks.
Most existing graph visualization methods based on dimension reduction are limited to relatively small graphs due to performance issues. In this work, we propose a novel dimension reduction method for graph visualization, called t-Distributed Stochastic Graph Neighbor Embedding (t-SGNE). t-SGNE is specifically designed to visualize cluster structures in the graph. As a variant of the standard t-SNE method, t-SGNE avoids the time-consuming computations of pairwise similarity. Instead, it uses the neighbor structures of the graph to reduce the time complexity from quadratic to linear, thus supporting larger graphs. In addition, to suit t-SGNE, we combined Laplacian Eigenmaps with the shortest path algorithm in graphs to form the graph embedding algorithm ShortestPath Laplacian Eigenmaps Embedding (SPLEE). Performing SPLEE to obtain a high-dimensional embedding of the large-scale graph and then using t-SGNE to reduce its dimension for visualization, we are able to visualize graphs with up to 300K nodes and 1M edges within 5 minutes and achieve approximately 10% improvement in visualization quality. Codes and data are available at https://github.com/Charlie-XIAO/embedding-visualization-test.
The embedding of Biomedical Knowledge Graphs (BKGs) generates robust representations, valuable for a variety of artificial intelligence applications, including predicting drug combinations and reasoning disease-drug relationships. Meanwhile, contrastive learning (CL) is widely employed to enhance the distinctiveness of these representations. However, constructing suitable contrastive pairs for CL, especially within Knowledge Graphs (KGs), has been challenging. In this paper, we proposed a novel node-based contrastive learning method for knowledge graph embedding, NC-KGE. NC-KGE enhances knowledge extraction in embeddings and speeds up training convergence by constructing appropriate contrastive node pairs on KGs. This scheme can be easily integrated with other knowledge graph embedding (KGE) methods. For downstream task such as biochemical relationship prediction, we have incorporated a relation-aware attention mechanism into NC-KGE, focusing on the semantic relationships and node interactions. Extensive experiments show that NC-KGE performs competitively with state-of-the-art models on public datasets like FB15k-237 and WN18RR. Particularly in biomedical relationship prediction tasks, NC-KGE outperforms all baselines on datasets such as PharmKG8k-28, DRKG17k-21, and BioKG72k-14, especially in predicting drug combination relationships. We release our code at https://github.com/zhi520/NC-KGE.
Knowledge graph embedding (KGE) aims to map entities and relations of a knowledge graph (KG) into a low-dimensional and dense vector space via contrasting the positive and negative triples. In the training process of KGEs, negative sampling is essential to find high-quality negative triples since KGs only contain positive triples. Most existing negative sampling methods assume that non-existent triples with high scores are high-quality negative triples. However, negative triples sampled by these methods are likely to contain noise. Specifically, they ignore that non-existent triples with high scores might also be true facts due to the incompleteness of KGs, which are usually called false negative triples. To alleviate the above issue, we propose an easily pluggable denoising mixup method called DeMix, which generates high-quality triples by refining sampled negative triples in a self-supervised manner. Given a sampled unlabeled triple, DeMix firstly classifies it into a marginal pseudo-negative triple or a negative triple based on the judgment of the KGE model itself. Secondly, it selects an appropriate mixup partner for the current triple to synthesize a partially positive or a harder negative triple. Experimental results on the knowledge graph completion task show that the proposed DeMix is superior to other negative sampling techniques, ensuring corresponding KGEs a faster convergence and better link prediction results.
Knowledge graph (KG) embedding is a fundamental task in natural language processing, and various methods have been proposed to explore semantic patterns in distinctive ways. In this paper, we propose to learn an ensemble by leveraging existing methods in a relation-aware manner. However, exploring these semantics using relation-aware ensemble leads to a much larger search space than general ensemble methods. To address this issue, we propose a divide-search-combine algorithm RelEns-DSC that searches the relation-wise ensemble weights independently. This algorithm has the same computation cost as general ensemble methods but with much better performance. Experimental results on benchmark datasets demonstrate the effectiveness of the proposed method in efficiently searching relation-aware ensemble weights and achieving state-of-the-art embedding performance. The code is public at https://github.com/LARS-research/RelEns.
The design and development of text-based knowledge graph completion (KGC) methods leveraging textual entity descriptions are at the forefront of research. These methods involve advanced optimization techniques such as soft prompts and contrastive learning to enhance KGC models. The effectiveness of text-based methods largely hinges on the quality and richness of the training data. Large language models (LLMs) can utilize straightforward prompts to alter text data, thereby enabling data augmentation for KGC. Nevertheless, LLMs typically demand substantial computational resources. To address these issues, we introduce a framework termed constrained prompts for KGC (CP-KGC). This CP-KGC framework designs prompts that adapt to different datasets to enhance semantic richness. Additionally, CP-KGC employs a context constraint strategy to effectively identify polysemous entities within KGC datasets. Through extensive experimentation, we have verified the effectiveness of this framework. Even after quantization, the LLM (Qwen-7B-Chat-int4) still enhances the performance of text-based KGC methods \footnote{Code and datasets are available at \href{https://github.com/sjlmg/CP-KGC}{https://github.com/sjlmg/CP-KGC}}. This study extends the performance limits of existing models and promotes further integration of KGC with LLMs.
Multimodal movie genre classification has always been regarded as a demanding multi-label classification task due to the diversity of multimodal data such as posters, plot summaries, trailers and metadata. Although existing works have made great progress in modeling and combining each modality, they still face three issues: 1) unutilized group relations in metadata, 2) unreliable attention allocation, and 3) indiscriminative fused features. Given that the knowledge graph has been proven to contain rich information, we present a novel framework that exploits the knowledge graph from various perspectives to address the above problems. As a preparation, the metadata is processed into a domain knowledge graph. A translate model for knowledge graph embedding is adopted to capture the relations between entities. Firstly we retrieve the relevant embedding from the knowledge graph by utilizing group relations in metadata and then integrate it with other modalities. Next, we introduce an Attention Teacher module for reliable attention allocation based on self-supervised learning. It learns the distribution of the knowledge graph and produces rational attention weights. Finally, a Genre-Centroid Anchored Contrastive Learning module is proposed to strengthen the discriminative ability of fused features. The embedding space of anchors is initialized from the genre entities in the knowledge graph. To verify the effectiveness of our framework, we collect a larger and more challenging dataset named MM-IMDb 2.0 compared with the MM-IMDb dataset. The experimental results on two datasets demonstrate that our model is superior to the state-of-the-art methods. We will release the code in the near future.
We present the Multidimensional Hopfield Network (DHN), a natural generalisation of the Hopfield Network. In our theoretical investigations we focus on DHNs with a certain activation function and provide energy functions for them. We conclude that these DHNs are convergent in finite time, and are equivalent to greedy methods that aim to find graph clusterings of locally minimal cuts. We also show that the general framework of DHNs encapsulates several previously known algorithms used for generating graph embeddings and clusterings. Namely, the Cleora graph embedding algorithm, the Louvain method, and the Newmans method can be cast as DHNs with appropriate activation function and update rule. Motivated by these findings we provide a generalisation of Newmans method to the multidimensional case.
Developing text mining approaches to mine aspects from customer reviews has been well-studied due to its importance in understanding customer needs and product attributes. In contrast, it remains unclear how to predict the future emerging aspects of a new product that currently has little review information. This task, which we named product aspect forecasting, is critical for recommending new products, but also challenging because of the missing reviews. Here, we propose ForeSeer, a novel textual mining and product embedding approach progressively trained on temporal product graphs for this novel product aspect forecasting task. ForeSeer transfers reviews from similar products on a large product graph and exploits these reviews to predict aspects that might emerge in future reviews. A key novelty of our method is to jointly provide review, product, and aspect embeddings that are both time-sensitive and less affected by extremely imbalanced aspect frequencies. We evaluated ForeSeer on a real-world product review system containing 11,536,382 reviews and 11,000 products over 3 years. We observe that ForeSeer substantially outperformed existing approaches with at least 49.1\% AUPRC improvement under the real setting where aspect associations are not given. ForeSeer further improves future link prediction on the product graph and the review aspect association prediction. Collectively, Foreseer offers a novel framework for review forecasting by effectively integrating review text, product network, and temporal information, opening up new avenues for online shopping recommendation and e-commerce applications.
Ontology matching (OM) entails the identification of semantic relationships between concepts within two or more knowledge graphs (KGs) and serves as a critical step in integrating KGs from various sources. Recent advancements in deep OM models have harnessed the power of transformer-based language models and the advantages of knowledge graph embedding. Nevertheless, these OM models still face persistent challenges, such as a lack of reference alignments, runtime latency, and unexplored different graph structures within an end-to-end framework. In this study, we introduce a novel self-supervised learning OM framework with input ontologies, called LaKERMap. This framework capitalizes on the contextual and structural information of concepts by integrating implicit knowledge into transformers. Specifically, we aim to capture multiple structural contexts, encompassing both local and global interactions, by employing distinct training objectives. To assess our methods, we utilize the Bio-ML datasets and tasks. The findings from our innovative approach reveal that LaKERMap surpasses state-of-the-art systems in terms of alignment quality and inference time. Our models and codes are available here: https://github.com/ellenzhuwang/lakermap.
Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.
Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.
Subsampling is effective in Knowledge Graph Embedding (KGE) for reducing overfitting caused by the sparsity in Knowledge Graph (KG) datasets. However, current subsampling approaches consider only frequencies of queries that consist of entities and their relations. Thus, the existing subsampling potentially underestimates the appearance probabilities of infrequent queries even if the frequencies of their entities or relations are high. To address this problem, we propose Model-based Subsampling (MBS) and Mixed Subsampling (MIX) to estimate their appearance probabilities through predictions of KGE models. Evaluation results on datasets FB15k-237, WN18RR, and YAGO3-10 showed that our proposed subsampling methods actually improved the KG completion performances for popular KGE models, RotatE, TransE, HAKE, ComplEx, and DistMult.
Node2vec is a graph embedding method that learns a vector representation for each node of a weighted graph while seeking to preserve relative proximity and global structure. Numerical experiments suggest Node2vec struggles to recreate the topology of the input graph. To resolve this we introduce a topological loss term to be added to the training loss of Node2vec which tries to align the persistence diagram (PD) of the resulting embedding as closely as possible to that of the input graph. Following results in computational optimal transport, we carefully adapt entropic regularization to PD metrics, allowing us to measure the discrepancy between PDs in a differentiable way. Our modified loss function can then be minimized through gradient descent to reconstruct both the geometry and the topology of the input graph. We showcase the benefits of this approach using demonstrative synthetic examples.
Graph embedding has become an increasingly important technique for analyzing graph-structured data. By representing nodes in a graph as vectors in a low-dimensional space, graph embedding enables efficient graph processing and analysis tasks like node classification, link prediction, and visualization. In this paper, we propose a novel force-directed graph embedding method that utilizes the steady acceleration kinetic formula to embed nodes in a way that preserves graph topology and structural features. Our method simulates a set of customized attractive and repulsive forces between all node pairs with respect to their hop distance. These forces are then used in Newton's second law to obtain the acceleration of each node. The method is intuitive, parallelizable, and highly scalable. We evaluate our method on several graph analysis tasks and show that it achieves competitive performance compared to state-of-the-art unsupervised embedding techniques.
Link prediction is a key aspect of graph machine learning, with applications as diverse as disease prediction, social network recommendations, and drug discovery. It involves predicting new links that may form between network nodes. Despite the clear importance of link prediction, existing models have significant shortcomings. Graph Convolutional Networks, for instance, have been proven to be highly efficient for link prediction on a variety of datasets. However, they encounter severe limitations when applied to short-path networks and ego networks, resulting in poor performance. This presents a critical problem space that this work aims to address. In this paper, we present the Node Centrality and Similarity Based Parameterised Model (NCSM), a novel method for link prediction tasks. NCSM uniquely integrates node centrality and similarity measures as edge features in a customised Graph Neural Network (GNN) layer, effectively leveraging the topological information of large networks. This model represents the first parameterised GNN-based link prediction model that considers topological information. The proposed model was evaluated on five benchmark graph datasets, each comprising thousands of nodes and edges. Experimental results highlight NCSM's superiority over existing state-of-the-art models like Graph Convolutional Networks and Variational Graph Autoencoder, as it outperforms them across various metrics and datasets. This exceptional performance can be attributed to NCSM's innovative integration of node centrality, similarity measures, and its efficient use of topological information.
Knowledge graph (KG) embedding has been used to benefit the diagnosis of animal diseases by analyzing electronic medical records (EMRs), such as notes and veterinary records. However, learning representations to capture entities and relations with literal information in KGs is challenging as the KGs show heterogeneous properties and various types of literal information. Meanwhile, the existing methods mostly aim to preserve graph structures surrounding target nodes without considering different types of literals, which could also carry significant information. In this paper, we propose a knowledge graph embedding model for the efficient diagnosis of animal diseases, which could learn various types of literal information and graph structure and fuse them into unified representations, namely LiteralKG. Specifically, we construct a knowledge graph that is built from EMRs along with literal information collected from various animal hospitals. We then fuse different types of entities and node feature information into unified vector representations through gate networks. Finally, we propose a self-supervised learning task to learn graph structure in pretext tasks and then towards various downstream tasks. Experimental results on link prediction tasks demonstrate that our model outperforms the baselines that consist of state-of-the-art models. The source code is available at https://github.com/NSLab-CUK/LiteralKG.
The way we analyse clinical texts has undergone major changes over the last years. The introduction of language models such as BERT led to adaptations for the (bio)medical domain like PubMedBERT and ClinicalBERT. These models rely on large databases of archived medical documents. While performing well in terms of accuracy, both the lack of interpretability and limitations to transfer across languages limit their use in clinical setting. We introduce a novel light-weight graph-based embedding method specifically catering radiology reports. It takes into account the structure and composition of the report, while also connecting medical terms in the report through the multi-lingual SNOMED Clinical Terms knowledge base. The resulting graph embedding uncovers the underlying relationships among clinical terms, achieving a representation that is better understandable for clinicians and clinically more accurate, without reliance on large pre-training datasets. We show the use of this embedding on two tasks namely disease classification of X-ray reports and image classification. For disease classification our model is competitive with its BERT-based counterparts, while being magnitudes smaller in size and training data requirements. For image classification, we show the effectiveness of the graph embedding leveraging cross-modal knowledge transfer and show how this method is usable across different languages.