liu.seSearch for publications in DiVA
Change search
Link to record
Permanent link

Direct link
BETA
Wei-Kleiner, Fang
Alternative names
Publications (10 of 12) Show all publications
Sundvall, E., Wei-Kleiner, F., Freire, S. M. & Lambrix, P. (2017). Querying archetype-based Electronic Health Records using Hadoop and Dewey encoding of openEHR models. In: Rebecca Randell, Ronald Cornet, Colin McCowan, Niels Peek, Philip J. Scott (Ed.), Rebecca Randell; Ronald Cornet; Colin McCowan; Niels Peek; Philip J. Scott (Ed.), Informatics for Health: Connected Citizen-Led Wellness and Population Health. Paper presented at Informatics for Health 2017, Manchester, UK, April 2017 (pp. 406-410). Amsterdam, The Netherlands: IOS Press
Open this publication in new window or tab >>Querying archetype-based Electronic Health Records using Hadoop and Dewey encoding of openEHR models
2017 (English)In: Informatics for Health: Connected Citizen-Led Wellness and Population Health / [ed] Rebecca Randell; Ronald Cornet; Colin McCowan; Niels Peek; Philip J. Scott, Amsterdam, The Netherlands: IOS Press, 2017, p. 406-410Conference paper, Published paper (Refereed)
Abstract [en]

Archetype-based Electronic Health Record (EHR) systems using generic reference models from e.g. openEHR, ISO 13606 or CIMI should be easy to update and reconfigure with new types (or versions) of data models or entries, ideally with very limited programming or manual database tweaking. Exploratory research (e.g. epidemiology) leading to ad-hoc querying on a population-wide scale can be a challenge in such environments. This publication describes implementation and test of an archetype-aware Dewey encoding optimization that can be used to produce such systems in environments supporting relational operations, e.g. RDBMs and distributed map-reduce frameworks like Hadoop. Initial testing was done using a nine-node 2.2 GHz quad-core Hadoop cluster querying a dataset consisting of targeted extracts from 4+ million real patient EHRs, query results with sub-minute response time were obtained.

Place, publisher, year, edition, pages
Amsterdam, The Netherlands: IOS Press, 2017
Series
Studies in Health Technology and Informatics, ISSN 0926-9630 ; 235
Keywords
medical record systems, computerzied; database management systems; Dewey encoding; Archetypes; open EHR; Hadoop; Epidemiology; XML
National Category
Computer Sciences Other Medical Engineering
Identifiers
urn:nbn:se:liu:diva-136902 (URN)10.3233/978-1-61499-753-5-406 (DOI)28423824 (PubMedID)978-1-61499-752-8 (ISBN)978-1-61499-753-5 (ISBN)
Conference
Informatics for Health 2017, Manchester, UK, April 2017
Funder
Swedish e‐Science Research Center
Available from: 2017-04-28 Created: 2017-04-28 Last updated: 2019-07-03Bibliographically approved
Freire, S. M., Teodoro, D., Wei-Kleiner, F., Sundvall, E., Karlsson, D. & Lambrix, P. (2016). Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data. PLoS ONE, 11(3), Article ID e0150069.
Open this publication in new window or tab >>Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data
Show others...
2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0150069Article in journal (Refereed) Published
Abstract [en]

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

Place, publisher, year, edition, pages
Public Library Science, 2016
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-125961 (URN)10.1371/journal.pone.0150069 (DOI)000371992300032 ()26958859 (PubMedID)
Funder
Swedish e‐Science Research Center
Note

Funding agencies: Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES Foundation - Brazil) [4055/11]; Conselho Brasileiro de Desenvolvimento Cientifico e Tecnologico (CNPq) [150916/2013-2]

Available from: 2016-03-09 Created: 2016-03-09 Last updated: 2018-03-22
Wei-Kleiner, F. (2016). Tree decomposition-based indexing for efficient shortest path and nearest neighbors query answering on graphs. Journal of computer and system sciences (Print), 82(1), 23-44
Open this publication in new window or tab >>Tree decomposition-based indexing for efficient shortest path and nearest neighbors query answering on graphs
2016 (English)In: Journal of computer and system sciences (Print), ISSN 0022-0000, E-ISSN 1090-2724, Vol. 82, no 1, p. 23-44Article in journal (Refereed) Published
Abstract [en]

We propose TEDI, an indexing for solving shortest path, and k Nearest Neighbors (kNN) problems. TEDI is based on the tree decomposition methodology. The graph is first decomposed into a tree in which the node contains vertices. The shortest paths are stored in such nodes. These local shortest paths together with the tree structure constitute the index of the graph. Based on this index, algorithms can be executed to solve the shortest path, as well as the kNN problem more efficiently. Our experimental results show that TEDI offers orders-of-magnitude performance improvement over existing approaches on the index construction time, the index size and the query answering. (C) 2015 Elsevier Inc. All rights reserved.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2016
Keywords
Graphs algorithms; Graph indexing; Shortest path; Tree decomposition; k Nearest Neighbors problems
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-122642 (URN)10.1016/j.jcss.2015.06.008 (DOI)000363092400003 ()
Available from: 2015-11-16 Created: 2015-11-13 Last updated: 2018-01-10
Lambrix, P., Wei-Kleiner, F. & Dragisic, Z. (2015). Completing the is-a structure in light-weight ontologies. Journal of Biomedical Semantics, 6, Article ID 12.
Open this publication in new window or tab >>Completing the is-a structure in light-weight ontologies
2015 (English)In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 6, article id 12Article in journal (Refereed) Published
Abstract [en]

 Background: With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologies are a key technology in this effort. However, developing ontologies is not an easy task and often the resulting ontologies are not complete. In addition to being problematic for the correct modelling of a domain, such incomplete ontologies, when used in semantically-enabled applications, can lead to valid conclusions being missed.

Results: We consider the problem of repairing missing is-a relations in ontologies. We formalize the problem as a generalized TBox abduction problem. Based on this abduction framework, we present complexity results for the existence, relevance and necessity decision problems for the generalized TBox abduction problem with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

Conclusions: Semantically-enabled applications need high quality ontologies and one key aspect is their completeness. We have introduced a framework and system that provides an environment for supporting domain experts to complete the is-a structure of ontologies. We have shown the usefulness of the approach in different experiments. For the two Anatomy ontologies from the Ontology Alignment Evaluation Initiative, we repaired 94 and 58 initial given missing is-a relations, respectively, and detected and repaired additionally, 47 and 10 missing is-a relations. In an experiment with BioTop without given missing is-a relations, we detected and repaired 40 new missing is-a relations.

National Category
Computer Sciences Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:liu:diva-116628 (URN)10.1186/s13326-015-0002-8 (DOI)000353197200001 ()25883780 (PubMedID)
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2015-03-29 Created: 2015-03-29 Last updated: 2018-01-11
Dragisic, Z., Lambrix, P. & Wei-Kleiner, F. (2014). A System for Debugging Missing Is-a Structure in EL Ontologies. In: Proceedings of the Third International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM14: . Paper presented at Third International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2014), May 26, 2014, Anissaras/Hersonissou, Greece (pp. 51-58).
Open this publication in new window or tab >>A System for Debugging Missing Is-a Structure in EL Ontologies
2014 (English)In: Proceedings of the Third International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM14, 2014, p. 51-58Conference paper, Published paper (Refereed)
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 1162
Keywords
ontologies, knowledge representation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-107320 (URN)
Conference
Third International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2014), May 26, 2014, Anissaras/Hersonissou, Greece
Funder
Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)
Available from: 2014-06-10 Created: 2014-06-10 Last updated: 2018-01-11Bibliographically approved
Wei-Kleiner, F., Dragisic, Z. & Lambrix, P. (2014). Abduction Framework for Repairing Incomplete EL Ontologies:  Complexity Results and Algorithms. In: Proceedings of the 28th AAAI Conference on Artificial Intelligence: . Paper presented at 28th AAAI Conference on Artificial Intelligence (pp. 1120-1127). Palo Alto, CA, USA: AAAI Press
Open this publication in new window or tab >>Abduction Framework for Repairing Incomplete EL Ontologies:  Complexity Results and Algorithms
2014 (English)In: Proceedings of the 28th AAAI Conference on Artificial Intelligence, Palo Alto, CA, USA: AAAI Press, 2014, p. 1120-1127Conference paper, Published paper (Refereed)
Abstract [en]

In this paper we consider the problem of repairing  missing is-a relations in ontologies.We formalize the problem as a generalized TBox abduction problem (GTAP). Based on this abduction framework, we  present complexity results for the existence, relevance and necessity decision problems for the GTAP with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

Place, publisher, year, edition, pages
Palo Alto, CA, USA: AAAI Press, 2014
Keywords
ontology; ontology debugging; semantic web, knowledge representation; abductive reasoning
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-109039 (URN)2-s2.0-84908159683 (Scopus ID)9781577356783 (ISBN)
Conference
28th AAAI Conference on Artificial Intelligence
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2014-07-31 Created: 2014-07-31 Last updated: 2018-01-11
Dragisic, Z., Lambrix, P. & Wei-Kleiner, F. (2014). Completing the is-a structure of biomedical ontologies. In: Helena Galhardas, Erhard Rahm (Ed.), Data Integration in the Life Sciences 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014. Proceedings: . Paper presented at 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014 (pp. 66-80). Berlin: Springer Science+Business Media B.V.
Open this publication in new window or tab >>Completing the is-a structure of biomedical ontologies
2014 (English)In: Data Integration in the Life Sciences 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014. Proceedings / [ed] Helena Galhardas, Erhard Rahm, Berlin: Springer Science+Business Media B.V., 2014, p. 66-80Conference paper, Published paper (Refereed)
Abstract [en]

Ontologies in the biomedical domain are becoming a key element for data integration and search. The usefulness of the applications which use ontologies is often directly influenced by the quality of ontologies, as incorrect or incomplete ontologies might lead to wrong or incomplete results for the applications. Therefore, there is an increasing need for repairing defects in ontologies. In this paper we focus on completing ontologies. We provide an algorithm for completing the is-a structure in TeX ontologies which covers many biomedical ontologies. Further, we present an implemented system based on the algorithm as well as an evaluation using three biomedical ontologies.

Place, publisher, year, edition, pages
Berlin: Springer Science+Business Media B.V., 2014
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 8574
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-108848 (URN)10.1007/978-3-319-08590-6_7 (DOI)000345519500007 ()978-3-319-08589-0 (ISBN)978-3-319-08590-6 (ISBN)
Conference
10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2014-07-08 Created: 2014-07-08 Last updated: 2018-07-17Bibliographically approved
Wei-Kleiner, F. (2013). Finding nearest neighbors in road networks: a tree decomposition method. In: EDBT '13 Proceedings of the Joint EDBT/ICDT 2013 Workshops: . Paper presented at EDBT/ICDT Workshops, March 18-22, 2013, Genoa, Italy (pp. 233-240). New York: Association for Computing Machinery (ACM)
Open this publication in new window or tab >>Finding nearest neighbors in road networks: a tree decomposition method
2013 (English)In: EDBT '13 Proceedings of the Joint EDBT/ICDT 2013 Workshops, New York: Association for Computing Machinery (ACM), 2013, p. 233-240Conference paper, Published paper (Refereed)
Abstract [en]

Finding k Nearest Neighbors in one category of POIs (point of interests) belongs to the most frequently issued queries in the navigating systems or online maps. This problem can be formulated as given a graph G(V, E), a vertex u and SV, finding k nearest neighbors of u in S. Classic Dijkstra's algorithm offers an optimal solution if S = V holds, but the performance deteriorates as S is of smaller size. Other approaches such as pre-computing and storing all the shortest distances require too much storage, thus suffer from drawbacks of scalability.

To address these problems, we propose TIkNN (stands for Tree decomposition-based Indexing for kNN), an indexing and query processing scheme for kNN query answering. TIkNN is based on the tree decomposition methodology. The graph is first decomposed into a tree in which each node (a.k.a. bag) contains more than one vertex from graph. The shortest paths are stored in such bags and these local paths together with the tree are the components of the index of the graph. Based on this index, step-wise query processing over the tree can be executed to find the nearest neighbors.

Our experimental results show that TIkNN offers orders-of-magnitude performance improvement over Dijkstra's algorithm on query answering, while the storage requirement for the index structure is relatively small.

Place, publisher, year, edition, pages
New York: Association for Computing Machinery (ACM), 2013
Keywords
graphs, indexing, k nearest neighbors, shortest path, tree decomposition
National Category
Computer Systems
Identifiers
urn:nbn:se:liu:diva-94575 (URN)10.1145/2457317.2457355 (DOI)978-1-4503-1599-9 (ISBN)
Conference
EDBT/ICDT Workshops, March 18-22, 2013, Genoa, Italy
Available from: 2013-06-26 Created: 2013-06-26 Last updated: 2013-08-01Bibliographically approved
Lambrix, P., Wei-Kleiner, F., Dragisic, Z. & Ivanova, V. (2013). Repairing missing is-a structure in ontologies is an abductive reasoning problem. In: Patrick Lambrix; Guilin Qi; Matthew Horridge; Bijan Parsia (Ed.), Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings: . Paper presented at Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013), Montpellier, France, May 27, 2013 (pp. 33-44). Rheinisch-Westfaelische Technische Hochschule Aachen University
Open this publication in new window or tab >>Repairing missing is-a structure in ontologies is an abductive reasoning problem
2013 (English)In: Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings / [ed] Patrick Lambrix; Guilin Qi; Matthew Horridge; Bijan Parsia, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2013, p. 33-44Conference paper, Published paper (Refereed)
Abstract [en]

With the increased use of ontologies in semantically-enabled applications, the issue of debugging defects in ontologies has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Debugging consists of the phases of detection and repairing. In this paper we focus on the repairing phase of a particular kind of defects, i.e., the missing relations in the is-a hierarchy. We show that this can be formalized as an abduction problem. Further, we define properties for the ontology, the set of is-a relations to repair and the domain expert, as well as preference criteria on solutions and discuss the influences of these properties and criteria on the existence of solutions for the abduction problem. We also discuss the consequences of our analyses of the repairing problem for the development and use of debugging systems.

Place, publisher, year, edition, pages
Rheinisch-Westfaelische Technische Hochschule Aachen University, 2013
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 999
Keywords
ontology debugging, ontology engineering, knowledge representation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-93928 (URN)
Conference
Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013), Montpellier, France, May 27, 2013
Funder
Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)
Available from: 2013-06-12 Created: 2013-06-12 Last updated: 2018-01-11Bibliographically approved
Meier, M., Schmidt, M., Wei, F. & Lausen, G. (2013). Semantic query optimization in the presence of types. Journal of computer and system sciences (Print), 79(6), 937-957
Open this publication in new window or tab >>Semantic query optimization in the presence of types
2013 (English)In: Journal of computer and system sciences (Print), ISSN 0022-0000, E-ISSN 1090-2724, Vol. 79, no 6, p. 937-957Article in journal (Refereed) Published
Abstract [en]

Both semantic and type-based query optimization rely on the idea that queries may exhibit non-trivial rewritings if the state space of the database is restricted. While these two problems have always been studied as separate problems in previous work, in this paper we present a unifying, logic-based query optimization framework that builds upon the classical chase algorithm and brings both problems together. As a major challenge, our novel setting requires chasing conjunctive queries with union and negation in the presence of dependencies containing negation and disjunction. Tackling this problem, we study the applicability of the chase in this setting, develop novel conditions that guarantee its termination, identify fragments for which minimal query computation (w.r.t. a generic cost function) is always possible, and investigate the complexity of related decision problems.

Place, publisher, year, edition, pages
Elsevier, 2013
Keywords
Systems – relational databases; Query processing; Query optimization; Types; Constraints; Chase
National Category
Computer Systems
Identifiers
urn:nbn:se:liu:diva-94572 (URN)10.1016/j.jcss.2013.01.010 (DOI)
Available from: 2013-06-26 Created: 2013-06-26 Last updated: 2017-12-06Bibliographically approved
Organisations

Search in DiVA

Show all publications