Graph BI & analytics: current state and future challenges

In an increasingly competitive market, making well-informed decisions requires the analysis of a wide range of heterogeneous, large and complex data. This paper focuses on the emerging field of graph warehousing. Graphs are widespread structures that yield a great expressive power. They are used for modeling highly complex and interconnected domains, and efficiently solving emerging big data application. This paper presents the current status and open challenges of graph BI and analytics, and motivates the need for new warehousing frameworks aware of the topological nature of graphs. We survey the topics of graph modeling, management, processing and analysis in graph warehouses. Then we conclude by discussing future research directions and positioning them within a unified architecture of a graph BI and analytics framework.Peer ReviewedPostprint (author's final draft

Cypher: An Evolving Query Language for Property Graphs

International audienceThe Cypher property graph query language is an evolving language, originally designed and implemented as part of the Neo4j graph database, and it is currently used by several commercial database products and researchers. We describe Cypher 9, which is the first version of the language governed by the openCypher Implementers Group. We first introduce the language by example, and describe its uses in industry. We then provide a formal semantic definition of the core read-query features of Cypher, including its variant of the property graph data model, and its " ASCII Art " graph pattern matching mechanism for expressing subgraphs of interest to an application. We compare the features of Cypher to other property graph query languages, and describe extensions, at an advanced stage of development, which will form part of Cypher 10, turning the language into a compositional language which supports graph projections and multiple named graphs

A Distributed Path Query Engine for Temporal Property Graphs

Property graphs are a common form of linked data, with path queries used to traverse and explore them for enterprise transactions and mining. Temporal property graphs are a recent variant where time is a first-class entity to be queried over, and their properties and structure vary over time. These are seen in social, telecom, transit and epidemic networks. However, current graph databases and query engines have limited support for temporal relations among graph entities, no support for time-varying entities and/or do not scale on distributed resources. We address this gap by extending a linear path query model over property graphs to include intuitive temporal predicates and aggregation operators over temporal graphs. We design a distributed execution model for these temporal path queries using the interval-centric computing model, and develop a novel cost model to select an efficient execution plan from several. We perform detailed experiments of our Granite distributed query engine using both static and dynamic temporal property graphs as large as 52M vertices, 218M edges and 325M properties, and a 1600-query workload, derived from the LDBC benchmark. We often offer sub-second query latencies on a commodity cluster, which is 149x-1140x faster compared to industry-leading Neo4J shared-memory graph database and the JanusGraph / Spark distributed graph query engine. Granite also completes 100% of the queries for all graphs, compared to only 32-92% workload completion by the baseline systems. Further, our cost model selects a query plan that is within 10% of the optimal execution time in 90% of the cases. Despite the irregular nature of graph processing, we exhibit a weak-scaling efficiency >= 60% on 8 nodes and >= 40% on 16 nodes, for most query workloads.Comment: An extended version of the paper that appears in IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 202

Scalable Data Integration for Linked Data

Linked Data describes an extensive set of structured but heterogeneous datasources where entities are connected by formal semantic descriptions. In thevision of the Semantic Web, these semantic links are extended towards theWorld Wide Web to provide as much machine-readable data as possible forsearch queries. The resulting connections allow an automatic evaluation to findnew insights into the data. Identifying these semantic connections betweentwo data sources with automatic approaches is called link discovery. We derivecommon requirements and a generic link discovery workflow based on similaritiesbetween entity properties and associated properties of ontology concepts. Mostof the existing link discovery approaches disregard the fact that in times ofBig Data, an increasing volume of data sources poses new demands on linkdiscovery. In particular, the problem of complex and time-consuming linkdetermination escalates with an increasing number of intersecting data sources.To overcome the restriction of pairwise linking of entities, holistic clusteringapproaches are needed to link equivalent entities of multiple data sources toconstruct integrated knowledge bases. In this context, the focus on efficiencyand scalability is essential. For example, reusing existing links or backgroundinformation can help to avoid redundant calculations. However, when dealingwith multiple data sources, additional data quality problems must also be dealtwith. This dissertation addresses these comprehensive challenges by designingholistic linking and clustering approaches that enable reuse of existing links.Unlike previous systems, we execute the complete data integration workflowvia a distributed processing system. At first, the LinkLion portal will beintroduced to provide existing links for new applications. These links act asa basis for a physical data integration process to create a unified representationfor equivalent entities from many data sources. We then propose a holisticclustering approach to form consolidated clusters for same real-world entitiesfrom many different sources. At the same time, we exploit the semantic typeof entities to improve the quality of the result. The process identifies errorsin existing links and can find numerous additional links. Additionally, theentity clustering has to react to the high dynamics of the data. In particular,this requires scalable approaches for continuously growing data sources withmany entities as well as additional new sources. Previous entity clusteringapproaches are mostly static, focusing on the one-time linking and clustering ofentities from few sources. Therefore, we propose and evaluate new approaches for incremental entity clustering that supports the continuous addition of newentities and data sources. To cope with the ever-increasing number of LinkedData sources, efficient and scalable methods based on distributed processingsystems are required. Thus we propose distributed holistic approaches to linkmany data sources based on a clustering of entities that represent the samereal-world object. The implementation is realized on Apache Flink. In contrastto previous approaches, we utilize efficiency-enhancing optimizations for bothdistributed static and dynamic clustering. An extensive comparative evaluationof the proposed approaches with various distributed clustering strategies showshigh effectiveness for datasets from multiple domains as well as scalability on amulti-machine Apache Flink cluster

Streamlining Temporal Formal Verification over Columnar Databases

Recent findings demonstrate how database technology enhances the computation of formal verification tasks expressible in linear time logic for finite traces (LTLf). Human-readable declarative languages also help the common practitioner to express temporal constraints in a straightforward and accessible language. Notwithstanding the former, this technology is in its infancy, and therefore, few optimization algorithms are known for dealing with massive amounts of information audited from real systems. We, therefore, present four novel algorithms subsuming entire LTLf expressions while outperforming previous state-of-the-art implementations on top of KnoBAB, thus postulating the need for the corresponding, leading to the formulation of novel xtLTLf-derived algebraic operators

Bench-Ranking: ettekirjutav analüüsimeetod suurte teadmiste graafide päringutele

Relatsiooniliste suurandmete (BD) töötlemisraamistike kasutamine suurte teadmiste graafide töötlemiseks kätkeb endas võimalust päringu jõudlust optimeerimida. Kaasaegsed BD-süsteemid on samas keerulised andmesüsteemid, mille konfiguratsioonid omavad olulist mõju jõudlusele. Erinevate raamistike ja konfiguratsioonide võrdlusuuringud pakuvad kogukonnale parimaid tavasid parema jõudluse saavutamiseks. Enamik neist võrdlusuuringutest saab liigitada siiski vaid kirjeldavaks ja diagnostiliseks analüütikaks. Lisaks puudub ühtne standard nende uuringute võrdlemiseks kvantitatiivselt järjestatud kujul. Veelgi enam, suurte graafide töötlemiseks vajalike konveierite kavandamine eeldab täiendavaid disainiotsuseid mis tulenevad mitteloomulikust (relatsioonilisest) graafi töötlemise paradigmast. Taolisi disainiotsuseid ei saa automaatselt langetada, nt relatsiooniskeemi, partitsioonitehnika ja salvestusvormingute valikut. Käesolevas töös käsitleme kuidas me antud uurimuslünga täidame. Esmalt näitame disainiotsuste kompromisside mõju BD-süsteemide jõudluse korratavusele suurte teadmiste graafide päringute tegemisel. Lisaks näitame BD-raamistike jõudluse kirjeldavate ja diagnostiliste analüüside piiranguid suurte graafide päringute tegemisel. Seejärel uurime, kuidas lubada ettekirjutavat analüütikat järjestamisfunktsioonide ja mitmemõõtmeliste optimeerimistehnikate (nn "Bench-Ranking") kaudu. See lähenemine peidab kirjeldava tulemusanalüüsi keerukuse, suunates praktiku otse teostatavate teadlike otsusteni.Leveraging relational Big Data (BD) processing frameworks to process large knowledge graphs yields a great interest in optimizing query performance. Modern BD systems are yet complicated data systems, where the configurations notably affect the performance. Benchmarking different frameworks and configurations provides the community with best practices for better performance. However, most of these benchmarking efforts are classified as descriptive and diagnostic analytics. Moreover, there is no standard for comparing these benchmarks based on quantitative ranking techniques. Moreover, designing mature pipelines for processing big graphs entails considering additional design decisions that emerge with the non-native (relational) graph processing paradigm. Those design decisions cannot be decided automatically, e.g., the choice of the relational schema, partitioning technique, and storage formats. Thus, in this thesis, we discuss how our work fills this timely research gap. Particularly, we first show the impact of those design decisions’ trade-offs on the BD systems’ performance replicability when querying large knowledge graphs. Moreover, we showed the limitations of the descriptive and diagnostic analyses of BD frameworks’ performance for querying large graphs. Thus, we investigate how to enable prescriptive analytics via ranking functions and Multi-Dimensional optimization techniques (called ”Bench-Ranking”). This approach abstracts out from the complexity of descriptive performance analysis, guiding the practitioner directly to actionable informed decisions.https://www.ester.ee/record=b553332

Advanced Methods for Entity Linking in the Life Sciences

The amount of knowledge increases rapidly due to the increasing number of available data sources. However, the autonomy of data sources and the resulting heterogeneity prevent comprehensive data analysis and applications. Data integration aims to overcome heterogeneity by unifying different data sources and enriching unstructured data. The enrichment of data consists of different subtasks, amongst other the annotation process. The annotation process links document phrases to terms of a standardized vocabulary. Annotated documents enable effective retrieval methods, comparability of different documents, and comprehensive data analysis, such as finding adversarial drug effects based on patient data. A vocabulary allows the comparability using standardized terms. An ontology can also represent a vocabulary, whereas concepts, relationships, and logical constraints additionally define an ontology. The annotation process is applicable in different domains. Nevertheless, there is a difference between generic and specialized domains according to the annotation process. This thesis emphasizes the differences between the domains and addresses the identified challenges. The majority of annotation approaches focuses on the evaluation of general domains, such as Wikipedia. This thesis evaluates the developed annotation approaches with case report forms that are medical documents for examining clinical trials. The natural language provides different challenges, such as similar meanings using different phrases. The proposed annotation method, AnnoMap, considers the fuzziness of natural language. A further challenge is the reuse of verified annotations. Existing annotations represent knowledge that can be reused for further annotation processes. AnnoMap consists of a reuse strategy that utilizes verified annotations to link new documents to appropriate concepts. Due to the broad spectrum of areas in the biomedical domain, different tools exist. The tools perform differently regarding a particular domain. This thesis proposes a combination approach to unify results from different tools. The method utilizes existing tool results to build a classification model that can classify new annotations as correct or incorrect. The results show that the reuse and the machine learning-based combination improve the annotation quality compared to existing approaches focussing on the biomedical domain. A further part of data integration is entity resolution to build unified knowledge bases from different data sources. A data source consists of a set of records characterized by attributes. The goal of entity resolution is to identify records representing the same real-world entity. Many methods focus on linking data sources consisting of records being characterized by attributes. Nevertheless, only a few methods can handle graph-structured knowledge bases or consider temporal aspects. The temporal aspects are essential to identify the same entities over different time intervals since these aspects underlie certain conditions. Moreover, records can be related to other records so that a small graph structure exists for each record. These small graphs can be linked to each other if they represent the same. This thesis proposes an entity resolution approach for census data consisting of person records for different time intervals. The approach also considers the graph structure of persons given by family relationships. For achieving qualitative results, current methods apply machine-learning techniques to classify record pairs as the same entity. The classification task used a model that is generated by training data. In this case, the training data is a set of record pairs that are labeled as a duplicate or not. Nevertheless, the generation of training data is a time-consuming task so that active learning techniques are relevant for reducing the number of training examples. The entity resolution method for temporal graph-structured data shows an improvement compared to previous collective entity resolution approaches. The developed active learning approach achieves comparable results to supervised learning methods and outperforms other limited budget active learning methods. Besides the entity resolution approach, the thesis introduces the concept of evolution operators for communities. These operators can express the dynamics of communities and individuals. For instance, we can formulate that two communities merged or split over time. Moreover, the operators allow observing the history of individuals. Overall, the presented annotation approaches generate qualitative annotations for medical forms. The annotations enable comprehensive analysis across different data sources as well as accurate queries. The proposed entity resolution approaches improve existing ones so that they contribute to the generation of qualitative knowledge graphs and data analysis tasks