Publications


Books
Kietz, Jörg-Uwe, Fischer, Simon, Lavrač, Nada & Podpečan, Vid (2011). Planning to Learn and Service-Oriented Knowledge Discovery (SoKD 2011). Athens, Greece.
d'Amato, Claudia, Fanizzi, Nicola, Fortuna, Blaz, Lawrynowicz, Agnieszka & Svatek, Vojtech (2011). Proceedings of the 3rd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS). Heraklion, Greece.
Antulov-Fantulin, N, Šmuc, T & Morzy, M (2011). Proceedings of the ECML/PKDD Discovery Challenge Workshop 2011.
Fischer, Simon & Mierswa, Ingo (2011). Proceedings of the Second RapidMiner Community Meeting and Conference (RCOMM). Dublin, Ireland.
Brazdil, P, Bernstein, A & Kietz, J (2010). Proc. of the 3rd Planning to Learn Workshop (WS9) at ECAI.
d'Amato, C, Fanizzi, N, Grobelnik, M, Ławrynowicz, A & Svatek, V (2010). Proceedings of the 2nd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS).
Hilario, Melanie, Lavrač, Nada, Podpečan, Vid & Kok, Joost P (2010). Proceedings of the 3rd International Workshop on Third-Generation Data Mining: Towards Service-Oriented Knowledge Discovery (SoKD), held in conjunction with ECML/PKDD.
Fischer, Simon & Mierswa, Ingo (2010). Proceedings of the First RapidMiner Community Meeting and Conference (RCOMM). Dortmund, Germany.
Articles in Journals and Conference Proceedings
Šmuc, Tom, Antonov-Fantulin, Nino & Morzy, Mikołaj (September 2011). ECML/PKDD Discovery Challenge 2011 (VLChallenge 2011). Athens, Greece.
Antulov-Fantulin, N., Bosnjak, M., Zlatic, V., Grcar, M. & Smuc, T. (January 2012). Memory biased random walk approach to synthetic clickstream generation. ArXiv e-prints. Retrieved from: http://arxiv.org/[...]
Do, Huyen, Kalousis, Alexandros, Wang, Jun & Woznica, Adam (2012). A Metric Learning Perspective of SVM: on the relation of LMNN and SVM. To appear in the proceedings of AI-STATS 2012.
Klein, Julie, Jupp, Simon, Moulos, Panagiotis, Fernandez, Myriem, Buffin-Meyer, Bénédicte, Casemayou, Audrey, Chaaya, Rana, Charonis, Aristidis, Bascands, Jean-Loup, Stevens, Robert & Schanstra, Joost P. (2012). A novel web application to access multi-omics data on kidney disease. Faseb Journal.
Serban, Floarea, Vanschoren, Joaquin, Kietz, Jörg-Uwe & Bernstein, Abraham (2012). A Survey of Intelligent Assistants for Data Analysis. ACM Computing Surveys, 1 - 36. Retrieved from: http://merlin.ifi.uzh.ch/[...]
Jupp, Simon, Horridge, Matthew, Iannone, Luigi, Klein, Julie, Owen, Stuart, Schanstra, Joost, Stevens, Robert & Wolstencroft, Katy (2012). Populous: A tool for populating ontology templates. Journal of Biomedical Semantics.
Nguyen P., Kalousis A & Hilario, M (2011). 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).
Ławrynowicz, A., Potoniec, J., Konieczny, L., Madziar, M., Nowak, A. & Pawlak, K. T. (2011). 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).
Eales, James M, Demetriou, George & Stevens, Robert (2011). An exercise in kidney factomics: From article titles to RDF knowledge base. bio-ontologies 2011, a SIG held in conjuction with ISMB 2011. Retrieved from: http://bio-ontologies.knowledgeblog.org
Eales, J, Demetriou, G & Stevens, R (2011). An exercise in kidney factomics: From article titles to RDF knowledge base. Proceedings of the Bio-ontologies SIG, ISMB 2011. Retrieved from: http://www.manchester.ac.uk/[...]
Lawrynowicz, Agnieszka, Potoniec, Jedrzej, Konieczny, Lukasz, Madziar, Michal, Nowak, Aleksandra & Pawlak, Krzysztof T. (2011). ASPARAGUS - A System for Automatic SPARQL Query Results Aggregation Using Semantics. Computational Collective Intelligence. Technologies and Applications - Third International Conference (ICCCI 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).
Eales, James, Demetriou, George & Stevens, Robert (2011). Creating a focused corpus of factual outcomes from biomedical experiments. Mining Complex Entities from biomedical Data (MIND 2011), a workshop held in conjuction with PKDD 2011). Retrieved from: http://www.cs.man.ac.uk/[...]
Eales, J, Demetriou, G & Stevens, R (2011). Creating a focused corpus of factual outcomes from biomedical experiments. Proceedings of the MIND workshop 2011 at ECML/PKDD. Retrieved from: http://www.manchester.ac.uk/[...]
Jupp, Simon, Klein, Julie, Schanstra, Joost & Stevens, Robert (2011). Developing a kidney and urinary pathway knowledge base. Journal of Biomedical Semantics, 2 (Suppl 2), S7. Retrieved from: http://www.jbiomedsem.com/[...]
Antulov-Fantulin, N, Bošnjak, M, Znidarsic, M, Grcar, M, Morzy, M & Šmuc, T (2011). ECML-PKDD 2011 Discovery Challenge Overview. In Proceedings of the ECML/PKDD Discovery Challenge Workshop 2011.
Ławrynowicz, Agnieszka & Potoniec, Jedrzej (2011). Fr-ONT: An Algorithm for Frequent Concept Mining with Formal Ontologies. Proc. of 19th International Symposium on Methodologies for Intelligent Systems (ISMIS 2011).
Moutselos, K, Maglogiannis, I & Chatziioannou, A (2011). GOrevenge: a novel generic reverse engineering method for the identification of critical molecular players, through the use of ontologies. IEEE Trans Biomed Eng., (58(12):3522-7). Retrieved from: http://www.ncbi.nlm.nih.gov/[...]
Moulos, P, Valavanis, I, Klein, J, Maglogiannis, I, Schanstra, J & Chatziioannou, A (2011). Intelligent Selection of human miRNAs and mouse mRNAs related to Obstructive Nephropathy. In Proc of Artificial Intelligence Applications in Biomedicine (AIAB 2011).
Jozefowski, Lukasz, Lawrynowicz, Agnieszka, Jozefowska, Joanna, Potoniec, Jedrzej & Lukaszewski, Tomasz (2011). 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.
Wang, Jun, Do, Huyen, Woznica, Adam & Kalousis, Alexandros (2011). Metric Learning with Multiple Kernels. In proceedings of the 25th Neural Information Processing Systems (NIPS) Conference.
Afzal, Hammad, Eales, James, Stevens, Robert & Nenadic, Goran (2011). Mining semantic networks of bioinformatics e-resources from the literature. Journal of Biomedical Semantics, 2 (Suppl 1:S4). Retrieved from: http://www.jbiomedsem.com/[...]
Jupp, Simon, Klein, Julie, Moulos, Panagiotis, Schanstra, Joost & Stevens, Robert (2011). Ontologies Come of Age with the iKUP Browser (CEUR Workshop Proceedings). Proceedings of the Workshop Ontologies Come of Age in the Semantic Web, International Semantic Web Conference, (809), 25-28. Retrieved from: http://ceur-ws.org/[...]
Hilario, Melanie, Nguyen, Phong, Do, Huyen, Woznica, Adam & Kalousis, Alexandros (2011). Ontology-Based Meta-Mining of Knowledge Discovery Workflows. In Jankowski, N., Duchs, W. & Grabczewski, K., Meta-Learning in Computational Intelligence (p. 273-316). Springer.
Podpečan, Vid, Zemenova, Monika & Lavrač, Nada (2011). Orange4WS environment for service-oriented data mining. Computer Journal, 17.
Jupp, Simon, Horridge, Matthew, Iannone, Luigi, Klein, Julie, Stuart, Owen, Schanstra, Joost, Wolstencroft, Katy & Stevens, Robert (2011). Populous: a tool for building OWL ontologies from templates. BMC Bioinformatics, 13 (Suppl 1), S5. Retrieved from: http://www.biomedcentral.com/[...]
Potoniec, Jedrzej & Lawrynowicz, Agnieszka (2011). 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.
Moulos, P, Valavanis, I, Klein, J, Maglogiannis, I, Schanstra, J & Chatziioannou, A (2011). 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.
Stevens, Robert, Jupp, Simon, Klein, Julie & Schanstra, Joost (2011). Using Semantic Web Technologies to Manage Complexity and Change in Biomedical Data. 33rd Engineering in Medicine and Biology Conference. Retrieved from: http://www.cs.man.ac.uk/[...]
Woznica, Adam & Kalousis, Alexandros (2010). A New Framework for Dissimilarity and Similarity Learning. Advances in Knowledge Discovery and Data Mining, 14th Pacific-Asia Conference, PAKDD, 386-397.
Doukas, Charalampos, Maglogiannis, Ilias & Chatziioannou, Aristotle (2010). A Scientific Gateway for Distributed Mining of Biomedical Image Data utilizing Web Services. Proceedings of the 5th EGEE User Forum 2010 Conference.
Woznica, Adam & Kalousis, Alexandros (2010). Adaptive Distances on Sets of Vectors. IEEE International Conference on Data Mining (ICDM), 579-588.
Woznica, Adam, Kalousis, Alexandros & Hilario, Melanie (2010). Adaptive Matching Based Kernels for Labelled Graphs. Advances in Knowledge Discovery and Data Mining, Proceedings of the 14th Pacific-Asia Conference (PAKDD), 374-385.
Dakna, Mohammed, Harris, Keith, Kalousis, Alexandros, Carpentier, Sebastien, Kolch, Walter, Schanstra, Joost P, Haubitz, Marion, Vlahou, Antonia, Mischak, Harald & Girolami, Mark (2010). Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers. BMC Bioinformatics, 594 (11).
Doukas, Charalampos, Goudas, Theodosis, Fischer, Simon, Mierswa, Ingo, Chatziioannou, Aristotle & Maglogiannis, Ilias (2010). An Open Data Mining Framework for the Analysis of Medical Images: Application on Obstructive Nephropathy Microscopy Images. Proc. of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 4108-4111.
Serban, Floarea, Kietz, Jörg-Uwe & Bernstein, Abraham (2010). An Overview of Intelligent Data Assistants for Data Analysis. Proceedings of the 3rd Planning to Learn Workshop (WS9) at ECAI, 7-14.
Valavanis, Ioannis, Caubet, Cécile, Maglogiannis, Ilias, Klein, Julie, Schanstra, Joost P & Chatziioannou, Aristotle (2010). Analysis of pediatric obstructive nephropathy using protein antibody arrays and computational techniques. Proc. of the 10th IEEE International Special Topic Conference on Information Technology in Biomedicine (ITAB 2010).
Serban, Floarea (2010). Auto-experimentation of KDD Workflows based on Ontological Planning. The 9th International Semantic Web Conference (ISWC 2010), Doctoral Consortium, 313-320.
Kietz, Jörg-Uwe, Serban, Floarea, Bernstein, Abraham & Fischer, Simon (2010). Data Mining Workflow Templates for Intelligent Discovery Assistance and Auto-Experimentation. Proceedings of the ECML/PKDD-10 Workshop on Third Generation Data Mining: Towards Service-Oriented Knowledge Discovery (SoKD-10), 1-12.
Kietz, Jörg-Uwe, Serban, Floarea, Bernstein, Abraham & Fischer, Simon (2010). Data Mining Workflow Templates for Intelligent Discovery Assistance in RapidMiner. In Fischer, Simon & Mierswa, Ingo, Proceedings of the First RapidMiner Community Meeting and Conference. Retrieved from: http://www.rcomm2010.org/
Moutselos, Konstantinos, Maglogiannis, Ilias & Chatziioannou, Aristotle (2010). 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. Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 6709-6712.
Jupp, Simon, Klein, Julie, Schanstra, Joost P & Stevens, Robert (2010). Developing a Kidney and Urinary Pathway Knowledge Base. Bio-ontologies SIG.
Chatziioannou, Aristotle, Kanaris, Ioannis, Doukas, Charalampos, Thermou, Ypapanti & Maglogiannis, Ilias (2010). Enabling distributed Processing and Management of biological Data using the Grid and Web Technologies. Stud Health Technol Inform, (159), 249-54.
Kietz, Jörg-Uwe, Serban, Floarea & Bernstein, Abraham (2010). eProPlan: A Tool to Model Automatic Generation of Data Mining Workflows. Proc. of the 3rd Planning to Learn Workshop (WS9) at ECAI, 15-18.
Ławrynowicz, Agnieszka (2010). Foundations of frequent concept mining with formal ontologies. Proc. of the ECML/PKDD'10 Workshop on Third Generation Data Mining: Towards Service-oriented Knowledge Discovery (SoKD-10), 45-50.
Doukas, Charalampos, Chatziioannou, Aristotle & Maglogiannis, Ilias (2010). Intelligent Planning of Biomedical Image Mining Workflows. Proc of the 10th IEEE International Special Topic Conference on Information Technology in Biomedicine (ITAB 2010).
Jupp, Simon, Horridge, Matthew, Iannone, Luigi, Klein, Julie, Owen, Stuart, Schanstra, Joost, Stevens, Robert & Wolstencroft, Katy (2010). Populous: A tool for populating ontology templates. Semantic Web Applications and Tools for Life Sciences (SWAT4LS).
Tanti Wijaya, Derry, Kalousis, Alexandros & Hilario, Melanie (2010). Predicting Classifier Performance Using Data Set Descriptors and Data Mining Ontology. Proc. of the 3rd Planning to Learn Workshop, ECAI, 63-68.
Fischer, Simon & Mierswa, Ingo (2010). Proceedings of the First RapidMiner Community Meeting and Conference 2010 (September). Dortmund, Germany. Retrieved from: http://www.rcomm2010.org/ [2011-11-16]
Goudas, Theodosis, Doukas, Charalampos & Maglogiannis Ilias abd Chatziioannou, Aristotle (2010). Salient Regions Detection in Microscopic Kidney Biopsies Utilizing Image Analysis Techniques. Proceedings of the 12th Mediterranean Conference on Medical and Biological Engineering and Computing - MEDICON.
Boccard, Julien, Kalousis, Alexandros, Hilario, Melanie, Lantéric, Pierre, Hanafid, Mohamed, Mazerollese, Gérard, Wolfendera, Jean-Luc, Carrupta, Pierre-Alain & Rudaz, Serge (2010). 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, 20-27.
Kralj Novak, Petra, Vavpetič, Anže, Trajkovski, Igor & Lavrač, Nada (2010). Towards Semantic Data mining with g-SEGS. Proceedings of the 13th International Multiconference Information Society (IS 2010), 173-176.
Chatziioannou, Aristotle, Kanaris, Ioannis, Doukas, Charalampos & Maglogiannis, Ilias (2010). Using Grid Infrastructure for the Promotion of Biomedical Knowledge Mining. Proceedings of the 12th Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON).
Vlahou, Antonia, Allmaier, Guenter, Attwood, Teresa, Bongcam-Rudloff, Erik, Charonis, Aris, Frokiaer, Jorgen, Mischak, Harald, Schanstra, Joost P & Spasovski, Goce (2009). 2nd Combined Working Group and Management Committee Meeting of Urine and Kidney Proteomics COST Action. Proteomics - Clinical Applications, 3 (9), 1017-1022.
Hilario, Melanie, Kalousis, Alexandros, Nguyen, Phong & Woznica, Adam (2009). 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), 76-87.
Charalampos, Doukas, Maglogiannis, Ilias & Chatziioannou, Aristotle (2009). An open Web services-based framework for data mining of biomedical image data. 9th International Conference on Information Technology and Applications in Biomedicine (ITAB), 1-5.
Do, Huyen Thi Thanh, Kalousis, Alexandros & Hilario, Melanie (2009). 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).
Moutselos, Konstantinos, Kanaris, Ioannis, Chatziioannou, Aristotelis, Maglogiannis, Ilias & Kolisis, Fragiskos N (2009). KEGGconverter: A tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics, 324 (10).
Do, Huyen Thi Thanh, Kalousis, Alexandros, Woznica, Adam & Hilario, Melanie (2009). 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).
Kietz, Jörg-Uwe, Serban, Floarea, Bernstein, Avi & Fischer, Simon (2009). Towards Cooperative Planning of Data Mining Workflows. Service-oriented Knowledge Discovery (SoKD 2009), Workshop at ECML/PKDD 2009, 1-12.
Hilario, Melanie, Nguyen, Phong, Do, Huyen, Woznica, Adam & Kalousis, Alexandros. Ontology-Based Meta-Mining of Knowledge Discovery Workflows. Meta-Learning in Computational Intelligence.
Demos and Presentations
Goble, Carol (2011). Accelerating Scientists. The 3rd International Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (ICK3). Retrieved from: http://dl.dropbox.com/[...]
Eales, James, Demetriou, George & Stevens, Robert (2011). An exercise in kidney factomics: From article titles to RDF Knowledgebase. Intelligent Systems in Molecular Biology (ISMB).
Lawrynowicz, Agnieszka, Potoniec, Jedrzej, Konieczny, Lukasz, Madziar, Michal, Nowak, Aleksandra & Pawlak, Krzysztof T. (2011). ASPARAGUS - a system for automatic SPARQL query results aggregation using semantics. Demonstration at 8th Extended Semantic Web Conference (ESWC 2011).
Fischer, Simon (2011). Lost in Transformation: Data Mining Beyond Crisp. ECML/PKDD 2011 Industry Track, Athens, Greece.
Fischer, Simon (2011). Lost in Transformation: Data Mining Beyond Crisp. Third International Conference on Information Technologies and and Information Society, Dolenjske Toplice, Slovenia.
Fischer, Simon (2011). Lost in Transformation: Data Mining Beyond Crisp. International Classification Conference 2011, St. Andrews, Scotland.
Lawrynowicz, Agnieszka & Palma, Raul (2011). Ontology network for recommendation systems in digital multimedia repositories. Presentation at the Second Workshop on Applied Ontology (II Warsztaty Ontologii Stosowanej).
Jupp, Simon, Horridge, Matthew, Iannone, Luigi, Klein, Julie, Owen, Stuart, Schanstra, Joost, Wolstencroft, Katy & Stevens, Robert (2011). Populating Ontology Content with Populous (software demonstration). International Conference on Biomedical Ontologies (ICBO). Retrieved from: http://www.cs.man.ac.uk/[...]
Potoniec, Jedrzej & Lawrynowicz, Agnieszka (2011). RMonto: Ontological extension to RapidMiner. In Proc of the Poster and Demo Session of the ISWC 2011 - 10th International Semantic Web Conference.
Fischer, Simon (2011). The RapidMiner IDA Extension. Planning to Learn and Service-Oriented Knowledge Discovery, Workshop at ECML/PKDD 2011.
Jupp, Simon, Eales, James, Fischer, Simon, Land, Sebastian, Ramgolam, Rishi, Williams, Alan & Stevens, Robert (2011). The RapidMiner Plugin for Taverna: Bringing Data Mining Tools to bioinformatics Workflows. Bioinformatics Open Source Conference 2011, a SIG held in conjuction with ISMB 2011. Retrieved from: http://www.cs.man.ac.uk/[...]
Klein, Julie, Jupp, Simon, Bascands, Jean-Loup, Stevens, Robert & Schanstra, Joost P (2010). Development of an Open-Source Platform To Support Analysis, Integration and Representation of Kidney and Urinary Pathways (KUP)-Related -Omics Data. Renal Week.
Bernstein, Abraham, Hilario, Melanie & Kietz, Jörg-Uwe (2010). 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).
Jupp, Simon & Klein, Julie (2010). e-LICO: An e-Laboratory for Interdisciplinary Collaborative Research in Data-mining. Intelligent Systems in Molecular Biology.
Jupp, Simon, Eales, James, Fischer, Simon, Kietz, Jörg-Uwe, Ramgolam, Rishi, Williams, Alan, Stevens, Robert & Goble, Carole (2010). e-LICO: Delivering Data Mining to the Life Science Community. Microsoft e-Science Workshop.
Jupp, Simon, Klein, Julie, Schanstra, Joost P, Stevens, Robert, Woznica, Adam & Kalousis, Alexandros (2010). Integration of Kidney and Urinary Pathway Data for Knowledge Intensive Data Mining. Data Integration in the Life Science (DILS).
Jupp, Simon, Klein, Julie, Stevens, Robert & Schanstra, Joost P (2010). Kidney and Urinary Pathways Knowledge Base (part of e-LICO). EuroKUP COST Meeting.
Hilario, Melanie (2010). Optimizing the Knowledge Discovery Process through Semantic Meta-Mining. Proc. of the 2nd ESWC Workshop on Inductive Reasoning and Machine Learning for the Semantic Web (IRMLeS).
Klein, Julie, Jupp, Simon, Bascands, Jean-Loup, Stevens, Robert & Schanstra, Joost P (2009). Creating the Kidney and Urinary Pathways Ontology. EuroKUP COST Meeting.

Public Reports and Flyer

2010-annual-public-report.pdf (508.6 kB)

eLICO-annual-public-report-2009.pdf (415.2 kB)

eLICO-flyer.pdf (607.8 kB)