Predicting commuting flows based on infrastructure and land-use information is critical for urban planning and public policy development. However, it is a challenging task given the complex patterns of commuting flows. Conventional models, such as gravity model, are mainly derived from physics principles and limited by their predictive power in real-world scenarios where many factors need to be considered. Meanwhile, most existing machine learning-based methods ignore the spatial correlations and fail to model the influence of nearby regions. To address these issues, we propose Geo-contextual Multitask Embedding Learner (GMEL), a model that captures the spatial correlations from geographic contextual information for commuting flow prediction. Specifically, we first construct a geo-adjacency network containing the geographic contextual information. Then, an attention mechanism is proposed based on the framework of graph attention network (GAT) to capture the spatial correlations and encode geographic contextual information to embedding space. Two separate GATs are used to model supply and demand characteristics. A multitask learning framework is used to introduce stronger restrictions and enhance the effectiveness of the embedding representation. Finally, a gradient boosting machine is trained based on the learned embeddings to predict commuting flows. We evaluate our model using real-world datasets from New York City and the experimental results demonstrate the effectiveness of our proposal against the state of the art.
Human-curated knowledge graphs provide critical supportive information to various natural language processing tasks, but these graphs are usually incomplete, urging auto-completion of them. Prevalent graph embedding approaches, e.g., TransE, learn structured knowledge via representing graph elements into dense embeddings and capturing their triple-level relationship with spatial distance. However, they are hardly generalizable to the elements never visited in training and are intrinsically vulnerable to graph incompleteness. In contrast, textual encoding approaches, e.g., KG-BERT, resort to graph triple's text and triple-level contextualized representations. They are generalizable enough and robust to the incompleteness, especially when coupled with pre-trained encoders. But two major drawbacks limit the performance: (1) high overheads due to the costly scoring of all possible triples in inference, and (2) a lack of structured knowledge in the textual encoder. In this paper, we follow the textual encoding paradigm and aim to alleviate its drawbacks by augmenting it with graph embedding techniques -- a complementary hybrid of both paradigms. Specifically, we partition each triple into two asymmetric parts as in translation-based graph embedding approach, and encode both parts into contextualized representations by a Siamese-style textual encoder. Built upon the representations, our model employs both deterministic classifier and spatial measurement for representation and structure learning respectively. Moreover, we develop a self-adaptive ensemble scheme to further improve the performance by incorporating triple scores from an existing graph embedding model. In experiments, we achieve state-of-the-art performance on three benchmarks and a zero-shot dataset for link prediction, with highlights of inference costs reduced by 1-2 orders of magnitude compared to a textual encoding method.
Domain Adaptation is the process of alleviating distribution gaps between data from different domains. In this paper, we show that Domain Adaptation methods using pair-wise relationships between source and target domain data can be formulated as a Graph Embedding in which the domain labels are incorporated into the structure of the intrinsic and penalty graphs. Specifically, we analyse the loss functions of three existing state-of-the-art Supervised Domain Adaptation methods and demonstrate that they perform Graph Embedding. Moreover, we highlight some generalisation and reproducibility issues related to the experimental setup commonly used to demonstrate the few-shot learning capabilities of these methods. To assess and compare Supervised Domain Adaptation methods accurately, we propose a rectified evaluation protocol, and report updated benchmarks on the standard datasets Office31 (Amazon, DSLR, and Webcam), Digits (MNIST, USPS, SVHN, and MNIST-M) and VisDA (Synthetic, Real).
Hyperspectral image (HSI) clustering is a challenging task due to the high complexity of HSI data. Subspace clustering has been proven to be powerful for exploiting the intrinsic relationship between data points. Despite the impressive performance in the HSI clustering, traditional subspace clustering methods often ignore the inherent structural information among data. In this paper, we revisit the subspace clustering with graph convolution and present a novel subspace clustering framework called Graph Convolutional Subspace Clustering (GCSC) for robust HSI clustering. Specifically, the framework recasts the self-expressiveness property of the data into the non-Euclidean domain, which results in a more robust graph embedding dictionary. We show that traditional subspace clustering models are the special forms of our framework with the Euclidean data. Basing on the framework, we further propose two novel subspace clustering models by using the Frobenius norm, namely Efficient GCSC (EGCSC) and Efficient Kernel GCSC (EKGCSC). Both models have a globally optimal closed-form solution, which makes them easier to implement, train, and apply in practice. Extensive experiments on three popular HSI datasets demonstrate that EGCSC and EKGCSC can achieve state-of-the-art clustering performance and dramatically outperforms many existing methods with significant margins.
The task of link prediction for knowledge graphs is to predict missing relationships between entities. Knowledge graph embedding, which aims to represent entities and relations of a knowledge graph as low dimensional vectors in a continuous vector space, has achieved promising predictive performance. If an embedding model can cover different types of connectivity patterns and mapping properties of relations as many as possible, it will potentially bring more benefits for link prediction tasks. In this paper, we propose a novel embedding model, namely LineaRE, which is capable of modeling four connectivity patterns (i.e., symmetry, antisymmetry, inversion, and composition) and four mapping properties (i.e., one-to-one, one-to-many, many-to-one, and many-to-many) of relations. Specifically, we regard knowledge graph embedding as a simple linear regression task, where a relation is modeled as a linear function of two low-dimensional vector-presented entities with two weight vectors and a bias vector. Since the vectors are defined in a real number space and the scoring function of the model is linear, our model is simple and scalable to large knowledge graphs. Experimental results on multiple widely used real-world datasets show that the proposed LineaRE model significantly outperforms existing state-of-the-art models for link prediction tasks.
Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous chemical space and unclear design principles for small-molecule combinations, the computational drug-combination design has not seen generative models to meet its potential to accelerate resistance-overcoming drug combination discovery. We have developed the first deep generative model for drug combination design, by jointly embedding graph-structured domain knowledge and iteratively training a reinforcement learning-based chemical graph-set designer. First, we have developed Hierarchical Variational Graph Auto-Encoders (HVGAE) trained end-to-end to jointly embed gene-gene, gene-disease, and disease-disease networks. Novel attentional pooling is introduced here for learning disease-representations from associated genes' representations. Second, targeting diseases in learned representations, we have recast the drug-combination design problem as graph-set generation and developed a deep learning-based model with novel rewards. Specifically, besides chemical validity rewards, we have introduced a novel generative adversarial award, being generalized sliced Wasserstein, for chemically diverse molecules with distributions similar to known drugs. We have also designed a network principle-based reward for drug combinations. Numerical results indicate that, compared to graph embedding methods, HVGAE learns more informative and generalizable disease representations. Case studies on four diseases show that network-principled drug combinations tend to have low toxicity. The generated drug combinations collectively cover the disease module similar to FDA-approved drug combinations and could potentially suggest novel systems-pharmacology strategies.
Much progress has been made recently on text classification with methods based on neural networks. In particular, models using attention mechanism such as BERT have shown to have the capability of capturing the contextual information within a sentence or document. However, their ability of capturing the global information about the vocabulary of a language is more limited. This latter is the strength of Graph Convolutional Networks (GCN). In this paper, we propose VGCN-BERT model which combines the capability of BERT with a Vocabulary Graph Convolutional Network (VGCN). Local information and global information interact through different layers of BERT, allowing them to influence mutually and to build together a final representation for classification. In our experiments on several text classification datasets, our approach outperforms BERT and GCN alone, and achieve higher effectiveness than that reported in previous studies.
Graph representation learning is a fundamental task in various applications that strives to learn low-dimensional embeddings for nodes that can preserve graph topology information. However, many existing methods focus on static graphs while ignoring evolving graph patterns. Inspired by the success of graph convolutional networks(GCNs) in static graph embedding, we propose a novel k-core based temporal graph convolutional network, the CTGCN, to learn node representations for dynamic graphs. In contrast to previous dynamic graph embedding methods, CTGCN can preserve both local connective proximity and global structural similarity while simultaneously capturing graph dynamics. In the proposed framework, the traditional graph convolution is generalized into two phases, feature transformation and feature aggregation, which gives the CTGCN more flexibility and enables the CTGCN to learn connective and structural information under the same framework. Experimental results on 7 real-world graphs demonstrate that the CTGCN outperforms existing state-of-the-art graph embedding methods in several tasks, including link prediction and structural role classification. The source code of this work can be obtained from \url{https://github.com/jhljx/CTGCN}.
We present Karate Club a Python framework combining more than 30 state-of-the-art graph mining algorithms which can solve unsupervised machine learning tasks. The primary goal of the package is to make community detection, node and whole graph embedding available to a wide audience of machine learning researchers and practitioners. We designed Karate Club with an emphasis on a consistent application interface, scalability, ease of use, sensible out of the box model behaviour, standardized dataset ingestion, and output generation. This paper discusses the design principles behind this framework with practical examples. We show Karate Club's efficiency with respect to learning performance on a wide range of real world clustering problems, classification tasks and support evidence with regards to its competitive speed.
Getting deep convolutional neural networks to perform well requires a large amount of training data. When the available labelled data is small, it is often beneficial to use transfer learning to leverage a related larger dataset (source) in order to improve the performance on the small dataset (target). Among the transfer learning approaches, domain adaptation methods assume that distributions between the two domains are shifted and attempt to realign them. In this paper, we consider the domain adaptation problem from the perspective of dimensionality reduction and propose a generic framework based on graph embedding. Instead of solving the generalised eigenvalue problem, we formulate the graph-preserving criterion as a loss in the neural network and learn a domain-invariant feature transformation in an end-to-end fashion. We show that the proposed approach leads to a powerful Domain Adaptation framework; a simple LDA-inspired instantiation of the framework leads to state-of-the-art performance on two of the most widely used Domain Adaptation benchmarks, Office31 and MNIST to USPS datasets.
Graph-based clustering plays an important role in the clustering area. Recent studies about graph convolution neural networks have achieved impressive success on graph type data. However, in general clustering tasks, the graph structure of data does not exist such that the strategy to construct a graph is crucial for performance. Therefore, how to extend graph convolution networks into general clustering tasks is an attractive problem. In this paper, we propose a graph auto-encoder for general data clustering, which constructs the graph adaptively according to the generative perspective of graphs. The adaptive process is designed to induce the model to exploit the high-level information behind data and utilize the non-Euclidean structure sufficiently. We further design a novel mechanism with rigorous analysis to avoid the collapse caused by the adaptive construction. Via combining the generative model for network embedding and graph-based clustering, a graph auto-encoder with a novel decoder is developed such that it performs well in weighted graph used scenarios. Extensive experiments prove the superiority of our model.
Inductive representation learning on temporal graphs is an important step toward salable machine learning on real-world dynamic networks. The evolving nature of temporal dynamic graphs requires handling new nodes as well as capturing temporal patterns. The node embeddings, which are now functions of time, should represent both the static node features and the evolving topological structures. Moreover, node and topological features can be temporal as well, whose patterns the node embeddings should also capture. We propose the temporal graph attention (TGAT) layer to efficiently aggregate temporal-topological neighborhood features as well as to learn the time-feature interactions. For TGAT, we use the self-attention mechanism as building block and develop a novel functional time encoding technique based on the classical Bochner's theorem from harmonic analysis. By stacking TGAT layers, the network recognizes the node embeddings as functions of time and is able to inductively infer embeddings for both new and observed nodes as the graph evolves. The proposed approach handles both node classification and link prediction task, and can be naturally extended to include the temporal edge features. We evaluate our method with transductive and inductive tasks under temporal settings with two benchmark and one industrial dataset. Our TGAT model compares favorably to state-of-the-art baselines as well as the previous temporal graph embedding approaches.
Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.
Knowledge Graphs (KGs) have found many applications in industry and academic settings, which in turn, have motivated considerable research efforts towards large-scale information extraction from a variety of sources. Despite such efforts, it is well known that even state-of-the-art KGs suffer from incompleteness. Link Prediction (LP), the task of predicting missing facts among entities already a KG, is a promising and widely studied task aimed at addressing KG incompleteness. Among the recent LP techniques, those based on KG embeddings have achieved very promising performances in some benchmarks. Despite the fast growing literature in the subject, insufficient attention has been paid to the effect of the various design choices in those methods. Moreover, the standard practice in this area is to report accuracy by aggregating over a large number of test facts in which some entities are over-represented; this allows LP methods to exhibit good performance by just attending to structural properties that include such entities, while ignoring the remaining majority of the KG. This analysis provides a comprehensive comparison of embedding-based LP methods, extending the dimensions of analysis beyond what is commonly available in the literature. We experimentally compare effectiveness and efficiency of 16 state-of-the-art methods, consider a rule-based baseline, and report detailed analysis over the most popular benchmarks in the literature.
Graph embedding algorithms are used to efficiently represent (encode) a graph in a low-dimensional continuous vector space that preserves the most important properties of the graph. One aspect that is often overlooked is whether the graph is directed or not. Most studies ignore the directionality, so as to learn high-quality representations optimized for node classification. On the other hand, studies that capture directionality are usually effective on link prediction but do not perform well on other tasks. This preliminary study presents a novel text-enriched, direction-aware algorithm called DIAGRAM , based on a carefully designed multi-objective model to learn embeddings that preserve the direction of edges, textual features and graph context of nodes. As a result, our algorithm does not have to trade one property for another and jointly learns high-quality representations for multiple network analysis tasks. We empirically show that DIAGRAM significantly outperforms six state-of-the-art baselines, both direction-aware and oblivious ones,on link prediction and network reconstruction experiments using two popular datasets. It also achieves a comparable performance on node classification experiments against these baselines using the same datasets.
There is an emerging trend of embedding knowledge graphs (KGs) in continuous vector spaces in order to use those for machine learning tasks. Recently, many knowledge graph embedding (KGE) models have been proposed that learn low dimensional representations while trying to maintain the structural properties of the KGs such as the similarity of nodes depending on their edges to other nodes. KGEs can be used to address tasks within KGs such as the prediction of novel links and the disambiguation of entities. They can also be used for downstream tasks like question answering and fact-checking. Overall, these tasks are relevant for the semantic web community. Despite their popularity, the reproducibility of KGE experiments and the transferability of proposed KGE models to research fields outside the machine learning community can be a major challenge. Therefore, we present the KEEN Universe, an ecosystem for knowledge graph embeddings that we have developed with a strong focus on reproducibility and transferability. The KEEN Universe currently consists of the Python packages PyKEEN (Python KnowlEdge EmbeddiNgs), BioKEEN (Biological KnowlEdge EmbeddiNgs), and the KEEN Model Zoo for sharing trained KGE models with the community.
A collaborative network is a social network that is comprised of experts who cooperate with each other to fulfill a special goal. Analyzing this network yields meaningful information about the expertise of these experts and their subject areas. To perform the analysis, graph embedding techniques have emerged as an effective and promising tool. Graph embedding attempts to represent graph nodes as low-dimensional vectors. In this paper, we propose a graph embedding method, called ExEm, that uses dominating-set theory and deep learning approaches to capture node representations. ExEm finds dominating nodes of the collaborative network and constructs intelligent random walks that comprise of at least two dominating nodes. One dominating node should appear at the beginning of each path sampled to characterize the local neighborhoods. Moreover, the second dominating node reflects the global structure information. To learn the node embeddings, ExEm exploits three embedding methods including Word2vec, fastText and the concatenation of these two. The final result is the low-dimensional vectors of experts, called expert embeddings. The extracted expert embeddings can be applied to many applications. In order to extend these embeddings into the expert recommendation system, we introduce a novel strategy that uses expert vectors to calculate experts' scores and recommend experts. At the end, we conduct extensive experiments to validate the effectiveness of ExEm through assessing its performance over the multi-label classification, link prediction, and recommendation tasks on common datasets and our collected data formed by crawling the vast author Scopus profiles. The experiments show that ExEm outperforms the baselines especially in dense networks.
A graph embedding is a representation of graph vertices in a low-dimensional space, which approximately preserves properties such as distances between nodes. Vertex sequence-based embedding procedures use features extracted from linear sequences of nodes to create embeddings using a neural network. In this paper, we propose diffusion graphs as a method to rapidly generate vertex sequences for network embedding. Its computational efficiency is superior to previous methods due to simpler sequence generation, and it produces more accurate results. In experiments, we found that the performance relative to other methods improves with increasing edge density in the graph. In a community detection task, clustering nodes in the embedding space produces better results compared to other sequence-based embedding methods.
Knowledge graph embedding methods learn continuous vector representations for entities in knowledge graphs and have been used successfully in a large number of applications. We present a novel and scalable paradigm for the computation of knowledge graph embeddings, which we dub PYKE . Our approach combines a physical model based on Hooke's law and its inverse with ideas from simulated annealing to compute embeddings for knowledge graphs efficiently. We prove that PYKE achieves a linear space complexity. While the time complexity for the initialization of our approach is quadratic, the time complexity of each of its iterations is linear in the size of the input knowledge graph. Hence, PYKE's overall runtime is close to linear. Consequently, our approach easily scales up to knowledge graphs containing millions of triples. We evaluate our approach against six state-of-the-art embedding approaches on the DrugBank and DBpedia datasets in two series of experiments. The first series shows that the cluster purity achieved by PYKE is up to 26% (absolute) better than that of the state of art. In addition, PYKE is more than 22 times faster than existing embedding solutions in the best case. The results of our second series of experiments show that PYKE is up to 23% (absolute) better than the state of art on the task of type prediction while maintaining its superior scalability. Our implementation and results are open-source and are available at http://github.com/dice-group/PYKE.
In this paper, we focus on graph representation learning of heterogeneous information network (HIN), in which various types of vertices are connected by various types of relations. Most of the existing methods conducted on HIN revise homogeneous graph embedding models via meta-paths to learn low-dimensional vector space of HIN. In this paper, we propose a novel Heterogeneous Graph Structural Attention Neural Network (HetSANN) to directly encode structural information of HIN without meta-path and achieve more informative representations. With this method, domain experts will not be needed to design meta-path schemes and the heterogeneous information can be processed automatically by our proposed model. Specifically, we implicitly represent heterogeneous information using the following two methods: 1) we model the transformation between heterogeneous vertices through a projection in low-dimensional entity spaces; 2) afterwards, we apply the graph neural network to aggregate multi-relational information of projected neighborhood by means of attention mechanism. We also present three extensions of HetSANN, i.e., voices-sharing product attention for the pairwise relationships in HIN, cycle-consistency loss to retain the transformation between heterogeneous entity spaces, and multi-task learning with full use of information. The experiments conducted on three public datasets demonstrate that our proposed models achieve significant and consistent improvements compared to state-of-the-art solutions.