Interaction Network Analysis Using Semantic Similarity Based on Translation Embeddings

Biomedical knowledge graphs such as STITCH, SIDER, and Drugbank provide the basis for the discovery of associations between biomedical entities, e.g., interactions between drugs and targets. Link prediction is a paramount task and represents a building block for supporting knowledge discovery. Although several approaches have been proposed for effectively predicting links, the role of semantics has not been studied in depth. In this work, we tackle the problem of discovering interactions between drugs and targets, and propose SimTransE, a machine learning-based approach that solves this problem effectively. SimTransE relies on translating embeddings to model drug-target interactions and values of similarity across them. Grounded on the vectorial representation of drug-target interactions, SimTransE is able to discover novel drug-target interactions. We empirically study SimTransE using state-of-the-art benchmarks and approaches. Experimental results suggest that SimTransE is competitive with the state of the art, representing, thus, an effective alternative for knowledge discovery in the biomedical domain

Context-Based Entity Matching for Big Data

In the Big Data era, where variety is the most dominant dimension, the RDF data model enables the creation and integration of actionable knowledge from heterogeneous data sources. However, the RDF data model allows for describing entities under various contexts, e.g., people can be described from its demographic context, but as well from their professional contexts. Context-aware description poses challenges during entity matching of RDF datasets—the match might not be valid in every context. To perform a contextually relevant entity matching, the specific context under which a data-driven task, e.g., data integration is performed, must be taken into account. However, existing approaches only consider inter-schema and properties mapping of different data sources and prevent users from selecting contexts and conditions during a data integration process. We devise COMET, an entity matching technique that relies on both the knowledge stated in RDF vocabularies and a context-based similarity metric to map contextually equivalent RDF graphs. COMET follows a two-fold approach to solve the problem of entity matching in RDF graphs in a context-aware manner. In the first step, COMET computes the similarity measures across RDF entities and resorts to the Formal Concept Analysis algorithm to map contextually equivalent RDF entities. Finally, COMET combines the results of the first step and executes a 1-1 perfect matching algorithm for matching RDF entities based on the combined scores. We empirically evaluate the performance of COMET on testbed from DBpedia. The experimental results suggest that COMET accurately matches equivalent RDF graphs in a context-dependent manner

Formal Concept Analysis for Semantic Compression of Knowledge Graph Versions

International audienceRecent years have witnessed the increase of openly available knowledge graphs online. These graphs are often structured according to the W3C semantic web standard RDF. With this availability of information comes the challenge of coping with dataset versions as information may change in time and therefore deprecates the former knowledge graph. Several solutions have been proposed to deal with data versioning, mainly based on computing data deltas and having an incremental approach to keep track of the version history. In this article, we describe a novel method that relies on aggregating graph versions to obtain one single complete graph. Our solution semantically compresses similar and common edges together to obtain a final graph smaller than the sum of the distinct versioned ones. Technically, our method takes advantage of FCA to match graph elements together. We also describe how this compressed graph can be queried without being unzipped, using standard methods

SDM-RDFizer: An RML Interpreter for the Efficient Creation of RDF Knowledge Graphs

In recent years, the amount of data has increased exponentially, and knowledge graphs have gained attention as data structures to integrate data and knowledge harvested from myriad data sources. However, data complexity issues like large volume, high-duplicate rate, and heterogeneity usually characterize these data sources, being required data management tools able to address the negative impact of these issues on the knowledge graph creation process. In this paper, we propose the SDM-RDFizer, an interpreter of the RDF Mapping Language (RML), to transform raw data in various formats into an RDF knowledge graph. SDM-RDFizer implements novel algorithms to execute the logical operators between mappings in RML, allowing thus to scale up to complex scenarios where data is not only broad but has a high-duplication rate. We empirically evaluate the SDM-RDFizer performance against diverse testbeds with diverse configurations of data volume, duplicates, and heterogeneity. The observed results indicate that SDM-RDFizer is two orders of magnitude faster than state of the art, thus, meaning that SDM-RDFizer an interoperable and scalable solution for knowledge graph creation. SDM-RDFizer is publicly available as a resource through a Github repository and a DOI

Interaction Network Analysis Using Semantic Similarity Based on Translation Embeddings

Biomedical knowledge graphs such as STITCH, SIDER, and Drugbank provide the basis for the discovery of associations between biomedical entities, e.g., interactions between drugs and targets. Link prediction is a paramount task and represents a building block for supporting knowledge discovery. Although several approaches have been proposed for effectively predicting links, the role of semantics has not been studied in depth. In this work, we tackle the problem of discovering interactions between drugs and targets, and propose SimTransE, a machine learning-based approach that solves this problem effectively. SimTransE relies on translating embeddings to model drug-target interactions and values of similarity across them. Grounded on the vectorial representation of drug-target interactions, SimTransE is able to discover novel drug-target interactions. We empirically study SimTransE using state-of-the-art benchmarks and approaches. Experimental results suggest that SimTransE is competitive with the state of the art, representing, thus, an effective alternative for knowledge discovery in the biomedical domain

Interaction Network Analysis Using Semantic Similarity Based on Translation Embeddings

Biomedical knowledge graphs such as STITCH, SIDER, and Drugbank provide the basis for the discovery of associations between biomedical entities, e.g., interactions between drugs and targets. Link prediction is a paramount task and represents a building block for supporting knowledge discovery. Although several approaches have been proposed for effectively predicting links, the role of semantics has not been studied in depth. In this work, we tackle the problem of discovering interactions between drugs and targets, and propose SimTransE, a machine learning-based approach that solves this problem effectively. SimTransE relies on translating embeddings to model drug-target interactions and values of similarity across them. Grounded on the vectorial representation of drug-target interactions, SimTransE is able to discover novel drug-target interactions. We empirically study SimTransE using state-of-the-art benchmarks and approaches. Experimental results suggest that SimTransE is competitive with the state of the art, representing, thus, an effective alternative for knowledge discovery in the biomedical domain

Embedding Knowledge Graphs Attentive to Positional and Centrality Qualities

International audienceKnowledge graphs embeddings (KGE) are lately at the center of many artificial intelligence studies due to their applicability for solving downstream tasks, including link prediction and node classification. However, most Knowledge Graph embedding models encode, into the vector space, only the local graph structure of an entity, i.e., information of the 1-hop neighborhood. Capturing not only local graph structure but global features of entities are crucial for prediction tasks on Knowledge Graphs. This work proposes a novel KGE method named Graph Feature Attentive Neural Network (GFA-NN) that computes graphical features of entities. As a consequence, the resulting embeddings are attentive to two types of global network features. First, nodes’ relative centrality is based on the observation that some of the entities are more “prominent” than the others. Second, the relative position of entities in the graph. GFA-NN computes several centrality values per entity, generates a random set of reference nodes’ entities, and computes a given entity’s shortest path to each entity in the reference set. It then learns this information through optimization of objectives specified on each of these features. We investigate GFA-NN on several link prediction benchmarks in the inductive and transductive setting and show that GFA-NN achieves on-par or better results than state-of-the-art KGE solutions

Spatial concept learning and inference on geospatial polygon data

Geospatial knowledge has always been an essential driver for many societal aspects. This concerns in particular urban planning and urban growth management. To gain insights from geospatial data and guide decisions usually authoritative and open data sources are used, combined with user or citizen sensing data. However, we see a great potential for improving geospatial analytics by combining geospatial data with the rich terminological knowledge, e.g., provided by the Linked Open Data Cloud. Having semantically explicit, integrated geospatial and terminological knowledge, expressed by means of established vocabularies and ontologies, cross-domain spatial analytics can be performed. One analytics technique working on terminological knowledge is inductive concept learning, an approach that learns classifiers expressed as logical concept descriptions. In this paper, we extend inductive concept learning to infer and make use of the spatial context of entities in spatio-terminological data. We propose a formalism for extracting and making spatial relations explicit such that they can be exploited to learn spatial concept descriptions, enabling ‘spatially aware’ concept learning. We further provide an implementation of this formalism and demonstrate its capabilities in different evaluation scenarios