With the increasing speed of technological advancements, the pharmaceutical and healthcare industry needs to break up departmental data silos with Knowledge Graphs and AI to understand the value of their data. At PhUSE EU Connect 2018 we will introduce the innovative approach of PoolParty Semantic Suite to make the most out of your data with semantic data integration. Our partner Findwise, global experts in search-driven solutions for the pharmaceutical and healthcare industry, presents a series of four blog posts to help you understand how knowledge graphs and AI can leverage your data-driven innovation and improve healthcare outcome. We face grand societal challenges pinned down in the 17 UN sustainability goals and specifically number 3 Good Health and Well-being. Humans live a longer life, which shifts the population pyramid.

In our previous post of this blog post series about knowledge graphs and AI in the pharmaceutical and healthcare industry, you got an overview of the challenges knowledge-intensive organizations face to be able to support data-driven innovation and improve healthcare outcome. In this blog post, you will learn by the hand of a use case about how connecting your siloed departmental data with external authoritative resources will leverage the value of your content assets. Visit us at PhUSE EU Connect 2018, where we will introduce the innovative approach of PoolParty Semantic Suite to make the most out of your data with semantic data integration. Stay tuned for upcoming blog posts that will help you understand how knowledge graphs and AI can leverage your organization. Our partner Findwise, global experts in search-driven solutions for the pharmaceutical and healthcare industry, are bringing all their expertise in information management and knowledge engineering into this blog post series. A smart semantic information engine will connect a variety of information systems relevant within the pharmaceutical and healthcare industry.

This paper introduces TakeFive, a new semantic role labeling method that transforms a text into a frame-oriented knowledge graph. It performs dependency parsing, identifies the words that evoke lexical frames, locates the roles and fillers for each frame, runs coercion techniques, and formalises the results as a knowledge graph. This formal representation complies with the frame semantics used in Framester, a factual-linguistic linked data resource. The obtained precision, recall and F1 values indicate that TakeFive is competitive with other existing methods such as SEMAFOR, Pikes, PathLSTM and FRED. We finally discuss how to combine TakeFive and FRED, obtaining higher values of precision, recall and F1. Keywords: Semantic Role Labeling, Frame Semantics, Framester, Dependency Parsing, Role Oriented Knowledge Graphs 1. Introduction Most knowledge in linked data and knowledge graphs is of a relational nature: people participating in events, products having prices, artifacts with parts, works of art produced by artists, beers sold at a bar, etc. For that reason, a good part of integration and interoperability ends up consisting in aligning relations among heterogeneous schemas and data. This limit makes interoperability difficult.

Knowledge graph embedding aims at modeling entities and relations with low-dimensional vectors. Most previous methods require that all entities should be seen during training, which is unpractical for real-world knowledge graphs with new entities emerging on a daily basis. Recent efforts on this issue suggest training a neighborhood aggregator in conjunction with the conventional entity and relation embeddings, which may help embed new entities inductively via their existing neighbors. However, their neighborhood aggregators neglect the unordered and unequal natures of an entity's neighbors. To this end, we summarize the desired properties that may lead to effective neighborhood aggregators. We also introduce a novel aggregator, namely, Logic Attention Network (LAN), which addresses the properties by aggregating neighbors with both rules- and network-based attention weights. By comparing with conventional aggregators on two knowledge graph completion tasks, we experimentally validate LAN's superiority in terms of the desired properties.

In this paper, we conduct an empirical investigation of neural query graph ranking approaches for the task of complex question answering over knowledge graphs. We experiment with six different ranking models and propose a novel self-attention based slot matching model which exploits the inherent structure of query graphs, our logical form of choice. Our proposed model generally outperforms the other models on two QA datasets over the DBpedia knowledge graph, evaluated in different settings. In addition, we show that transfer learning from the larger of those QA datasets to the smaller dataset yields substantial improvements, effectively offsetting the general lack of training data.

Many knowledge graph embedding methods operate on triples and are therefore implicitly limited by a very local view of the entire knowledge graph. We present a new framework MOHONE to effectively model higher order network effects in knowledge-graphs, thus enabling one to capture varying degrees of network connectivity (from the local to the global). Our framework is generic, explicitly models the network scale, and captures two different aspects of similarity in networks: (a) shared local neighborhood and (b) structural role-based similarity. First, we introduce methods that learn network representations of entities in the knowledge graph capturing these varied aspects of similarity. We then propose a fast, efficient method to incorporate the information captured by these network representations into existing knowledge graph embeddings. We show that our method consistently and significantly improves the performance on link prediction of several different knowledge-graph embedding methods including TRANSE, TRANSD, DISTMULT, and COMPLEX(by at least 4 points or 17% in some cases).

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%).

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 neutral 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.

Knowledge graphs contain knowledge about the world and provide a structured representation of this knowledge. Current knowledge graphs contain only a small subset of what is true in the world. Link prediction approaches aim at predicting new links for a knowledge graph given the existing links among the entities. Tensor factorization approaches have proved promising for such link prediction problems. Proposed in 1927, Canonical Polyadic (CP) decomposition is among the first tensor factorization approaches. CP generally performs poorly for link prediction as it learns two independent embedding vectors for each entity, whereas they are really tied. We present a simple enhancement of CP (which we call SimplE) to allow the two embeddings of each entity to be learned dependently. The complexity of SimplE grows linearly with the size of embeddings. The embeddings learned through SimplE are interpretable, and certain types of background knowledge 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. SimplE's code is available on GitHub at https://github.com/Mehran-k/SimplE.

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.