Publications

2011

Journal articles, book chapters, publications in peer-reviewed conferences and workshops

  • Hammad Afzal, James Eales, Robert Stevens, Goran Nenadic. Mining semantic networks of bioinformatics e-resources from the literature, Journal of Biomedical Semantics 2011, 2(Suppl 1):S4. doi:10.1186/2041-1480-2-S1-S4.
  • Melanie Hilario, Phong Nguyen, Huyen Do, Adam Woznica, Alexandros Kalousis. Ontology-Based Meta-Mining of Knowledge Discovery Workflows. In N. Jankowski, W. Duchs, K. Grabczewski (Eds), Meta-Learning in Computational Intelligence, pp. 273-316. Springer, 2011.
  • Ławrynowicz A., Potoniec J., Fr-ONT: An Algorithm for Frequent Concept Mining with Formal Ontologies, In Proc. of 19th International Symposium on Methodologies for Intelligent Systems (ISMIS 2011), Warsaw, Poland, LNAI, Springer-Verlag, 2011.
  • Ławrynowicz A., Potoniec J., Konieczny L., Madziar M., Nowak A. and K. T. Pawlak: A prototype system for semantic aggregation of SPARQL query results, In Proc. of the 3nd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS 2011), Heraklion, Greece.
  • Claudia d'Amato, Nicola Fanizzi, Blaz Fortuna, Agnieszka Lawrynowicz, Vojtech Svatek (eds.). Proc. of the 3nd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS 2011). Heraklion, Greece.
  • P. Moulos, I. Valavanis, J. Klein, I. Maglogiannis, J. Schanstra, and A. Chatziioannou, "Unifying the Integration, Analysis and Interpretation of multi-omic datasets: Exploration of the disease networks of Obstructive Nephropathy in children", In Proc of 33th Annual International Conference of the IEEE Engineering in Medicine and Biology, EMBC11 Boston, USA, 2011.
  • P. Moulos, I. Valavanis, J. Klein, I. Maglogiannis, J. Schanstra, and A. Chatziioannou, "Intelligent Selection of human miRNAs and mouse mRNAs related to Obstructive Nephropathy", In Proc of Artificial Intelligence Applications in Biomedicine (AIAB 2011), Corfu, Greece, 2011
  • P. Nguyen, A. Kalousis and M. Hilario, "A meta-mining infrastructure to support KD workflow optimization". In: Proc. of the ECML/PKDD-11 Workshop on Planning to Learn and Service-Oriented Knowledge Discovery (PlanSoKD-2011).
  • L. Jozefowski, A. Lawrynowicz, J. Jozefowska, J. Potoniec, and T. Lukaszewski. Kernels for measuring similarity of EL++ description logic concepts. In Proc of the ECML/PKDD’2011 workshop CoLISD: Collective Learning and Inference on Structured Data, September 2011.
  • J. Potoniec and A. Lawrynowicz. RMonto - towards KDD workflows for ontology-based data mining. In Proc of the ECML/PKDD’2011 workshop PlanSoKD 2011 - Workshop on Planning to Learn and Service- Oriented Knowledge Discovery, September 2011.
  • Lawrynowicz A., Potoniec J., Konieczny L., Madziar M., Nowak A. and K. T. Pawlak:: ASPARAGUS - A System for Automatic SPARQL Query Results Aggregation Using Semantics. In ICCCI (1). Vol. 6922 of LNCS, Springer, (2011): 304-313

 

Invited talks, posters and demos, project presentations

 

  • Ławrynowicz A., Potoniec J., Konieczny L., Madziar M., Nowak A. and K. T. Pawlak: ASPARAGUS - a system for automatic SPARQL query results aggregation using semantics, Demonstration at 8th Extended Semantic Web Conference (ESWC 2011), Heraklion, Greece.
  • Ławrynowicz A., Palma R., Ontology network for recommendation systems in digital multimedia repositories, Presentation at the Second Workshop on Applied Ontology (II Warsztaty Ontologii Stosowanej), Kazimierz Dolny, Poland, 12-13 April 2011
  • J. Potoniec and A. Lawrynowicz. RMonto: Ontological extension to RapidMiner. In Proc of the Poster and Demo Session of the ISWC 2011 - 10th International Semantic Web Conference, 2011
  • Jupp, Simon, Eales, James, Fischer, Simon, Land, Sebastian, Ramgolam, Rishi, Williams, Alan & Stevens, Robert (2011). Combining RapidMiner operators with bioinformatics services - a powerful combination. RapidMiner Community Meeting and Conference, (RCOMM) 2011. Retrieved from: http://www.cs.man.ac.uk/[...]
  • Bošnjak, M, Antulov-Fantulin, N, Šmuc, T & Gamberger, D (2011). Constructing recommender systems workflow templates in RapidMiner. In Fischer, Simon & Mierswa, Ingo, Proceedings of the RapidMiner Community Meeting And Conference (RCOMM 2011).

 

2010

Journal articles, book chapters, publications in peer-reviewed conferences and workshops

  • Claudia d'Amato, Nicola Fanizzi, Marko Grobelnik, Agnieszka Lawrynowicz, Vojtech Svatek (eds.). Proc. of the 2nd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS 2010). Heraklion, Greece.
  • Julien Boccard, Alexandros Kalousis, Melanie Hilario, et al. Standard Machine Learning Algorithms Applied to UPLC-TOF/MS Metabolic Fingerprinting for the Discovery of Wound Biomarkers in Arabidopsis thaliana. Chemometrics and Intelligent Laboratory Systems, Elsevier, 104:1(2010), pp. 20-27.
  • Pavel Brazdil, Abraham Bernstein, Jörg-Uwe Kietz (eds.). Proc. of the 3rd Planning to Learn Workshop (WS9) at ECAI 2010.
  • Ilias Maglogiannis, Charalampos Doukas and Aristotle Chatziioannou, “Enabling Distributed Mining of Biomedical Image Data Utilizing Web Services Technology”, In Proc. of  8th ICICTH, International Conference on Information Communication Technologies in Health, July, 2010, Samos Island, Greece.
  • A. Chatziioannou , I. Kanaris, C. Doukas, Ilias Maglogiannis. Using Grid Infrastructure for the Promotion of Biomedical Knowledge Mining. In: Proceedings of the 12th Mediterranean Conference on Medical and Biological Engineering and Computing. MEDICON 2010, May 27-30, 2010, Chalkidiki, Greece.
  • T. Goudas, C. Doukas, Ilias Maglogiannis, A. Chatziioannou. Salient Regions Detection in Microscopic Kidney Biopsies Utilizing Image Analysis Techniques. In: Proceedings of the 12th Mediterranean Conference on Medical and Biological Engineering and Computing– MEDICON 2010, May 27-30, 2010, Chalkidiki, Greece.
  • A. Chatziioannou, I. Kanaris,  C. Doukas, Y. Thermou, I. Maglogiannis. Enabling distributed Processing and Management of biological Data using the Grid and Web Technologies. 8th HealthGrid 2010 Conference, June 28-30, 2010, Paris, France, Stud Health Technol Inform. 2010;159:249-54.
  • M. Dakna, H. Keith, A. Kalousis, S. Carpentier, W. Kolch, J. P. Schanstra, M. Haubitz, A. Vlahou, H. Mischak, M. Girolami.Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers. BMC Bioinformatics 2010,11:594 (10 December 2010).
  • C. Doukas, Ilias Maglogiannis, A. Chatziioannou. A Scientific Gateway for Distributed Mining of Biomedical Image Data utilizing Web Services. In: Proceedings of the 5th EGEE User Forum, 2010 Conference, April 12-16, 2010, Upsalla, Sweden.
  • C. Doukas,  A. Chatziioannou, I. Maglogiannis. Intelligent Planning of Biomedical Image Mining Workflows. In Proc. of the 10th IEEE International Special Topic Conference on Technology in Biomedicine (ITAB 2010), Corfu, Greece.
  • C. Doukas, T. Goudas, S. Fischer, I. Mierswa, A. Chatziioannou and I. Maglogiannis. An Open Data Mining Framework for the Analysis of Medical Images: Application on Obstructive Nephropathy Microscopy Images. In: Proc. of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2010, Buenos Aires, Argentina, 4108-4111.
  • K. Moutselos, I. Maglogiannis, A. Chatziioannou. Delineation and interpretation of gene networks towards their effect in cellular physiology- A reverse engineering approach for the identification of critical molecular players, through the use of ontologies. In: Proc. of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2010, Buenos Aires, Argentina, 6709-6712.
  • Simon Fischer and Ingo Mierswa. Proceedings of the First RapidMiner Community Meeting and Conference (RCOMM). September 2010, Dortmund, Germany.
  • Melanie Hilario, Nada Lavrač, Vid Podpečan, Joost Kok. Proceedings of the 3rd International Workshop on Third-Generation Data Mining: Towards Service-Oriented Knowledge Discovery (SoKD'10), held in conjunction with ECML/PKDD-2010, Barcelona.
  • Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, and Katy Wolstencroft. Populous: A tool for populating ontology templates. Semantic Web Applications and Tools for Life Sciences (SWAT4LS). Dec 2010.
  • Simon Jupp, Julie Klein, Joost Schanstra and Robert Stevens. Developing a Kidney and Urinary Pathway Knowledge Base. Bio-ontologies 2010, Boston, USA.
  • Jörg-Uwe Kietz, Floarea Serban, Abraham Bernstein, Simon Fischer, Data Mining Workflow Templates for Intelligent Discovery Assistance in RapidMiner, Proc of RCOMM'10 2010. (inproceedings)
  • Jörg-Uwe Kietz, Floarea Serban and Abraham Bernstein. eProPlan: A Tool to Model Automatic Generation of Data Mining Workflows  In: Pavel Brazdil, Abraham Bernstein, Jörg-Uwe Kietz (eds.): Proc. of the 3rd Planning to Learn Workshop (WS9) at ECAI 2010.
  • Jörg-Uwe Kietz, Floarea Serban, Abraham Bernstein and Simon Fischer. Data Mining Workflow Templates for Intelligent Discovery Assistance and Auto-Experimentation. In: Proc. of the ECML/PKDD-10 Workshop on Third Generation Data Mining: Towards Service-Oriented Knowledge Discovery (SoKD-10).
  • Agnieszka Ławrynowicz. Foundations of frequent concept mining with formal ontologies. In Proc. of the ECML/PKDD'10 Workshop on Third Generation Data Mining: Towards Service-oriented Knowledge Discovery (SoKD-10), pages 45-50, 2010.
  • Petra Kralj Novak, Anže Vavpetič, Igor Trajkovski, Nada Lavrač. Towards Semantic Data mining with g-SEGS. In: Proceedings of the 13th International Multiconference Information Society (IS 2010), October 2010, pp173-176.
  • Floarea Serban, Jörg-Uwe Kietz and Abraham Bernstein. An Overview of Intelligent Data Assistants for Data Analysis  In: Pavel Brazdil, Abraham Bernstein, Jörg-Uwe Kietz (eds.): Proc. of the 3rd Planning to Learn Workshop (WS9) at ECAI 2010.
  • I. Valavanis, C. Caubet, I. Maglogiannis, J. Klein, J.P. Schanstra, A. Chatziioannou. Analysis of pediatric obstructive nephropathy using protein antibody arrays and computational techniques. In Proc. of the 10th IEEE International Special Topic Conference on Information Technology in Biomedicine (ITAB 2010), Corfu, Greece.
  • Derry Tanti Wijaya, Alexandros Kalousis, Melanie Hilario. Predicting Classifier Performance Using Data Set Descriptors and Data Mining Ontology. Proc. of the 3rd Planning to Learn Workshop, ECAI 2010, Lisbon, Portugal, pp. 60-68.
  • Adam Woznica, Alexandros Kalousis. A New Framework for Dissimilarity and Similarity Learning. Advances in Knowledge Discovery and Data Mining, 14th Pacific-Asia Conference, PAKDD 2010, Hyderabad, India, June 21-24, 2010. Springer, pp. 386-397.
  • Adam Woznica, Alexandros Kalousis. Adaptive Distances on Sets of Vectors. IEEE International Conference on Data Mining (ICDM 2010),Sydney, Australia, December 14-17, 2010, pp. 579-588.
  • Adam Woznica, Alexandros Kalousis, Melanie Hilario. Adaptive Matching Based Kernels for Labelled Graphs. Advances in Knowledge Discovery and Data Mining, 14th Pacific-Asia Conference, PAKDD 2010, Hyderabad, India, June 21-24, 2010. Springer, pp. 374-385.

Invited talks, posters and demos, project presentations

  • Abraham Bernstein, Melanie Hilario, Jörg-Uwe Kietz. e-LICO: An e-Laboratory for Interdisciplinary Collaborative Research in Data Mining and Data-Intensive Sciences. "News from the Front" Session, Extended Semantic Web Conference (ESWC-10), Heraklion, Greece, June 2010.
  • Melanie Hilario. Optimizing the Knowledge Discovery Process through Semantic Meta-Mining (Invited talk). In  Proc. of the 2nd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS 2010). Heraklion, Greece, May 2010.
  • Simon Jupp, James Eales, Simon Fischer, Jörg-Uwe Kietz, Rishi Ramgolam, Alan Williams, Robert Stevens, Carole Goble. e-LICO: Delivering Data Mining to the Life Science Community. Microsoft e-Science Workshop 2010, 11-13 October, Berkeley, CA.
  • Simon Jupp and Julie Klein. e-LICO an e-Laboratory for Interdisciplinary Collaborative Research in Data-mining. Intelligent Systems in Molecular Biology Poster and Demo. 2010. Boston, USA.
  • Simon Jupp, Julie Klein, Joost Schanstra, Robert Stevens, Adam Woznica, Alexandros Kalousis. Integration of Kidney and Urinary Pathway Data for Knowledge Intensive Data Mining. Demonstration, Data Integration in the Life Science (DILS  2010). Gothenburg, Sweden.
  • Simon Jupp, Julie Klein, Robert Stevens, Joost Schanstra. Kidney and Urinary Pathways Knowledge Base (part of e-LICO). EuroKUP COST Meeting, Rotterdam, The Netherlands, March 20-21, 2010.
  • Julie Klein, Simon Jupp, Jean-Loup Bascands, Robert Stevens, Joost Schanstra. Development of an Open-Source Platform To Support Analysis, Integration and Representation of Kidney and Urinary Pathways (KUP)-Related – Omics Data. Renal Week 2010, Denver.

 

2009

  • Huyen Thi Thanh Do, Alexandros Kalousis, Adam Woznica, Melanie Hilario. Margin and Radius Based Multiple Kernel Learning. Proc. of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD 2009), Springer.
  • Huyen Thi Thanh Do, Alexandros Kalousis, Melanie Hilario. Feature Weighting Using Margin and Radius Based Error Bound Optimization in SVMs. Proc. of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD 2009), Springer.
  • Charalampos Doukas, Ilias Maglogiannis, Aristotle Chatziioannou. An open web services-based framework for data mining of biomedical image data. Information Technology and Applications in Biomedicine, 2009. ITAB 2009. 9th International Conference on 4-7 Nov. 2009. DOI:10.1109/ITAB.2009.5394403.
  • Melanie Hilario, Alexandros Kalousis, Phong Nguyen, Adam Woznica. A Data Mining Ontology for Algorithm Selection and Meta-Learning.  Proc of the ECML/PKDD09 Workshop on Third Generation Data Mining: Towards Service-oriented Knowledge Discovery (SoKD-09), Bled, Slovenia, September 2009, pp. 76-87. 
  • Jörg-Uwe Kietz, Floarea Serban, Abraham Bernstein and Simon Fischer: Towards Cooperative Planning of Data Mining Workflows,  Proc of the ECML/PKDD09 Workshop on Third Generation Data Mining: Towards Service-oriented Knowledge Discovery (SoKD-09), Bled, Slovenia, September 2009, pp. 1-12. 
  • K.Moutselos, I.Kanaris, A.Chatziioannou, I. Maglogiannis, F.N. Kolisis. KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics 10:324, 2009. DOI:10.1186/1471-2105-10-324.
  • Antonia Vlahou, Guenter Allmaier, Teresa Attwood, Erik Bongcam-Rudloff, Aris Charonis, Jorgen Frokiaer, Harald Mischak, Joost Schanstra, Goce Spasovski, EuroKUP. 2nd Combined Working Group and Management Committee Meeting of Urine and Kidney Proteomics COST Action 29-30 March 2009, Nafplio, Greece. Proteomics – Clinical Applications, Volume 3, Issue 9, Date: September 2009, pages 1017-1022. DOI:10.1002/prca.200900087

Invited talks

  • Julie Klein, Simon Jupp, Jean-Loup Bascands, Robert Stevens, Joost Schanstra. Creating the Kidney and Urinary Pathways Ontology. EuroKUP COST Meeting, Sheffield, UK, October 31st to November 1st 2009.