The polypharmacy side effect prediction problem considers cases in which two drugs taken individually do not result in a particular side effect; however, when the two drugs are taken in combination, the side effect manifests. In this work, we demonstrate that multi-relational knowledge graph completion achieves state-of-the-art results on the polypharmacy side effect prediction problem. Empirical results show that our approach is particularly effective when the protein targets of the drugs are well-characterized. In contrast to prior work, our approach provides more interpretable predictions and hypotheses for wet lab validation.
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Incompleteness is a common problem for existing knowledge graphs (KGs), and the completion of KG which aims to predict links between entities is challenging. Most existing KG completion methods only consider the direct relation between nodes and ignore the relation paths which contain useful information for link prediction. Recently, a few methods take relation paths into consideration but pay less attention to the order of relations in paths which is important for reasoning. In addition, these path-based models always ignore nonlinear contributions of path features for link prediction. To solve these problems, we propose a novel KG completion method named OPTransE. Instead of embedding both entities of a relation into the same latent space as in previous methods, we project the head entity and the tail entity of each relation into different spaces to guarantee the order of relations in the path. Meanwhile, we adopt a pooling strategy to extract nonlinear and complex features of different paths to further improve the performance of link prediction. Experimental results on two benchmark datasets show that the proposed model OPTransE performs better than state-of-the-art methods.
Knowledge graph embedding aims to learn distributed representations for entities and relations, and is proven to be effective in many applications. Crossover interactions --- bi-directional effects between entities and relations --- help select related information when predicting a new triple, but haven't been formally discussed before. In this paper, we propose CrossE, a novel knowledge graph embedding which explicitly simulates crossover interactions. It not only learns one general embedding for each entity and relation as most previous methods do, but also generates multiple triple specific embeddings for both of them, named interaction embeddings. We evaluate embeddings on typical link prediction tasks and find that CrossE achieves state-of-the-art results on complex and more challenging datasets. Furthermore, we evaluate embeddings from a new perspective --- giving explanations for predicted triples, which is important for real applications. In this work, an explanation for a triple is regarded as a reliable closed-path between the head and the tail entity. Compared to other baselines, we show experimentally that CrossE, benefiting from interaction embeddings, is more capable of generating reliable explanations to support its predictions.
Knowledge graph (KG) completion aims to fill the missing facts in a KG, where a fact is represented as a triple in the form of $(subject, relation, object)$. Current KG completion models compel two-thirds of a triple provided (e.g., $subject$ and $relation$) to predict the remaining one. In this paper, we propose a new model, which uses a KG-specific multi-layer recurrent neural network (RNN) to model triples in a KG as sequences. It outperformed several state-of-the-art KG completion models on the conventional entity prediction task for many evaluation metrics, based on two benchmark datasets and a more difficult dataset. Furthermore, our model is enabled by the sequential characteristic and thus capable of predicting the whole triples only given one entity. Our experiments demonstrated that our model achieved promising performance on this new triple prediction task.
We introduce a new method DOLORES for learning knowledge graph embeddings that effectively captures contextual cues and dependencies among entities and relations. First, we note that short paths on knowledge graphs comprising of chains of entities and relations can encode valuable information regarding their contextual usage. We operationalize this notion by representing knowledge graphs not as a collection of triples but as a collection of entity-relation chains, and learn embeddings for entities and relations using deep neural models that capture such contextual usage. In particular, our model is based on Bi-Directional LSTMs and learn deep representations of entities and relations from constructed entity-relation chains. We show that these representations can very easily be incorporated into existing models to significantly advance the state of the art on several knowledge graph prediction tasks like link prediction, triple classification, and missing relation type prediction (in some cases by at least 9.5%).
Multi-hop reasoning is an effective approach for query answering (QA) over incomplete knowledge graphs (KGs). The problem can be formulated in a reinforcement learning (RL) setup, where a policy-based agent sequentially extends its inference path until it reaches a target. However, in an incomplete KG environment, the agent receives low-quality rewards corrupted by false negatives in the training data, which harms generalization at test time. Furthermore, since no golden action sequence is used for training, the agent can be misled by spurious search trajectories that incidentally lead to the correct answer. We propose two modeling advances to address both issues: (1) we reduce the impact of false negative supervision by adopting a pretrained one-hop embedding model to estimate the reward of unobserved facts; (2) we counter the sensitivity to spurious paths of on-policy RL by forcing the agent to explore a diverse set of paths using randomly generated edge masks. Our approach significantly improves over existing path-based KGQA models on several benchmark datasets and is comparable or better than embedding-based models.
Knowledge graphs (KGs) model facts about the world, they consist of nodes (entities such as companies and people) that are connected by edges (relations such as founderOf). Facts encoded in KGs are frequently used by search applications to augment result pages. When presenting a KG fact to the user, providing other facts that are pertinent to that main fact can enrich the user experience and support exploratory information needs. KG fact contextualization is the task of augmenting a given KG fact with additional and useful KG facts. The task is challenging because of the large size of KGs, discovering other relevant facts even in a small neighborhood of the given fact results in an enormous amount of candidates. We introduce a neural fact contextualization method (NFCM) to address the KG fact contextualization task. NFCM first generates a set of candidate facts in the neighborhood of a given fact and then ranks the candidate facts using a supervised learning to rank model. The ranking model combines features that we automatically learn from data and that represent the query-candidate facts with a set of hand-crafted features we devised or adjusted for this task. In order to obtain the annotations required to train the learning to rank model at scale, we generate training data automatically using distant supervision on a large entity-tagged text corpus. We show that ranking functions learned on this data are effective at contextualizing KG facts. Evaluation using human assessors shows that it significantly outperforms several competitive baselines.
Link prediction for knowledge graphs is the task of predicting missing relationships between entities. Previous work on link prediction has focused on shallow, fast models which can scale to large knowledge graphs. However, these models learn less expressive features than deep, multi-layer models -- which potentially limits performance. In this work, we introduce ConvE, a multi-layer convolutional network model for link prediction, and report state-of-the-art results for several established datasets. We also show that the model is highly parameter efficient, yielding the same performance as DistMult and R-GCN with 8x and 17x fewer parameters. Analysis of our model suggests that it is particularly effective at modelling nodes with high indegree -- which are common in highly-connected, complex knowledge graphs such as Freebase and YAGO3. In addition, it has been noted that the WN18 and FB15k datasets suffer from test set leakage, due to inverse relations from the training set being present in the test set -- however, the extent of this issue has so far not been quantified. We find this problem to be severe: a simple rule-based model can achieve state-of-the-art results on both WN18 and FB15k. To ensure that models are evaluated on datasets where simply exploiting inverse relations cannot yield competitive results, we investigate and validate several commonly used datasets -- deriving robust variants where necessary. We then perform experiments on these robust datasets for our own and several previously proposed models, and find that ConvE achieves state-of-the-art Mean Reciprocal Rank across all datasets.
Inferring missing links in knowledge graphs (KG) has attracted a lot of attention from the research community. In this paper, we tackle a practical query answering task involving predicting the relation of a given entity pair. We frame this prediction problem as an inference problem in a probabilistic graphical model and aim at resolving it from a variational inference perspective. In order to model the relation between the query entity pair, we assume that there exists an underlying latent variable (paths connecting two nodes) in the KG, which carries the equivalent semantics of their relations. However, due to the intractability of connections in large KGs, we propose to use variation inference to maximize the evidence lower bound. More specifically, our framework (\textsc{Diva}) is composed of three modules, i.e. a posterior approximator, a prior (path finder), and a likelihood (path reasoner). By using variational inference, we are able to incorporate them closely into a unified architecture and jointly optimize them to perform KG reasoning. With active interactions among these sub-modules, \textsc{Diva} is better at handling noise and coping with more complex reasoning scenarios. In order to evaluate our method, we conduct the experiment of the link prediction task on multiple datasets and achieve state-of-the-art performances on both datasets.
To address the sparsity and cold start problem of collaborative filtering, researchers usually make use of side information, such as social networks or item attributes, to improve recommendation performance. This paper considers the knowledge graph as the source of side information. To address the limitations of existing embedding-based and path-based methods for knowledge-graph-aware recommendation, we propose Ripple Network, an end-to-end framework that naturally incorporates the knowledge graph into recommender systems. Similar to actual ripples propagating on the surface of water, Ripple Network stimulates the propagation of user preferences over the set of knowledge entities by automatically and iteratively extending a user's potential interests along links in the knowledge graph. The multiple "ripples" activated by a user's historically clicked items are thus superposed to form the preference distribution of the user with respect to a candidate item, which could be used for predicting the final clicking probability. Through extensive experiments on real-world datasets, we demonstrate that Ripple Network achieves substantial gains in a variety of scenarios, including movie, book and news recommendation, over several state-of-the-art baselines.
The aim of knowledge graphs is to gather knowledge about the world and provide a structured representation of this knowledge. Current knowledge graphs are far from complete. To address the incompleteness of the knowledge graphs, link prediction approaches have been developed which make probabilistic predictions about new links in a knowledge graph given the existing links. Tensor factorization approaches have proven promising for such link prediction problems. In this paper, we develop a simple tensor factorization model called SimplE, through a slight modification of the Polyadic Decomposition model from 1927. The complexity of SimplE grows linearly with the size of embeddings. The embeddings learned through SimplE are interpretable, and certain types of expert knowledge in terms of logical rules can be incorporated into these embeddings through weight tying. We prove SimplE is fully-expressive and derive a bound on the size of its embeddings for full expressivity. We show empirically that, despite its simplicity, SimplE outperforms several state-of-the-art tensor factorization techniques.
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