Interactive multidimensional modeling of linked data for exploratory OLAP

Exploratory OLAP aims at coupling the precision and detail of corporate data with the information wealth of LOD. While some techniques to create, publish, and query RDF cubes are already available, little has been said about how to contextualize these cubes with situational data in an on-demand fashion. In this paper we describe an approach, called iMOLD, that enables non-technical users to enrich an RDF cube with multidimensional knowledge by discovering aggregation hierarchies in LOD. This is done through a user-guided process that recognizes in the LOD the recurring modeling patterns that express roll-up relationships between RDF concepts, then translates these patterns into aggregation hierarchies to enrich the RDF cube. Two families of aggregation patterns are identified, based on associations and generalization respectively, and the algorithms for recognizing them are described. To evaluate iMOLD in terms of efficiency and effectiveness we compare it with a related approach in the literature, we propose a case study based on DBpedia, and we discuss the results of a test made with real users.Peer ReviewedPostprint (author's final draft

Interactive Multidimensional Modeling of Linked Data for Exploratory OLAP

Exploratory OLAP aims at coupling the precision and detail of corporate data with the information wealth of LOD. While some techniques to create, publish, and query RDF cubes are already available, little has been said about how to contextualize these cubes with situational data in an on-demand fashion. In this paper we describe an approach, called iMOLD, that enables non-technical users to enrich an RDF cube with multidimensional knowledge by discovering aggregation hierarchies in LOD. This is done through a user-guided process that recognizes in the LOD the recurring modeling patterns that express roll- up relationships between RDF concepts, then translates these patterns into aggregation hierarchies to enrich the RDF cube. Two families of aggregation patterns are identified, based on associations and generalization respectively, and the algorithms for recognizing them are described. To evaluate iMOLD in terms of efficiency and effectiveness we compare it with a related approach in the literature, we propose a case study based on DBpedia, and we discuss the results of a test made with real users

Functional inferences over heterogeneous data

Inference enables an agent to create new knowledge from old or discover implicit relationships between concepts in a knowledge base (KB), provided that appropriate techniques are employed to deal with ambiguous, incomplete and sometimes erroneous data. The ever-increasing volumes of KBs on the web, available for use by automated systems, present an opportunity to leverage the available knowledge in order to improve the inference process in automated query answering systems. This thesis focuses on the FRANK (Functional Reasoning for Acquiring Novel Knowledge) framework that responds to queries where no suitable answer is readily contained in any available data source, using a variety of inference operations. Most question answering and information retrieval systems assume that answers to queries are stored in some form in the KB, thereby limiting the range of answers they can find. We take an approach motivated by rich forms of inference using techniques, such as regression, for prediction. For instance, FRANK can answer “what country in Europe will have the largest population in 2021?" by decomposing Europe geo-spatially, using regression on country population for past years and selecting the country with the largest predicted value. Our technique, which we refer to as Rich Inference, combines heuristics, logic and statistical methods to infer novel answers to queries. It also determines what facts are needed for inference, searches for them, and then integrates the diverse facts and their formalisms into a local query-specific inference tree. Our primary contribution in this thesis is the inference algorithm on which FRANK works. This includes (1) the process of recursively decomposing queries in way that allows variables in the query to be instantiated by facts in KBs; (2) the use of aggregate functions to perform arithmetic and statistical operations (e.g. prediction) to infer new values from child nodes; and (3) the estimation and propagation of uncertainty values into the returned answer based on errors introduced by noise in the KBs or errors introduced by aggregate functions. We also discuss many of the core concepts and modules that constitute FRANK. We explain the internal “alist” representation of FRANK that gives it the required flexibility to tackle different kinds of problems with minimal changes to its internal representation. We discuss the grammar for a simple query language that allows users to express queries in a formal way, such that we avoid the complexities of natural language queries, a problem that falls outside the scope of this thesis. We evaluate the framework with datasets from open sources

A BIM - GIS Integrated Information Model Using Semantic Web and RDF Graph Databases

In recent years, 3D virtual indoor and outdoor urban modelling has become an essential geospatial information framework for civil and engineering applications such as emergency response, evacuation planning, and facility management. Building multi-sourced and multi-scale 3D urban models are in high demand among architects, engineers, and construction professionals to achieve these tasks and provide relevant information to decision support systems. Spatial modelling technologies such as Building Information Modelling (BIM) and Geographical Information Systems (GIS) are frequently used to meet such high demands. However, sharing data and information between these two domains is still challenging. At the same time, the semantic or syntactic strategies for inter-communication between BIM and GIS do not fully provide rich semantic and geometric information exchange of BIM into GIS or vice-versa. This research study proposes a novel approach for integrating BIM and GIS using semantic web technologies and Resources Description Framework (RDF) graph databases. The suggested solution's originality and novelty come from combining the advantages of integrating BIM and GIS models into a semantically unified data model using a semantic framework and ontology engineering approaches. The new model will be named Integrated Geospatial Information Model (IGIM). It is constructed through three stages. The first stage requires BIMRDF and GISRDF graphs generation from BIM and GIS datasets. Then graph integration from BIM and GIS semantic models creates IGIMRDF. Lastly, the information from IGIMRDF unified graph is filtered using a graph query language and graph data analytics tools. The linkage between BIMRDF and GISRDF is completed through SPARQL endpoints defined by queries using elements and entity classes with similar or complementary information from properties, relationships, and geometries from an ontology-matching process during model construction. The resulting model (or sub-model) can be managed in a graph database system and used in the backend as a data-tier serving web services feeding a front-tier domain-oriented application. A case study was designed, developed, and tested using the semantic integrated information model for validating the newly proposed solution, architecture, and performance

Federated knowledge base debugging in DL-Lite A

Due to the continuously growing amount of data the federation of different and distributed data sources gained increasing attention. In order to tackle the challenge of federating heterogeneous sources a variety of approaches has been proposed. Especially in the context of the Semantic Web the application of Description Logics is one of the preferred methods to model federated knowledge based on a well-defined syntax and semantics. However, the more data are available from heterogeneous sources, the higher the risk is of inconsistency – a serious obstacle for performing reasoning tasks and query answering over a federated knowledge base. Given a single knowledge base the process of knowledge base debugging comprising the identification and resolution of conflicting statements have been widely studied while the consideration of federated settings integrating a network of loosely coupled data sources (such as LOD sources) has mostly been neglected. In this thesis we tackle the challenging problem of debugging federated knowledge bases and focus on a lightweight Description Logic language, called DL-LiteA, that is aimed at applications requiring efficient and scalable reasoning. After introducing formal foundations such as Description Logics and Semantic Web technologies we clarify the motivating context of this work and discuss the general problem of information integration based on Description Logics. The main part of this thesis is subdivided into three subjects. First, we discuss the specific characteristics of federated knowledge bases and provide an appropriate approach for detecting and explaining contradictive statements in a federated DL-LiteA knowledge base. Second, we study the representation of the identified conflicts and their relationships as a conflict graph and propose an approach for repair generation based on majority voting and statistical evidences. Third, in order to provide an alternative way for handling inconsistency in federated DL-LiteA knowledge bases we propose an automated approach for assessing adequate trust values (i.e., probabilities) at different levels of granularity by leveraging probabilistic inference over a graphical model. In the last part of this thesis, we evaluate the previously developed algorithms against a set of large distributed LOD sources. In the course of discussing the experimental results, it turns out that the proposed approaches are sufficient, efficient and scalable with respect to real-world scenarios. Moreover, due to the exploitation of the federated structure in our algorithms it further becomes apparent that the number of identified wrong statements, the quality of the generated repair as well as the fineness of the assessed trust values profit from an increasing number of integrated sources

Towards Data Sharing across Decentralized and Federated IoT Data Analytics Platforms

In the past decade the Internet-of-Things concept has overwhelmingly entered all of the fields where data are produced and processed, thus, resulting in a plethora of IoT platforms, typically cloud-based, that centralize data and services management. In this scenario, the development of IoT services in domains such as smart cities, smart industry, e-health, automotive, are possible only for the owner of the IoT deployments or for ad-hoc business one-to-one collaboration agreements. The realization of "smarter" IoT services or even services that are not viable today envisions a complete data sharing with the usage of multiple data sources from multiple parties and the interconnection with other IoT services. In this context, this work studies several aspects of data sharing focusing on Internet-of-Things. We work towards the hyperconnection of IoT services to analyze data that goes beyond the boundaries of a single IoT system. This thesis presents a data analytics platform that: i) treats data analytics processes as services and decouples their management from the data analytics development; ii) decentralizes the data management and the execution of data analytics services between fog, edge and cloud; iii) federates peers of data analytics platforms managed by multiple parties allowing the design to scale into federation of federations; iv) encompasses intelligent handling of security and data usage control across the federation of decentralized platforms instances to reduce data and service management complexity. The proposed solution is experimentally evaluated in terms of performances and validated against use cases. Further, this work adopts and extends available standards and open sources, after an analysis of their capabilities, fostering an easier acceptance of the proposed framework. We also report efforts to initiate an IoT services ecosystem among 27 cities in Europe and Korea based on a novel methodology. We believe that this thesis open a viable path towards a hyperconnection of IoT data and services, minimizing the human effort to manage it, but leaving the full control of the data and service management to the users' will

Systems approaches to drug repositioning

PhD ThesisDrug discovery has overall become less fruitful and more costly, despite vastly increased biomedical knowledge and evolving approaches to Research and Development (R&D). One complementary approach to drug discovery is that of drug repositioning which focusses on identifying novel uses for existing drugs. By focussing on existing drugs that have already reached the market, drug repositioning has the potential to both reduce the timeframe and cost of getting a disease treatment to those that need it. Many marketed examples of repositioned drugs have been found via serendipitous or rational observations, highlighting the need for more systematic methodologies. Systems approaches have the potential to enable the development of novel methods to understand the action of therapeutic compounds, but require an integrative approach to biological data. Integrated networks can facilitate systems-level analyses by combining multiple sources of evidence to provide a rich description of drugs, their targets and their interactions. Classically, such networks can be mined manually where a skilled person can identify portions of the graph that are indicative of relationships between drugs and highlight possible repositioning opportunities. However, this approach is not scalable. Automated procedures are required to mine integrated networks systematically for these subgraphs and bring them to the attention of the user. The aim of this project was the development of novel computational methods to identify new therapeutic uses for existing drugs (with particular focus on active small molecules) using data integration. A framework for integrating disparate data relevant to drug repositioning, Drug Repositioning Network Integration Framework (DReNInF) was developed as part of this work. This framework includes a high-level ontology, Drug Repositioning Network Integration Ontology (DReNInO), to aid integration and subsequent mining; a suite of parsers; and a generic semantic graph integration platform. This framework enables the production of integrated networks maintaining strict semantics that are important in, but not exclusive to, drug repositioning. The DReNInF is then used to create Drug Repositioning Network Integration (DReNIn), a semantically-rich Resource Description Framework (RDF) dataset. A Web-based front end was developed, which includes a SPARQL Protocol and RDF Query Language (SPARQL) endpoint for querying this dataset. To automate the mining of drug repositioning datasets, a formal framework for the definition of semantic subgraphs was established and a method for Drug Repositioning Semantic Mining (DReSMin) was developed. DReSMin is an algorithm for mining semantically-rich networks for occurrences of a given semantic subgraph. This algorithm allows instances of complex semantic subgraphs that contain data about putative drug repositioning opportunities to be identified in a computationally tractable fashion, scaling close to linearly with network data. The ability of DReSMin to identify novel Drug-Target (D-T) associations was investigated. 9,643,061 putative D-T interactions were identified and ranked, with a strong correlation between highly scored associations and those supported by literature observed. The 20 top ranked associations were analysed in more detail with 14 found to be novel and six found to be supported by the literature. It was also shown that this approach better prioritises known D-T interactions, than other state-of-the-art methodologies. The ability of DReSMin to identify novel Drug-Disease (Dr-D) indications was also investigated. As target-based approaches are utilised heavily in the field of drug discovery, it is necessary to have a systematic method to rank Gene-Disease (G-D) associations. Although methods already exist to collect, integrate and score these associations, these scores are often not a reliable re flection of expert knowledge. Therefore, an integrated data-driven approach to drug repositioning was developed using a Bayesian statistics approach and applied to rank 309,885 G-D associations using existing knowledge. Ranked associations were then integrated with other biological data to produce a semantically-rich drug discovery network. Using this network it was shown that diseases of the central nervous system (CNS) provide an area of interest. The network was then systematically mined for semantic subgraphs that capture novel Dr-D relations. 275,934 Dr-D associations were identified and ranked, with those more likely to be side-effects filtered. Work presented here includes novel tools and algorithms to enable research within the field of drug repositioning. DReNIn, for example, includes data that previous comparable datasets relevant to drug repositioning have neglected, such as clinical trial data and drug indications. Furthermore, the dataset may be easily extended using DReNInF to include future data as and when it becomes available, such as G-D association directionality (i.e. is the mutation a loss-of-function or gain-of-function). Unlike other algorithms and approaches developed for drug repositioning, DReSMin can be used to infer any types of associations captured in the target semantic network. Moreover, the approaches presented here should be more generically applicable to other fields that require algorithms for the integration and mining of semantically rich networks.European and Physical Sciences Research Council (EPSRC) and GS

Supporting Explainable AI on Semantic Constraint Validation

There is a rising number of knowledge graphs available published through various sources. The enormous amount of linked data strives to give entities a semantic context. Using SHACL, the entities can be validated with respect to their context. On the other hand, an increasing usage of AI models in productive systems comes with a great responsibility in various areas. Predictive models like linear, logistic regression, and tree-based models, are still frequently used as they come with a simple structure, which allows for interpretability. However, explaining models includes verifying whether the model makes predictions based on human constraints or scientific facts. This work proposes to use the semantic context of the entities in knowledge graphs to validate predictive models with respect to user-defined constraints; therefore, providing a theoretical framework for a model-agnostic validation engine based on SHACL. In a second step, the model validation results are summarized in the case of a decision tree and visualized model-coherently. Finally, the performance of the framework is evaluated based on a Python implementation

Report on shape analysis and matching and on semantic matching

In GRAVITATE, two disparate specialities will come together in one working platform for the archaeologist: the fields of shape analysis, and of metadata search. These fields are relatively disjoint at the moment, and the research and development challenge of GRAVITATE is precisely to merge them for our chosen tasks. As shown in chapter 7 the small amount of literature that already attempts join 3D geometry and semantics is not related to the cultural heritage domain. Therefore, after the project is done, there should be a clear ‘before-GRAVITATE’ and ‘after-GRAVITATE’ split in how these two aspects of a cultural heritage artefact are treated.This state of the art report (SOTA) is ‘before-GRAVITATE’. Shape analysis and metadata description are described separately, as currently in the literature and we end the report with common recommendations in chapter 8 on possible or plausible cross-connections that suggest themselves. These considerations will be refined for the Roadmap for Research deliverable.Within the project, a jargon is developing in which ‘geometry’ stands for the physical properties of an artefact (not only its shape, but also its colour and material) and ‘metadata’ is used as a general shorthand for the semantic description of the provenance, location, ownership, classification, use etc. of the artefact. As we proceed in the project, we will find a need to refine those broad divisions, and find intermediate classes (such as a semantic description of certain colour patterns), but for now the terminology is convenient – not least because it highlights the interesting area where both aspects meet.On the ‘geometry’ side, the GRAVITATE partners are UVA, Technion, CNR/IMATI; on the metadata side, IT Innovation, British Museum and Cyprus Institute; the latter two of course also playing the role of internal users, and representatives of the Cultural Heritage (CH) data and target user’s group. CNR/IMATI’s experience in shape analysis and similarity will be an important bridge between the two worlds for geometry and metadata. The authorship and styles of this SOTA reflect these specialisms: the first part (chapters 3 and 4) purely by the geometry partners (mostly IMATI and UVA), the second part (chapters 5 and 6) by the metadata partners, especially IT Innovation while the joint overview on 3D geometry and semantics is mainly by IT Innovation and IMATI. The common section on Perspectives was written with the contribution of all

Scalable Quality Assessment of Linked Data

In a world where the information economy is booming, poor data quality can lead to adverse consequences, including social and economical problems such as decrease in revenue. Furthermore, data-driven indus- tries are not just relying on their own (proprietary) data silos, but are also continuously aggregating data from different sources. This aggregation could then be re-distributed back to “data lakes”. However, this data (including Linked Data) is not necessarily checked for its quality prior to its use. Large volumes of data are being exchanged in a standard and interoperable format between organisations and published as Linked Data to facilitate their re-use. Some organisations, such as government institutions, take a step further and open their data. The Linked Open Data Cloud is a witness to this. However, similar to data in data lakes, it is challenging to determine the quality of this heterogeneous data, and subsequently to make this information explicit to data consumers. Despite the availability of a number of tools and frameworks to assess Linked Data quality, the current solutions do not aggregate a holistic approach that enables both the assessment of datasets and also provides consumers with quality results that can then be used to find, compare and rank datasets’ fitness for use. In this thesis we investigate methods to assess the quality of (possibly large) linked datasets with the intent that data consumers can then use the assessment results to find datasets that are fit for use, that is; finding the right dataset for the task at hand. Moreover, the benefits of quality assessment are two-fold: (1) data consumers do not need to blindly rely on subjective measures to choose a dataset, but base their choice on multiple factors such as the intrinsic structure of the dataset, therefore fostering trust and reputation between the publishers and consumers on more objective foundations; and (2) data publishers can be encouraged to improve their datasets so that they can be re-used more. Furthermore, our approach scales for large datasets. In this regard, we also look into improving the efficiency of quality metrics using various approximation techniques. However the trade-off is that consumers will not get the exact quality value, but a very close estimate which anyway provides the required guidance towards fitness for use. The central point of this thesis is not on data quality improvement, nonetheless, we still need to understand what data quality means to the consumers who are searching for potential datasets. This thesis looks into the challenges faced to detect quality problems in linked datasets presenting quality results in a standardised machine-readable and interoperable format for which agents can make sense out of to help human consumers identifying the fitness for use dataset. Our proposed approach is more consumer-centric where it looks into (1) making the assessment of quality as easy as possible, that is, allowing stakeholders, possibly non-experts, to identify and easily define quality metrics and to initiate the assessment; and (2) making results (quality metadata and quality reports) easy for stakeholders to understand, or at least interoperable with other systems to facilitate a possible data quality pipeline. Finally, our framework is used to assess the quality of a number of heterogeneous (large) linked datasets, where each assessment returns a quality metadata graph that can be consumed by agents as Linked Data. In turn, these agents can intelligently interpret a dataset’s quality with regard to multiple dimensions and observations, and thus provide further insight to consumers regarding its fitness for use