Minimizing adverse reactions caused by drug-drug interactions has always been a momentous research topic in clinical pharmacology. Detecting all possible interactions through clinical studies before a drug is released to the market is a demanding task. The power of big data is opening up new approaches to discover various drug-drug interactions. However, these discoveries contain a huge amount of noise and provide knowledge bases far from complete and trustworthy ones to be utilized. Most existing studies focus on predicting binary drug-drug interactions between drug pairs but ignore other interactions. In this paper, we propose a novel framework, called PRD, to predict drug-drug interactions. The framework uses the graph embedding that can overcome data incompleteness and sparsity issues to achieve multiple DDI label prediction. First, a large-scale drug knowledge graph is generated from different sources. Then, the knowledge graph is embedded with comprehensive biomedical text into a common low dimensional space. Finally, the learned embeddings are used to efficiently compute rich DDI information through a link prediction process. To validate the effectiveness of the proposed framework, extensive experiments were conducted on real-world datasets. The results demonstrate that our model outperforms several state-of-the-art baseline methods in terms of capability and accuracy.
Knowledge Graph Embedding methods aim at representing entities and relations in a knowledge base as points or vectors in a continuous vector space. Several approaches using embeddings have shown promising results on tasks such as link prediction, entity recommendation, question answering, and triplet classification. However, only a few methods can compute low-dimensional embeddings of very large knowledge bases without needing state-of-the-art computational resources. In this paper, we propose KG2Vec, a simple and fast approach to Knowledge Graph Embedding based on the skip-gram model. Instead of using a predefined scoring function, we learn it relying on Long Short-Term Memories. We show that our embeddings achieve results comparable with the most scalable approaches on knowledge graph completion as well as on a new metric. Yet, KG2Vec can embed large graphs in lesser time by processing more than 250 million triples in less than 7 hours on common hardware.
A visual-relational knowledge graph (KG) is a multi-relational graph whose entities are associated with images. We explore novel machine learning approaches for answering visual-relational queries in web-extracted knowledge graphs. To this end, we have created ImageGraph, a KG with 1,330 relation types, 14,870 entities, and 829,931 images crawled from the web. With visual-relational KGs such as ImageGraph one can introduce novel probabilistic query types in which images are treated as first-class citizens. Both the prediction of relations between unseen images as well as multi-relational image retrieval can be expressed with specific families of visual-relational queries. We introduce novel combinations of convolutional networks and knowledge graph embedding methods to answer such queries. We also explore a zero-shot learning scenario where an image of an entirely new entity is linked with multiple relations to entities of an existing KG. The resulting multi-relational grounding of unseen entity images into a knowledge graph serves as a semantic entity representation. We conduct experiments to demonstrate that the proposed methods can answer these visual-relational queries efficiently and accurately.
Knowledge Graphs (KGs) are becoming essential to information systems that require access to structured data. Several approaches have been recently proposed, for obtaining vector representations of KGs suitable for Machine Learning tasks, based on identifying and extracting relevant graph substructures using uniform and biased random walks. However, such approaches lead to representations comprising mostly "popular", instead of "relevant", entities in the KG. In KGs, in which different types of entities often exist (such as in Linked Open Data), a given target entity may have its own distinct set of most "relevant" nodes and edges. We propose specificity as an accurate measure of identifying most relevant, entity-specific, nodes and edges. We develop a scalable method based on bidirectional random walks to compute specificity. Our experimental evaluation results show that specificity-based biased random walks extract more "meaningful" (in terms of size and relevance) RDF substructures compared to the state-of-the-art and, the graph embedding learned from the extracted substructures, outperform existing techniques in the task of entity recommendation in DBpedia.
We introduce KBGAN, an adversarial learning framework to improve the performances of a wide range of existing knowledge graph embedding models. Because knowledge graphs typically only contain positive facts, sampling useful negative training examples is a non-trivial task. Replacing the head or tail entity of a fact with a uniformly randomly selected entity is a conventional method for generating negative facts, but the majority of the generated negative facts can be easily discriminated from positive facts, and will contribute little towards the training. Inspired by generative adversarial networks (GANs), we use one knowledge graph embedding model as a negative sample generator to assist the training of our desired model, which acts as the discriminator in GANs. This framework is independent of the concrete form of generator and discriminator, and therefore can utilize a wide variety of knowledge graph embedding models as its building blocks. In experiments, we adversarially train two translation-based models, TransE and TransD, each with assistance from one of the two probability-based models, DistMult and ComplEx. We evaluate the performances of KBGAN on the link prediction task, using three knowledge base completion datasets: FB15k-237, WN18 and WN18RR. Experimental results show that adversarial training substantially improves the performances of target embedding models under various settings.
We study feature propagation on graph, an inference process involved in graph representation learning tasks. It's to spread the features over the whole graph to the $t$-th orders, thus to expand the end's features. The process has been successfully adopted in graph embedding or graph neural networks, however few works studied the convergence of feature propagation. Without convergence guarantees, it may lead to unexpected numerical overflows and task failures. In this paper, we first define the concept of feature propagation on graph formally, and then study its convergence conditions to equilibrium states. We further link feature propagation to several established approaches such as node2vec and structure2vec. In the end of this paper, we extend existing approaches from represent nodes to edges (edge2vec) and demonstrate its applications on fraud transaction detection in real world scenario. Experiments show that it is quite competitive.
The success of graph embeddings or node representation learning in a variety of downstream tasks, such as node classification, link prediction, and recommendation systems, has led to their popularity in recent years. Representation learning algorithms aim to preserve local and global network structure by identifying node neighborhood notions. However, many existing algorithms generate embeddings that fail to properly preserve the network structure, or lead to unstable representations due to random processes (e.g., random walks to generate context) and, thus, cannot generate to multi-graph problems. In this paper, we propose RECS, a novel, stable graph embedding algorithmic framework. RECS learns graph representations using connection subgraphs by employing the analogy of graphs with electrical circuits. It preserves both local and global connectivity patterns, and addresses the issue of high-degree nodes. Further, it exploits the strength of weak ties and meta-data that have been neglected by baselines. The experiments show that RECS outperforms state-of-the-art algorithms by up to 36.85% on multi-label classification problem. Further, in contrast to baselines, RECS, being deterministic, is completely stable.
Embedding knowledge graphs (KGs) into continuous vector spaces is a focus of current research. Early works performed this task via simple models developed over KG triples. Recent attempts focused on either designing more complicated triple scoring models, or incorporating extra information beyond triples. This paper, by contrast, investigates the potential of using very simple constraints to improve KG embedding. We examine non-negativity constraints on entity representations and approximate entailment constraints on relation representations. The former help to learn compact and interpretable representations for entities. The latter further encode regularities of logical entailment between relations into their distributed representations. These constraints impose prior beliefs upon the structure of the embedding space, without negative impacts on efficiency or scalability. Evaluation on WordNet, Freebase, and DBpedia shows that our approach is simple yet surprisingly effective, significantly and consistently outperforming competitive baselines. The constraints imposed indeed improve model interpretability, leading to a substantially increased structuring of the embedding space. Code and data are available at https://github.com/iieir-km/ComplEx-NNE_AER.
Knowledge representation is a long-history topic in AI, which is very important. A variety of models have been proposed for knowledge graph embedding, which projects symbolic entities and relations into continuous vector space. However, most related methods merely focus on the data-fitting of knowledge graph, and ignore the interpretable semantic expression. Thus, traditional embedding methods are not friendly for applications that require semantic analysis, such as question answering and entity retrieval. 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 show that our model outperforms other state-of-the-art baselines substantially.
Recommender systems (RSs) have been the most important technology for increasing the business in Taobao, the largest online consumer-to-consumer (C2C) platform in China. The billion-scale data in Taobao creates three major challenges to Taobao's RS: scalability, sparsity and cold start. In this paper, we present our technical solutions to address these three challenges. The methods are based on the graph embedding framework. We first construct an item graph from users' behavior history. Each item is then represented as a vector using graph embedding. The item embeddings are employed to compute pairwise similarities between all items, which are then used in the recommendation process. To alleviate the sparsity and cold start problems, side information is incorporated into the embedding framework. We propose two aggregation methods to integrate the embeddings of items and the corresponding side information. Experimental results from offline experiments show that methods incorporating side information are superior to those that do not. Further, we describe the platform upon which the embedding methods are deployed and the workflow to process the billion-scale data in Taobao. Using online A/B test, we show that the online Click-Through-Rate (CTRs) are improved comparing to the previous recommendation methods widely used in Taobao, further demonstrating the effectiveness and feasibility of our proposed methods in Taobao's live production environment.
Recent years have witnessed the successful application of low-dimensional vector space representations of knowledge graphs to predict missing facts or find erroneous ones. However, it is not yet well-understood to what extent ontological knowledge, e.g. given as a set of (existential) rules, can be embedded in a principled way. To address this shortcoming, in this paper we introduce a general framework based on a view of relations as regions, which allows us to study the compatibility between ontological knowledge and different types of vector space embeddings. Our technical contribution is two-fold. First, we show that some of the most popular existing embedding methods are not capable of modelling even very simple types of rules, which in particular also means that they are not able to learn the type of dependencies captured by such rules. Second, we study a model in which relations are modelled as convex regions. We show particular that ontologies which are expressed using so-called quasi-chained existential rules can be exactly represented using convex regions, such that any set of facts which is induced using that vector space embedding is logically consistent and deductively closed with respect to the input ontology.
Word2Vec (W2V) and GloVe are popular, fast and efficient word embedding algorithms. Their embeddings are widely used and perform well on a variety of natural language processing tasks. Moreover, W2V has recently been adopted in the field of graph embedding, where it underpins several leading algorithms. However, despite their ubiquity and relatively simple model architecture, a theoretical understanding of what the embedding parameters of W2V and GloVe learn and why that is useful in downstream tasks has been lacking. We show that different interactions between PMI vectors reflect semantic word relationships, such as similarity and paraphrasing, that are encoded in low dimensional word embeddings under a suitable projection, theoretically explaining why embeddings of W2V and GloVe work. As a consequence, we also reveal an interesting mathematical interconnection between the considered semantic relationships themselves.
We consider the representation power of siamese-style similarity functions used in neural network-based graph embedding. The inner product similarity (IPS) with feature vectors computed via neural networks is commonly used for representing the strength of association between two nodes. However, only a little work has been done on the representation capability of IPS. A very recent work shed light on the nature of IPS and reveals that IPS has the capability of approximating any positive definite (PD) similarities. However, a simple example demonstrates the fundamental limitation of IPS to approximate non-PD similarities. We then propose a novel model named Shifted IPS (SIPS) that approximates any Conditionally PD (CPD) similarities arbitrary well. CPD is a generalization of PD with many examples such as negative Poincar\'e distance and negative Wasserstein distance, thus SIPS has a potential impact to significantly improve the applicability of graph embedding without taking great care in configuring the similarity function. Our numerical experiments demonstrate the SIPS's superiority over IPS. In theory, we further extend SIPS beyond CPD by considering the inner product in Minkowski space so that it approximates more general similarities.
Graph embedding is a central problem in social network analysis and many other applications, aiming to learn the vector representation for each node. While most existing approaches need to specify the neighborhood and the dependence form to the neighborhood, which may significantly degrades the flexibility of representation, we propose a novel graph node embedding method (namely GESF) via the set function technique. Our method can 1) learn an arbitrary form of representation function from neighborhood, 2) automatically decide the significance of neighbors at different distances, and 3) be applied to heterogeneous graph embedding, which may contain multiple types of nodes. Theoretical guarantee for the representation capability of our method has been proved for general homogeneous and heterogeneous graphs and evaluation results on benchmark data sets show that the proposed GESF outperforms the state-of-the-art approaches on producing node vectors for classification tasks.
Learning graph representations via low-dimensional embeddings that preserve relevant network properties is an important class of problems in machine learning. We here present a novel method to embed directed acyclic graphs. Following prior work, we first advocate for using hyperbolic spaces which provably model tree-like structures better than Euclidean geometry. Second, we view hierarchical relations as partial orders defined using a family of nested geodesically convex cones. We prove that these entailment cones admit an optimal shape with a closed form expression both in the Euclidean and hyperbolic spaces, and they canonically define the embedding learning process. Experiments show significant improvements of our method over strong recent baselines both in terms of representational capacity and generalization.
A simple framework Probabilistic Multi-view Graph Embedding (PMvGE) is proposed for multi-view feature learning with many-to-many associations so that it generalizes various existing multi-view methods. PMvGE is a probabilistic model for predicting new associations via graph embedding of the nodes of data vectors with links of their associations. Multi-view data vectors with many-to-many associations are transformed by neural networks to feature vectors in a shared space, and the probability of new association between two data vectors is modeled by the inner product of their feature vectors. While existing multi-view feature learning techniques can treat only either of many-to-many association or non-linear transformation, PMvGE can treat both simultaneously. By combining Mercer's theorem and the universal approximation theorem, we prove that PMvGE learns a wide class of similarity measures across views. Our likelihood-based estimator enables efficient computation of non-linear transformations of data vectors in large-scale datasets by minibatch SGD, and numerical experiments illustrate that PMvGE outperforms existing multi-view methods.
We propose a novel two-layered attention network based on Bidirectional Long Short-Term Memory for sentiment analysis. The novel two-layered attention network takes advantage of the external knowledge bases to improve the sentiment prediction. It uses the Knowledge Graph Embedding generated using the WordNet. We build our model by combining the two-layered attention network with the supervised model based on Support Vector Regression using a Multilayer Perceptron network for sentiment analysis. We evaluate our model on the benchmark dataset of SemEval 2017 Task 5. Experimental results show that the proposed model surpasses the top system of SemEval 2017 Task 5. The model performs significantly better by improving the state-of-the-art system at SemEval 2017 Task 5 by 1.7 and 3.7 points for sub-tracks 1 and 2 respectively.