Studying metabolic networks is vital for many areas such as novel drugs and bio-fuels. For biologists, a key challenge is that many reactions are impractical or expensive to be found through experiments. Our task is to recover the missing reactions. By exploiting the problem structure, we model reaction recovery as a hyperlink prediction problem, where each reaction is regarded as a hyperlink connecting its participating vertices (metabolites). Different from the traditional link prediction problem where two nodes form a link, a hyperlink can involve an arbitrary number of nodes. Since the cardinality of a hyperlink is variable, existing classifiers based on a fixed number of input features become infeasible. Traditional methods, such as common neighbors and Katz index, are not applicable either, since they are restricted to pairwise similarities. In this paper, we propose a novel hyperlink prediction algorithm, called Matrix Boosting (MATBoost). MATBoost conducts inference jointly in the incidence space and adjacency space by performing an iterative completion-matching optimization. We carry out extensive experiments to show that MATBoost achieves state-of-the-art performance. For a metabolic network with 1805 metabolites and 2583 reactions, our algorithm can successfully recover nearly 200 reactions out of 400 missing reactions.
Although hyperlinks are common in real world and can be used to model multi-way relationships, currently there are still limited research on hyperlink prediction. @cite_23 proposed a supervised HPLSF framework to predict hyperlinks in social networks. To deal with the variable number of features, HPLSF uses their entropy score as a fixed-length feature for training a classification model. To our best knowledge, this is the only algorithm that is specifically designed for hyperlink prediction in arbitrary-cardinality hypernetworks.
@cite_23
588318799 2535764243 2728059831 2020382732
Predicting the existence of links between pairwise objects in networks is a key problem in the study of social networks. However, relationships among objects are often more complex than simple pairwise relations. By restricting attention to dyads, it is possible that information valuable for many learning tasks can be lost. The hypernetwork relaxes the assumption that only two nodes can participate in a link, permitting instead an arbitrary number of nodes to participate in so-called hyperlinks or hyperedges, which is a more natural representation for complex, multi-party relations. However, the hyperlink prediction problem has yet to be studied. In this paper, we propose HPLSF (Hyperlink Prediction using Latent Social Features), a hyperlink prediction algorithm for hypernetworks. By exploiting the homophily property of social networks, HPLSF explores social features for hyperlink prediction. To handle the problem that social features are not always observable, a latent social feature learning scheme is developed. To cope with the arbitrary cardinality hyperlink issue in hypernetworks, we design a feature-embedding scheme to map the a priori arbitrarily-sized feature set associated with each hyperlink into a uniformly-sized auxiliary space. To address the fact that observed features and latent features may be not independent, we generalize a structural SVM to learn using both observed features and latent features. In experiments, we evaluate the proposed HPLSF framework on three large-scale hypernetwork datasets. Our results on the three diverse datasets demonstrate the effectiveness of the HPLSF algorithm. Although developed in the context of social networks, HPLSF is a general methodology and applies to arbitrary hypernetworks. The first objective towards the effective use of microblogging services such as Twitter for situational awareness during the emerging disasters is discovery of the disaster-related postings. Given the wide range of possible disasters, using a pre-selected set of disaster-related keywords for the discovery is suboptimal. An alternative that we focus on in this work is to train a classifier using a small set of labeled postings that are becoming available as a disaster is emerging. Our hypothesis is that utilizing large quantities of historical microblogs could improve the quality of classification, as compared to training a classifier only on the labeled data. We propose to use unlabeled microblogs to cluster words into a limited number of clusters and use the word clusters as features for classification. To evaluate the proposed semi-supervised approach, we used Twitter data from 6 different disasters. Our results indicate that when the number of labeled tweets is 100 or less, the proposed approach is superior to the standard classification based on the bag or words feature representation. Our results also reveal that the choice of the unlabeled corpus, the choice of word clustering algorithm, and the choice of hyperparameters can have a significant impact on the classification accuracy. 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 most datasets. Many important real-world systems, modeled naturally as complex networks, have heterogeneous interactions and complicated dependency structures. Link prediction in such networks must model the influences between heterogenous relationships and distinguish the formation mechanisms of each link type, a task which is beyond the simple topological features commonly used to score potential links. In this paper, we introduce a novel probabilistically weighted extension of the Adamic Adar measure for heterogenous information networks, which we use to demonstrate the potential benefits of diverse evidence, particularly in cases where homogeneous relationships are very sparse. However, we also expose some fundamental flaws of traditional unsupervised link prediction. We develop supervised learning approaches for relationship (link) prediction in multi-relational networks, and demonstrate that a supervised approach to link prediction can enhance performance. We present results on three diverse, real-world heterogeneous information networks and discuss the trends and tradeoffs of supervised and unsupervised link prediction in a multi-relational setting.