Graph representation learning is a fast-growing field where one of the main objectives is to generate meaningful representations of graphs in lower-dimensional spaces. The learned embeddings have been successfully applied to perform various prediction tasks, such as link prediction, node classification, clustering, and visualization. The collective effort of the graph learning community has delivered hundreds of methods, but no single method excels under all evaluation metrics such as prediction accuracy, running time, scalability, etc. This survey aims to evaluate all major classes of graph embedding methods by considering algorithmic variations, parameter selections, scalability, hardware and software platforms, downstream ML tasks, and diverse datasets. We organized graph embedding techniques using a taxonomy that includes methods from manual feature engineering, matrix factorization, shallow neural networks, and deep graph convolutional networks. We evaluated these classes of algorithms for node classification, link prediction, clustering, and visualization tasks using widely used benchmark graphs. We designed our experiments on top of PyTorch Geometric and DGL libraries and run experiments on different multicore CPU and GPU platforms. We rigorously scrutinize the performance of embedding methods under various performance metrics and summarize the results. Thus, this paper may serve as a comparative guide to help users select methods that are most suitable for their tasks.
Knowledge graph embedding (KGE) has shown great potential in automatic knowledge graph (KG) completion and knowledge-driven tasks. However, recent KGE models suffer from high training cost and large storage space, thus limiting their practicality in real-world applications. To address this challenge, based on the latest findings in the field of Contrastive Learning, we propose a novel KGE training framework called Hardness-aware Low-dimensional Embedding (HaLE). Instead of the traditional Negative Sampling, we design a new loss function based on query sampling that can balance two important training targets, Alignment and Uniformity. Furthermore, we analyze the hardness-aware ability of recent low-dimensional hyperbolic models and propose a lightweight hardness-aware activation mechanism. The experimental results show that in the limited training time, HaLE can effectively improve the performance and training speed of KGE models on five commonly-used datasets. After training just a few minutes, the HaLE-trained models are competitive compared to the state-of-the-art models in both low- and high-dimensional conditions.
We propose a novel software service recommendation model to help users find their suitable repositories in GitHub. Our model first designs a novel context-induced repository graph embedding method to leverage rich contextual information of repositories to alleviate the difficulties caused by the data sparsity issue. It then leverages sequence information of user-repository interactions for the first time in the software service recommendation field. Specifically, a deep-learning based sequential recommendation technique is adopted to capture the dynamics of user preferences. Comprehensive experiments have been conducted on a large dataset collected from GitHub against a list of existing methods. The results illustrate the superiority of our method in various aspects.
Unsupervised graph-level representation learning plays a crucial role in a variety of tasks such as molecular property prediction and community analysis, especially when data annotation is expensive. Currently, most of the best-performing graph embedding methods are based on Infomax principle. The performance of these methods highly depends on the selection of negative samples and hurt the performance, if the samples were not carefully selected. Inter-graph similarity-based methods also suffer if the selected set of graphs for similarity matching is low in quality. To address this, we focus only on utilizing the current input graph for embedding learning. We are motivated by an observation from real-world graph generation processes where the graphs are formed based on one or more global factors which are common to all elements of the graph (e.g., topic of a discussion thread, solubility level of a molecule). We hypothesize extracting these common factors could be highly beneficial. Hence, this work proposes a new principle for unsupervised graph representation learning: Graph-wise Common latent Factor EXtraction (GCFX). We further propose a deep model for GCFX, deepGCFX, based on the idea of reversing the above-mentioned graph generation process which could explicitly extract common latent factors from an input graph and achieve improved results on downstream tasks to the current state-of-the-art. Through extensive experiments and analysis, we demonstrate that, while extracting common latent factors is beneficial for graph-level tasks to alleviate distractions caused by local variations of individual nodes or local neighbourhoods, it also benefits node-level tasks by enabling long-range node dependencies, especially for disassortative graphs.
Knowledge Graphs (KGs), representing facts as triples, have been widely adopted in many applications. Reasoning tasks such as link prediction and rule induction are important for the development of KGs. Knowledge Graph Embeddings (KGEs) embedding entities and relations of a KG into continuous vector spaces, have been proposed for these reasoning tasks and proven to be efficient and robust. But the plausibility and feasibility of applying and deploying KGEs in real-work applications has not been well-explored. In this paper, we discuss and report our experiences of deploying KGEs in a real domain application: e-commerce. We first identity three important desiderata for e-commerce KG systems: 1) attentive reasoning, reasoning over a few target relations of more concerns instead of all; 2) explanation, providing explanations for a prediction to help both users and business operators understand why the prediction is made; 3) transferable rules, generating reusable rules to accelerate the deployment of a KG to new systems. While non existing KGE could meet all these desiderata, we propose a novel one, an explainable knowledge graph attention network that make prediction through modeling correlations between triples rather than purely relying on its head entity, relation and tail entity embeddings. It could automatically selects attentive triples for prediction and records the contribution of them at the same time, from which explanations could be easily provided and transferable rules could be efficiently produced. We empirically show that our method is capable of meeting all three desiderata in our e-commerce application and outperform typical baselines on datasets from real domain applications.
Here we study the semantic search and retrieval problem in biomedical digital libraries. First, we introduce MedGraph, a knowledge graph embedding-based method that provides semantic relevance retrieval and ranking for the biomedical literature indexed in PubMed. Second, we evaluate our method using PubMed's Best Match algorithm. Moreover, we compare our method MedGraph to a traditional TFIDF based algorithm. We use a dataset extracted from PubMed, including 30 million articles' metadata such as abstracts, author information, citation information, and extracted biological entity mentions. We do that by pulling a subset of the dataset to evaluate MedGraph using predefined queries with ground truth ranked results. To our knowledge, this technique has not been explored before in biomedical information retrieval. In addition, our results provide evidence that semantic approaches to search and relevance in biomedical digital libraries that rely on knowledge graph modeling offer better search relevance results when compared with traditional approaches in terms of objective metrics.
Many real-world graphs (networks) are heterogeneous with different types of nodes and edges. Heterogeneous graph embedding, aiming at learning the low-dimensional node representations of a heterogeneous graph, is vital for various downstream applications. Many meta-path based embedding methods have been proposed to learn the semantic information of heterogeneous graphs in recent years. However, most of the existing techniques overlook the graph structure information when learning the heterogeneous graph embeddings. This paper proposes a novel Structure-Aware Heterogeneous Graph Neural Network (SHGNN) to address the above limitations. In detail, we first utilize a feature propagation module to capture the local structure information of intermediate nodes in the meta-path. Next, we use a tree-attention aggregator to incorporate the graph structure information into the aggregation module on the meta-path. Finally, we leverage a meta-path aggregator to fuse the information aggregated from different meta-paths. We conducted experiments on node classification and clustering tasks and achieved state-of-the-art results on the benchmark datasets, which shows the effectiveness of our proposed method.
Adoption of recently developed methods from machine learning has given rise to creation of drug-discovery knowledge graphs (KG) that utilize the interconnected nature of the domain. Graph-based modelling of the data, combined with KG embedding (KGE) methods, are promising as they provide a more intuitive representation and are suitable for inference tasks such as predicting missing links. One common application is to produce ranked lists of genes for a given disease, where the rank is based on the perceived likelihood of association between the gene and the disease. It is thus critical that these predictions are not only pertinent but also biologically meaningful. However, KGs can be biased either directly due to the underlying data sources that are integrated or due to modeling choices in the construction of the graph, one consequence of which is that certain entities can get topologically overrepresented. We demonstrate the effect of these inherent structural imbalances, resulting in densely-connected entities being highly ranked no matter the context. We provide support for this observation across different datasets, models as well as predictive tasks. Further, we present various graph perturbation experiments which yield more support to the observation that KGE models can be more influenced by the frequency of entities rather than any biological information encoded within the relations. Our results highlight the importance of data modeling choices, and emphasizes the need for practitioners to be mindful of these issues when interpreting model outputs and during KG composition.
Learning the embeddings of knowledge graphs (KG) is vital in artificial intelligence, and can benefit various downstream applications, such as recommendation and question answering. In recent years, many research efforts have been proposed for knowledge graph embedding (KGE). However, most previous KGE methods ignore the semantic similarity between the related entities and entity-relation couples in different triples since they separately optimize each triple with the scoring function. To address this problem, we propose a simple yet efficient contrastive learning framework for tensor decomposition based (TDB) KGE, which can shorten the semantic distance of the related entities and entity-relation couples in different triples and thus improve the performance of KGE. We evaluate our proposed method on three standard KGE datasets: WN18RR, FB15k-237 and YAGO3-10. Our method can yield some new state-of-the-art results, achieving 51.2% MRR, 46.8% Hits@1 on the WN18RR dataset, 37.8% MRR, 28.6% Hits@1 on FB15k-237 dataset, and 59.1% MRR, 51.8% Hits@1 on the YAGO3-10 dataset.
We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on this prediction task. We show that using knowledge graph embeddings can increase the accuracy of effect prediction with neural networks. Furthermore, we have implemented a fine-tuning architecture that adapts the knowledge graph embeddings to the effect prediction task and leads to better performance. Finally, we evaluate certain characteristics of the knowledge graph embedding models to shed light on the individual model performance.
Graph embedding is a transformation of nodes of a network into a set of vectors. A good embedding should capture the underlying graph topology and structure, node-to-node relationship, and other relevant information about the graph, its subgraphs, and nodes themselves. If these objectives are achieved, an embedding is a meaningful, understandable, and often compressed representation of a network. Unfortunately, selecting the best embedding is a challenging task and very often requires domain experts. In this paper, we extend the framework for evaluating graph embeddings that was recently introduced by the authors. Now, the framework assigns two scores, local and global, to each embedding that measure the quality of an evaluated embedding for tasks that require good representation of local and, respectively, global properties of the network. The best embedding, if needed, can be selected in an unsupervised way, or the framework can identify a few embeddings that are worth further investigation. The framework is flexible, scalable, and can deal with undirected/directed, weighted/unweighted graphs.
Object encoding and identification are vital for robotic tasks such as autonomous exploration, semantic scene understanding, and re-localization. Previous approaches have attempted to either track objects or generate descriptors for object identification. However, such systems are limited to a "fixed" partial object representation from a single viewpoint. In a robot exploration setup, there is a requirement for a temporally "evolving" global object representation built as the robot observes the object from multiple viewpoints. Furthermore, given the vast distribution of unknown novel objects in the real world, the object identification process must be class-agnostic. In this context, we propose a novel temporal 3D object encoding approach, dubbed AirObject, to obtain global keypoint graph-based embeddings of objects. Specifically, the global 3D object embeddings are generated using a temporal convolutional network across structural information of multiple frames obtained from a graph attention-based encoding method. We demonstrate that AirObject achieves the state-of-the-art performance for video object identification and is robust to severe occlusion, perceptual aliasing, viewpoint shift, deformation, and scale transform, outperforming the state-of-the-art single-frame and sequential descriptors. To the best of our knowledge, AirObject is one of the first temporal object encoding methods. Source code is available at https://github.com/Nik-V9/AirObject.
Learning the manifold structure of remote sensing images is of paramount relevance for modeling and understanding processes, as well as to encapsulate the high dimensionality in a reduced set of informative features for subsequent classification, regression, or unmixing. Manifold learning methods have shown excellent performance to deal with hyperspectral image (HSI) analysis but, unless specifically designed, they cannot provide an explicit embedding map readily applicable to out-of-sample data. A common assumption to deal with the problem is that the transformation between the high-dimensional input space and the (typically low) latent space is linear. This is a particularly strong assumption, especially when dealing with hyperspectral images due to the well-known nonlinear nature of the data. To address this problem, a manifold learning method based on High Dimensional Model Representation (HDMR) is proposed, which enables to present a nonlinear embedding function to project out-of-sample samples into the latent space. The proposed method is compared to manifold learning methods along with its linear counterparts and achieves promising performance in terms of classification accuracy of a representative set of hyperspectral images.
Knowledge graphs (KGs) on COVID-19 have been constructed to accelerate the research process of COVID-19. However, KGs are always incomplete, especially the new constructed COVID-19 KGs. Link prediction task aims to predict missing entities for (e, r, t) or (h, r, e), where h and t are certain entities, e is an entity that needs to be predicted and r is a relation. This task also has the potential to solve COVID-19 related KGs' incomplete problem. Although various knowledge graph embedding (KGE) approaches have been proposed to the link prediction task, these existing methods suffer from the limitation of using a single scoring function, which fails to capture rich features of COVID-19 KGs. In this work, we propose the MDistMult model that leverages multiple scoring functions to extract more features from existing triples. We employ experiments on the CCKS2020 COVID-19 Antiviral Drugs Knowledge Graph (CADKG). The experimental results demonstrate that our MDistMult achieves state-of-the-art performance in link prediction task on the CADKG dataset
Increased attention has been paid over the last four years to dynamic network embedding. Existing dynamic embedding methods, however, consider the problem as limited to the evolution of a topology over a sequence of global, discrete states. We propose a novel embedding algorithm, WalkingTime, based on a fundamentally different handling of time, allowing for the local consideration of continuously occurring phenomena; while others consider global time-steps to be first-order citizens of the dynamic environment, we hold flows comprised of temporally and topologically local interactions as our primitives, without any discretization or alignment of time-related attributes being necessary. Keywords: dynamic networks , representation learning , dynamic graph embedding , time-respecting paths , temporal-topological flows , temporal random walks , temporal networks , real-attributed knowledge graphs , streaming graphs , online networks , asynchronous graphs , asynchronous networks , graph algorithms , deep learning , network analysis , datamining , network science
Steiner Tree Problem (STP) in graphs aims to find a tree of minimum weight in the graph that connects a given set of vertices. It is a classic NP-hard combinatorial optimization problem and has many real-world applications (e.g., VLSI chip design, transportation network planning and wireless sensor networks). Many exact and approximate algorithms have been developed for STP, but they suffer from high computational complexity and weak worst-case solution guarantees, respectively. Heuristic algorithms are also developed. However, each of them requires application domain knowledge to design and is only suitable for specific scenarios. Motivated by the recently reported observation that instances of the same NP-hard combinatorial problem may maintain the same or similar combinatorial structure but mainly differ in their data, we investigate the feasibility and benefits of applying machine learning techniques to solving STP. To this end, we design a novel model Vulcan based on novel graph neural networks and deep reinforcement learning. The core of Vulcan is a novel, compact graph embedding that transforms highdimensional graph structure data (i.e., path-changed information) into a low-dimensional vector representation. Given an STP instance, Vulcan uses this embedding to encode its pathrelated information and sends the encoded graph to a deep reinforcement learning component based on a double deep Q network (DDQN) to find solutions. In addition to STP, Vulcan can also find solutions to a wide range of NP-hard problems (e.g., SAT, MVC and X3C) by reducing them to STP. We implement a prototype of Vulcan and demonstrate its efficacy and efficiency with extensive experiments using real-world and synthetic datasets.
We study the problem of generating data poisoning attacks against Knowledge Graph Embedding (KGE) models for the task of link prediction in knowledge graphs. To poison KGE models, we propose to exploit their inductive abilities which are captured through the relationship patterns like symmetry, inversion and composition in the knowledge graph. Specifically, to degrade the model's prediction confidence on target facts, we propose to improve the model's prediction confidence on a set of decoy facts. Thus, we craft adversarial additions that can improve the model's prediction confidence on decoy facts through different inference patterns. Our experiments demonstrate that the proposed poisoning attacks outperform state-of-art baselines on four KGE models for two publicly available datasets. We also find that the symmetry pattern based attacks generalize across all model-dataset combinations which indicates the sensitivity of KGE models to this pattern.
In autonomous vehicles (AVs), early warning systems rely on collision prediction to ensure occupant safety. However, state-of-the-art methods using deep convolutional networks either fail at modeling collisions or are too expensive/slow, making them less suitable for deployment on AV edge hardware. To address these limitations, we propose sg2vec, a spatio-temporal scene-graph embedding methodology that uses Graph Neural Network (GNN) and Long Short-Term Memory (LSTM) layers to predict future collisions via visual scene perception. We demonstrate that sg2vec predicts collisions 8.11% more accurately and 39.07% earlier than the state-of-the-art method on synthesized datasets, and 29.47% more accurately on a challenging real-world collision dataset. We also show that sg2vec is better than the state-of-the-art at transferring knowledge from synthetic datasets to real-world driving datasets. Finally, we demonstrate that sg2vec performs inference 9.3x faster with an 88.0% smaller model, 32.4% less power, and 92.8% less energy than the state-of-the-art method on the industry-standard Nvidia DRIVE PX 2 platform, making it more suitable for implementation on the edge.
Nowadays, Knowledge graphs (KGs) have been playing a pivotal role in AI-related applications. Despite the large sizes, existing KGs are far from complete and comprehensive. In order to continuously enrich KGs, automatic knowledge construction and update mechanisms are usually utilized, which inevitably bring in plenty of noise. However, most existing knowledge graph embedding (KGE) methods assume that all the triple facts in KGs are correct, and project both entities and relations into a low-dimensional space without considering noise and knowledge conflicts. This will lead to low-quality and unreliable representations of KGs. To this end, in this paper, we propose a general multi-task reinforcement learning framework, which can greatly alleviate the noisy data problem. In our framework, we exploit reinforcement learning for choosing high-quality knowledge triples while filtering out the noisy ones. Also, in order to take full advantage of the correlations among semantically similar relations, the triple selection processes of similar relations are trained in a collective way with multi-task learning. Moreover, we extend popular KGE models TransE, DistMult, ConvE and RotatE with the proposed framework. Finally, the experimental validation shows that our approach is able to enhance existing KGE models and can provide more robust representations of KGs in noisy scenarios.
Presently with technology node scaling, an accurate prediction model at early design stages can significantly reduce the design cycle. Especially during logic synthesis, predicting cell congestion due to improper logic combination can reduce the burden of subsequent physical implementations. There have been attempts using Graph Neural Network (GNN) techniques to tackle congestion prediction during the logic synthesis stage. However, they require informative cell features to achieve reasonable performance since the core idea of GNNs is built on the message passing framework, which would be impractical at the early logic synthesis stage. To address this limitation, we propose a framework that can directly learn embeddings for the given netlist to enhance the quality of our node features. Popular random-walk based embedding methods such as Node2vec, LINE, and DeepWalk suffer from the issue of cross-graph alignment and poor generalization to unseen netlist graphs, yielding inferior performance and costing significant runtime. In our framework, we introduce a superior alternative to obtain node embeddings that can generalize across netlist graphs using matrix factorization methods. We propose an efficient mini-batch training method at the sub-graph level that can guarantee parallel training and satisfy the memory restriction for large-scale netlists. We present results utilizing open-source EDA tools such as DREAMPLACE and OPENROAD frameworks on a variety of openly available circuits. By combining the learned embedding on top of the netlist with the GNNs, our method improves prediction performance, generalizes to new circuit lines, and is efficient in training, potentially saving over $90 \%$ of runtime.