Knowledge graph embedding aims to represent entities and relations in a large-scale knowledge graph as elements in a continuous vector space. Existing methods, e.g., TransE and TransH, learn embedding representation by defining a global margin-based loss function over the data. However, the optimal loss function is determined during experiments whose parameters are examined among a closed set of candidates. Moreover, embeddings over two knowledge graphs with different entities and relations share the same set of candidate loss functions, ignoring the locality of both graphs. This leads to the limited performance of embedding related applications. In this paper, we propose a locally adaptive translation method for knowledge graph embedding, called TransA, to find the optimal loss function by adaptively determining its margin over different knowledge graphs. Experiments on two benchmark data sets demonstrate the superiority of the proposed method, as compared to the-state-of-the-art ones.
The strength of association between a pair of data vectors is represented by a nonnegative real number, called matching weight. For dimensionality reduction, we consider a linear transformation of data vectors, and define a matching error as the weighted sum of squared distances between transformed vectors with respect to the matching weights. Given data vectors and matching weights, the optimal linear transformation minimizing the matching error is solved by the spectral graph embedding of Yan et al. (2007). This method is a generalization of the canonical correlation analysis, and will be called as matching correlation analysis (MCA). In this paper, we consider a novel sampling scheme where the observed matching weights are randomly sampled from underlying true matching weights with small probability, whereas the data vectors are treated as constants. We then investigate a cross-validation by resampling the matching weights. Our asymptotic theory shows that the cross-validation, if rescaled properly, computes an unbiased estimate of the matching error with respect to the true matching weights. Existing ideas of cross-validation for resampling data vectors, instead of resampling matching weights, are not applicable here. MCA can be used for data vectors from multiple domains with different dimensions via an embarrassingly simple idea of coding the data vectors. This method will be called as cross-domain matching correlation analysis (CDMCA), and an interesting connection to the classical associative memory model of neural networks is also discussed.
Many scientific datasets are of high dimension, and the analysis usually requires visual manipulation by retaining the most important structures of data. Principal curve is a widely used approach for this purpose. However, many existing methods work only for data with structures that are not self-intersected, which is quite restrictive for real applications. A few methods can overcome the above problem, but they either require complicated human-made rules for a specific task with lack of convergence guarantee and adaption flexibility to different tasks, or cannot obtain explicit structures of data. To address these issues, we develop a new regularized principal graph learning framework that captures the local information of the underlying graph structure based on reversed graph embedding. As showcases, models that can learn a spanning tree or a weighted undirected $\ell_1$ graph are proposed, and a new learning algorithm is developed that learns a set of principal points and a graph structure from data, simultaneously. The new algorithm is simple with guaranteed convergence. We then extend the proposed framework to deal with large-scale data. Experimental results on various synthetic and six real world datasets show that the proposed method compares favorably with baselines and can uncover the underlying structure correctly.
Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches.
Several popular graph embedding techniques for representation learning and dimensionality reduction rely on performing computationally expensive eigendecompositions to derive a nonlinear transformation of the input data space. The resulting eigenvectors encode the embedding coordinates for the training samples only, and so the embedding of novel data samples requires further costly computation. In this paper, we present a method for the out-of-sample extension of graph embeddings using deep neural networks (DNN) to parametrically approximate these nonlinear maps. Compared with traditional nonparametric out-of-sample extension methods, we demonstrate that the DNNs can generalize with equal or better fidelity and require orders of magnitude less computation at test time. Moreover, we find that unsupervised pretraining of the DNNs improves optimization for larger network sizes, thus removing sensitivity to model selection.
We propose a simple discrete time semi-supervised graph embedding approach to link prediction in dynamic networks. The learned embedding reflects information from both the temporal and cross-sectional network structures, which is performed by defining the loss function as a weighted sum of the supervised loss from past dynamics and the unsupervised loss of predicting the neighborhood context in the current network. Our model is also capable of learning different embeddings for both formation and dissolution dynamics. These key aspects contributes to the predictive performance of our model and we provide experiments with three real--world dynamic networks showing that our method is comparable to state of the art methods in link formation prediction and outperforms state of the art baseline methods in link dissolution prediction.
In this paper, we tackle a problem of predicting phenotypes from structural connectomes. We propose that normalized Laplacian spectra can capture structural properties of brain networks, and hence graph spectral distributions are useful for a task of connectome-based classification. We introduce a kernel that is based on earth mover's distance (EMD) between spectral distributions of brain networks. We access performance of an SVM classifier with the proposed kernel for a task of classification of autism spectrum disorder versus typical development based on a publicly available dataset. Classification quality (area under the ROC-curve) obtained with the EMD-based kernel on spectral distributions is 0.71, which is higher than that based on simpler graph embedding methods.
The objective of knowledge graph embedding is to encode both entities and relations of knowledge graphs into continuous low-dimensional vector spaces. Previously, most works focused on symbolic representation of knowledge graph with structure information, which can not handle new entities or entities with few facts well. In this paper, we propose a novel deep architecture to utilize both structural and textual information of entities. Specifically, we introduce three neural models to encode the valuable information from text description of entity, among which an attentive model can select related information as needed. Then, a gating mechanism is applied to integrate representations of structure and text into a unified architecture. Experiments show that our models outperform baseline by margin on link prediction and triplet classification tasks. Source codes of this paper will be available on Github.
Knowledge graph embedding aims at translating the knowledge graph into numerical representations by transforming the entities and relations into continuous low-dimensional vectors. Recently, many methods [1, 5, 3, 2, 6] have been proposed to deal with this problem, but existing single-thread implementations of them are time-consuming for large-scale knowledge graphs. Here, we design a unified parallel framework to parallelize these methods, which achieves a significant time reduction without influencing the accuracy. We name our framework as ParaGraphE, which provides a library for parallel knowledge graph embedding. The source code can be downloaded from https://github.com/LIBBLE/LIBBLE-MultiThread/tree/master/ParaGraphE .
We propose graph-based predictable feature analysis (GPFA), a new method for unsupervised learning of predictable features from high-dimensional time series, where high predictability is understood very generically as low variance in the distribution of the next data point given the previous ones. We show how this measure of predictability can be understood in terms of graph embedding as well as how it relates to the information-theoretic measure of predictive information in special cases. We confirm the effectiveness of GPFA on different datasets, comparing it to three existing algorithms with similar objectives---namely slow feature analysis, forecastable component analysis, and predictable feature analysis---to which GPFA shows very competitive results.
Graph embedding provides an efficient solution for graph analysis by converting the graph into a low-dimensional space which preserves the structure information. In contrast to the graph structure data, the i.i.d. node embedding can be processed efficiently in terms of both time and space. Current semi-supervised graph embedding algorithms assume the labelled nodes are given, which may not be always true in the real world. While manually label all training data is inapplicable, how to select the subset of training data to label so as to maximize the graph analysis task performance is of great importance. This motivates our proposed active graph embedding (AGE) framework, in which we design a general active learning query strategy for any semi-supervised graph embedding algorithm. AGE selects the most informative nodes as the training labelled nodes based on the graphical information (i.e., node centrality) as well as the learnt node embedding (i.e., node classification uncertainty and node embedding representativeness). Different query criteria are combined with the time-sensitive parameters which shift the focus from graph based query criteria to embedding based criteria as the learning progresses. Experiments have been conducted on three public data sets and the results verified the effectiveness of each component of our query strategy and the power of combining them using time-sensitive parameters. Our code is available online at: https://github.com/vwz/AGE.
The volume of data generated by internet and social networks is increasing every day, and there is a clear need for efficient ways of extracting useful information from them. As those data can take different forms, it is important to use all the available data representations for prediction. In this paper, we focus our attention on supervised classification using both regular plain, tabular, data and structural information coming from a network structure. 14 techniques are investigated and compared in this study and can be divided in three classes: the first one uses only the plain data to build a classification model, the second uses only the graph structure and the last uses both information sources. The relative performances in these three cases are investigated. Furthermore, the effect of using a graph embedding and well-known indicators in spatial statistics is also studied. Possible applications are automatic classification of web pages or other linked documents, of people in a social network or of proteins in a biological complex system, to name a few. Based on our comparison, we draw some general conclusions and advices to tackle this particular classification task: some datasets can be better explained by their graph structure (graph-driven), or by their feature set (features-driven). The most efficient methods are discussed in both cases.
Representation learning has become an invaluable approach for learning from symbolic data such as text and graphs. However, while complex symbolic datasets often exhibit a latent hierarchical structure, state-of-the-art methods typically learn embeddings in Euclidean vector spaces, which do not account for this property. For this purpose, we introduce a new approach for learning hierarchical representations of symbolic data by embedding them into hyperbolic space -- or more precisely into an n-dimensional Poincar\'e ball. Due to the underlying hyperbolic geometry, this allows us to learn parsimonious representations of symbolic data by simultaneously capturing hierarchy and similarity. We introduce an efficient algorithm to learn the embeddings based on Riemannian optimization and show experimentally that Poincar\'e embeddings outperform Euclidean embeddings significantly on data with latent hierarchies, both in terms of representation capacity and in terms of generalization ability.
Knowledge representation is an important, long-history topic in AI, and there have been a large amount of work for knowledge graph embedding which projects symbolic entities and relations into low-dimensional, real-valued vector space. However, most embedding methods merely concentrate on data fitting and ignore the explicit semantic expression, leading to uninterpretable representations. Thus, traditional embedding methods have limited potentials for many applications such as question answering, and entity classification. To this end, this paper proposes a semantic representation method for knowledge graph \textbf{(KSR)}, which imposes a two-level hierarchical generative process that globally extracts many aspects and then locally assigns a specific category in each aspect for every triple. Since both aspects and categories are semantics-relevant, the collection of categories in each aspect is treated as the semantic representation of this triple. Extensive experiments justify our model outperforms other state-of-the-art baselines substantially.
Knowledge graph embedding aims at offering a numerical knowledge representation paradigm by transforming the entities and relations into continuous vector space. However, existing methods could not characterize the knowledge graph in a fine degree to make a precise prediction. There are two reasons: being an ill-posed algebraic system and applying an overstrict geometric form. As precise prediction is critical, we propose an manifold-based embedding principle (\textbf{ManifoldE}) which could be treated as a well-posed algebraic system that expands the position of golden triples from one point in current models to a manifold in ours. Extensive experiments show that the proposed models achieve substantial improvements against the state-of-the-art baselines especially for the precise prediction task, and yet maintain high efficiency.
Implementation and experiments of graph embedding algorithms.deep walk,LINE(Large-scale Information Network Embedding),node2vec,SDNE(Structural Deep Network Embedding),struc2vec
Recent works on representation learning for graph structured data predominantly focus on learning distributed representations of graph substructures such as nodes and subgraphs. However, many graph analytics tasks such as graph classification and clustering require representing entire graphs as fixed length feature vectors. While the aforementioned approaches are naturally unequipped to learn such representations, graph kernels remain as the most effective way of obtaining them. However, these graph kernels use handcrafted features (e.g., shortest paths, graphlets, etc.) and hence are hampered by problems such as poor generalization. To address this limitation, in this work, we propose a neural embedding framework named graph2vec to learn data-driven distributed representations of arbitrary sized graphs. graph2vec's embeddings are learnt in an unsupervised manner and are task agnostic. Hence, they could be used for any downstream task such as graph classification, clustering and even seeding supervised representation learning approaches. Our experiments on several benchmark and large real-world datasets show that graph2vec achieves significant improvements in classification and clustering accuracies over substructure representation learning approaches and are competitive with state-of-the-art graph kernels.
We propose a methodology that adapts graph embedding techniques (DeepWalk (Perozzi et al., 2014) and node2vec (Grover and Leskovec, 2016)) as well as cross-lingual vector space mapping approaches (Least Squares and Canonical Correlation Analysis) in order to merge the corpus and ontological sources of lexical knowledge. We also perform comparative analysis of the used algorithms in order to identify the best combination for the proposed system. We then apply this to the task of enhancing the coverage of an existing word embedding's vocabulary with rare and unseen words. We show that our technique can provide considerable extra coverage (over 99%), leading to consistent performance gain (around 10% absolute gain is achieved with w2v-gn-500K cf.\S 3.3) on the Rare Word Similarity dataset.
Patterns stored within pre-trained deep neural networks compose large and powerful descriptive languages that can be used for many different purposes. Typically, deep network representations are implemented within vector embedding spaces, which enables the use of traditional machine learning algorithms on top of them. In this short paper we propose the construction of a graph embedding space instead, introducing a methodology to transform the knowledge coded within a deep convolutional network into a topological space (i.e. a network). We outline how such graph can hold data instances, data features, relations between instances and features, and relations among features. Finally, we introduce some preliminary experiments to illustrate how the resultant graph embedding space can be exploited through graph analytics algorithms.
The problem of cross-platform binary code similarity detection aims at detecting whether two binary functions coming from different platforms are similar or not. It has many security applications, including plagiarism detection, malware detection, vulnerability search, etc. Existing approaches rely on approximate graph matching algorithms, which are inevitably slow and sometimes inaccurate, and hard to adapt to a new task. To address these issues, in this work, we propose a novel neural network-based approach to compute the embedding, i.e., a numeric vector, based on the control flow graph of each binary function, then the similarity detection can be done efficiently by measuring the distance between the embeddings for two functions. We implement a prototype called Gemini. Our extensive evaluation shows that Gemini outperforms the state-of-the-art approaches by large margins with respect to similarity detection accuracy. Further, Gemini can speed up prior art's embedding generation time by 3 to 4 orders of magnitude and reduce the required training time from more than 1 week down to 30 minutes to 10 hours. Our real world case studies demonstrate that Gemini can identify significantly more vulnerable firmware images than the state-of-the-art, i.e., Genius. Our research showcases a successful application of deep learning on computer security problems.