Timely identification of adverse drug reactions (ADRs) is highly important in the domains of public health and pharmacology. Early discovery of potential ADRs can limit their effect on patient lives and also make drug development pipelines more robust and efficient. Reliable in silico prediction of ADRs can be helpful in this context, and thus, it has been intensely studied. Recent works achieved promising results using machine learning. The presented work focuses on machine learning methods that use drug profiles for making predictions and use features from multiple data sources. We argue that despite promising results, existing works have limitations, especially regarding flexibility in experimenting with different data sets and/or predictive models. We suggest to address these limitations by generalization of the key principles used by the state of the art. Namely, we explore effects of: (1) using knowledge graphs-machine-readable interlinked representations of biomedical knowledge-as a convenient uniform representation of heterogeneous data; and (2) casting ADR prediction as a multi-label ranking problem. We present a specific way of using knowledge graphs to generate different feature sets and demonstrate favourable performance of selected off-the-shelf multi-label learning models in comparison with existing works. Our experiments suggest better suitability of certain multi-label learning methods for applications where ranking is preferred. The presented approach can be easily extended to other feature sources or machine learning methods, making it flexible for experiments tuned toward specific requirements of end users. Our work also provides a clearly defined and reproducible baseline for any future related experiments.

Abstract. Learning embeddings of entities and relations using neural architectures is an effective method of performing statistical learning on large-scale relational data, such as knowledge graphs. In this paper, we consider the problem of regularizing the training of neural knowledge graph embeddings by leveraging external background knowledge. We propose a principled and scalable method for leveraging equivalence and inversion axioms during the learning process, by imposing a set of modeldependent soft constraints on the predicate embeddings. The method has several advantages: i) the number of introduced constraints does not depend on the number of entities in the knowledge base; ii) regularities in the embedding space effectively reflect available background knowledge; iii) it yields more accurate results in link prediction tasks over non-regularized methods; and iv) it can be adapted to a variety of models, without affecting their scalability properties. We demonstrate the effectiveness of the proposed method on several large knowledge graphs. Our evaluation shows that it consistently improves the predictive accuracy of several neural knowledge graph embedding models (for instance, the MRR of TransE on WordNet increases by 11%) without compromising their scalability properties.

The tables embedded in Wikipedia articles contain rich, semi-structured encyclopaedic content. However, the cumulative content of these tables cannot be queried against. We thus propose methods to recover the semantics of Wikipedia tables and, in particular, to extract facts from them in the form of RDF triples. Our core method uses an existing Linked Data knowledge-base to find pre-existing relations between entities in Wikipedia tables, suggesting the same relations as holding for other entities in analogous columns on different rows. We find that such an approach extracts RDF triples from Wikipedia's tables at a raw precision of 40%. To improve the raw precision, we define a set of features for extracted triples that are tracked during the extraction phase. Using a manually labelled gold standard, we then test a variety of machine learning methods for classifying correct/incorrect triples. One such method extracts 7.9 million unique and novel RDF triples from over one million Wikipedia tables at an estimated precision of 81.5%.

Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is time-consuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model. It uses statistical relational learning on top of phosphorylation networks interpreted as knowledge graphs, a simple yet robust model for representing networked knowledge. Compared to a representative selection of six existing systems, our model has the highest kinome coverage and produces biologically valid high-confidence predictions not possible with the other tools. Specifically, we have experimentally validated predictions of previously unknown phosphorylations by the LATS1, AKT1, PKA and MST2 kinases in human. Thus, our tool is useful for focusing phosphoproteomic experiments, and facilitates the discovery of new phosphorylation reactions. Our model can be accessed publicly via an easy-to-use web interface (LinkPhinder).

Knowledge graph embedding (KGE) models have become popular means for making discoveries in knowledge graphs (e.g., RDF graphs) in an efficient and scalable manner. The key to success of these models is their ability to learn low-rank vector representations for knowledge graph entities and relations. Despite the rapid development of KGE models, state-of-the-art approaches have mostly focused on new ways to represent embeddings interaction functions (i.e., scoring functions). In this paper, we argue that the choice of other training components such as the loss function, hyperparameters and negative sampling strategies can also have substantial impact on the model efficiency. This area has been rather neglected by previous works so far and our contribution is towards closing this gap by a thorough analysis of possible choices of training loss functions, hyperparameters and negative sampling techniques. We finally investigate the effects of specific choices on the scalability and accuracy of knowledge graph embedding models.

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Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is time-consuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model. It uses statistical relational learning on top of phosphorylation networks interpreted as knowledge graphs, a simple yet robust model for representing networked knowledge. Compared to a representative selection of six existing systems, our model has the highest kinome coverage and produces biologically valid highconfidence predictions not possible with the other tools. Specifically, we have experimentally validated predictions of previously unknown phosphorylations by the LATS1, AKT1, PKA and MST2 kinases in human. Thus, our tool is useful for focusing phosphoproteomic experiments, and facilitates the discovery of new phosphorylation reactions.Our model can be accessed publicly via an easy-to-use web interface (LinkPhinder).

Abstract. Cardinality is an important structural aspect of data that has not received enough attention in the context of RDF knowledge bases (KBs). Information about cardinalities can be useful for data users and knowledge engineers when writing queries, reusing or engineering KBs. Such cardinalities can be declared using OWL and RDF constraint languages as constraints on the usage of properties over instance data. However, their declaration is optional and consistency with the instance data is not ensured. In this paper, we address the problem of mining cardinality bounds for properties to discover structural characteristics of KBs, and use these bounds to assess completeness. Because KBs are incomplete and error-prone, we apply statistical methods for filtering property usage and for finding accurate and robust patterns. Accuracy of the cardinality patterns is ensured by properly handling equality axioms (owl:sameAs); and robustness by filtering outliers. We report an implementation of our algorithm with two variants using SPARQL 1.1 and Apache Spark, and their evaluation on real-world and synthetic data.