Dipl.-Inf. Thomas Fober

Knowledge Engineering & Bioinformatics

^*The general prefix for the phone number is "+49 (0)6421-28". To get the correct email address, please add ".uni-marburg.de" .

SHORT CV

Education

Winter 2001 - Winter 2006:
Student in Computer Science (Minor: Business Management)
Universität Dortmund, Germany

Winter 2007/08 - Summer 2011:
PhD-Student in an interdisciplinary project from the field of
Pharmaceutical Chemistry and Computer Science, Philipps-Universität Marburg, Germany

Degrees

Diplom (German M.Sc.) in Computer Science
Universität Dortmund, Germany

Employment

2004, February - 2007, February
Student Assistant, Universität Dortmund, Germany

Since 2007, May
Research staff member (full time)
Department of Mathematics and Computer Science,
Philipps-Universität Marburg, Germany

Research Stays

Awards and Honors

2007: GMA/GI Computational Intelligence Young Author Award (official homepage)
2009: VDI/GMA Young Author Award (official homepage)

Invited Talks

Teaching

Summer 2007: Fuzzy Systems
Winter 2007/08: Logic and Discrete Mathematics
Summer 2008: Fuzzy Systems (Evaluation); Knowledge Engineering & Bioinformatics Seminar
Summer 2009: Computational Intelligence (Evaluation)
Winter 2009/10: Logic and Discrete Mathematics
Summer 2010: Computational Intelligence
Winter 2010/11: Introduction to Bioinformatics; Efficient Algorithms
Summer 2011: Database Systems
Summer 2012: Fuzzy Systems

Conferences (Organization)

International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2010), Westfalenhallen Dortmund, Germany, June 28 - July 02, 2010

Co-Organization of the Joint Conference of the German Classification Society (GfKl) and the German Association for Pattern Recognition (DAGM), Frankfurt a.M., Germany, August 31 - September 02, 2011

International Conference on Scalable Uncertainty Management (SUM 2012), Marburg, Germany, September 17 - 19, 2012

Reviewer Activities

International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems

Supervised Diploma/Master Thesis

Ralph Moritz: Kernbasierte Ähnlichkeitsmaße auf Graphen (Kernels on graphs), August, 2008

Imen Boukhris: Graph-based similarity of protein binding sites derived from quasi-clique detection, May, 2009

Timo Krotzky: Analyse und algorithmische Erweiterung von Methoden zum strukturellen Vergleich von Proteinbindestellen (Extension of methods for the structural comparison of protein binding sites), August, 2010 [ link to publisher]

Adil Paul: Effiziente Nächste-Nachbar Suche in dynamischen geometrischen Strukturen (Efficient nearest-neighbor search in dynamic geometrical structures), 2011

Mabou Bopda Constant: Entwurf und Analyse von Methoden zur Berechnung maximaler Cliquen im Produkt zweier euklidischer Graphen (Design of methods for the calculation of maximum cliques in the product of two Euclidean graphs), 2011

Datasets

• ATP/NADH dataset (zip-file containing two folders, each of which contains protein binding sites bind ATP or NADH ligands) [zip-file][description]
• Histogram-valued data (This data set is "non-standard" in the sense of being composed of "histogram-valued" attributes, that is, a set of attributes that assume a histogram as a value (and not, as usual, a single number or category). A precise description of the data can be found in this talk or this paper) [txt-file][description]
  

Publications / Talks

2006

Thomas Fober
Experimentelle Analyse Evolutionärer Algorithmen auf dem CEC 2005 Testfunktionensatz
[pdf][bibtex][DNB]
Technical Report, TR06-2-009, Universität Dortmund, Germany, July, 2006

2007

Thomas Fober, Eyke Hüllermeier, Marco Mernberger
Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules
[pdf][bibtex][slides(german)]
17. Workshop Computational Intelligence, Bommerholz, Germany, December, 2007

2008

Thomas Fober, Eyke Hüllermeier, Marco Mernberger
Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules
[pdf][bibtex]
German Conference on Bioinformatics, Dresden, Germany, September, 2008

Thomas Fober, Eyke Hüllermeier, Marco Mernberger
Evolutionary Construction of Multiple Graph Alignments for Mining Structured Biomolecular Data
[pdf][bibtex][slides]
Knowledge Discovery, Data Mining, und Maschinelles Lernen, Würzburg, Germany, October, 2008

2009

Thomas Fober
Evolutionary Methods for Protein Structure Comparison
[pdf (slides)]
Romanian-German Symposium on Mathematics and Its Applications, Sibiu, Romania, May, 2009

Thomas Fober, Eyke Hüllermeier
Fuzzy Modeling of Labeled Point Cloud Superposition for the Comparison of Protein Binding Sites
[pdf][bibtex][slides]
IFSA 2009 World Congress; EUSFLAT 2009 World Conference, Lisbon, Portugal, July, 2009

Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules
[pdf(draft)][supp][bibtex]
Oxford Bioinformatics 25(16): 2110 – 2117, August, 2009

Thomas Fober, Marco Mernberger, Vitalik Melnikov, Ralph Moritz, Eyke Hüllermeier
Extension and Empirical Comparison of Graph-Kernels for the Analysis of Protein Active Sites
[pdf][bibtex][slides]
Knowledge Discovery, Data Mining, und Maschinelles Lernen, Darmstadt, Germany, September, 2009

Thomas Fober, Marco Mernberger, Ralph Moritz, Eyke Hüllermeier
Graph-Kernels for the Comparative Analysis of Protein Active Sites
[pdf][bibtex]
German Conference on Bioinformatics, Halle (Saale), Germany, September, 2009

Imen Boukhris, Zied Elouedi, Thomas Fober, Marco Mernberger, Eyke Hüllermeier
Similarity Analysis of Protein Binding Sites: A Generalization of the Maximum Common Subgraph Measure based on Quasi-Clique Detection
[pdf(draft)][bibtex][slides]
IEEE International Conference on Intelligent Systems Design and Applications, Pisa, Italy, November, 2009

Thomas Fober, Gerhard Klebe, Eyke Hüllermeier
Efficient Construction of Multiple Geometrical Alignments for the Comparison of Protein Binding Sites
[pdf(draft)][bibtex][slides]
IEEE International Conference on Intelligent Systems Design and Applications, Pisa, Italy, November, 2009

Yu Yi, Thomas Fober, Eyke Hüllermeier
Fuzzy Operator Trees for Modeling Rating Functions
[pdf(draft)][bibtex]
International Journal of Computational Intelligence and Applications 8(4): 413 – 428, December, 2009

Thomas Fober, Eyke Hüllermeier
Multiple Geometrical Alignments for the Analysis of Protein Active Sites
[pdf][bibtex][slides]
19. Workshop Computational Intelligence, Bommerholz, Germany, December, 2009

2010

Thomas Fober, Eyke Hüllermeier
Similarity Measures for Protein Structures based on Fuzzy Histogram Comparison
[pdf(draft)][bibtex][slides(ppsx)]
IEEE World Congress on Computational Intelligence, Barcelona, Spain, July, 2010

Patrick Pfeffer, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe
GARLig: A fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm
[pdf(external link to publisher)][bibtex]
Journal of Chemical Information and Modeling 50(9): 1644 – 1659, September, 2010

Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Efficient Similarity Retrieval for Protein Binding Sites based on Histogram Comparison
[pdf][bibtex][slides(ppsx)]
German Conference on Bioinformatics, Braunschweig, Germany, September, 2010

2011

Thomas Fober, Gerhard Klebe, Eyke Hüllermeier
Local Clique Merging: An Extension of the Maximum Common Subgraph Measure for the Classification of Graph Structures
Joint Conference of the German Classification Society and the German Association for Pattern Recognition, Frankfurt a. M., Germany, August, 2011
[pdf][bibtex][slides(ppsx)]

Thomas Fober, Serghei Glinca, Gerhard Klebe, Eyke Hüllermeier
Superposition and Alignment of Labeled Point Clouds
[pdf(draft)][bibtex]
IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(6): 1653 – 1666, November, 2011

Thomas Fober, Weiwei Cheng, Eyke Hüllermeier
Focusing Search in Multiobjective Evolutionary Optimization through Preference Learning from User Feedback
[pdf][bibtex][slides]
21. Workshop Computational Intelligence, Dortmund, Germany, December, 2011

2012

Robin Senge, Thomas Fober, Maryam Nasiri, Eyke Hüllermeier
Fuzzy Pattern Trees: Ein alternativer Ansatz zu Fuzzy-Modellierung
[pdf][bibtex]
Automatisierungstechnik: Computational Intelligence, (to appear), Oldenbourg Verlag, München, Germany

Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Fingerprint Kernels for Protein Structure Comparison
[pdf][bibtex]
Molecular Informatics, to appear.

Matthias Leinweber, Lars Baumgärtner, Marco Mernberger, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe, Bernd Freisleben
GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites
[pdf][bibtex]
IEEE Conference on Digital Ecosystem Technologies - Complex Environment Engineering, Campione d'Italia, Italy, June, 2012

2013

Eyke Hüllermeier, Thomas Fober, Marco Mernberger
Classification
[bibtex][ link to publisher]
In: Dubitzky W., Wolkenhauer O., Cho K.-H., Yokota H. (Eds)
Encyclopedia of Systems Biology, (to appear), Springer, New York, USA

Eyke Hüllermeier, Thomas Fober, Marco Mernberger
Fuzzy Logic
[bibtex][ link to publisher]
In: Dubitzky W., Wolkenhauer O., Cho K.-H., Yokota H. (Eds)
Encyclopedia of Systems Biology, (to appear), Springer, New York, USA

Eyke Hüllermeier, Thomas Fober, Marco Mernberger
Case-based Reasoning
[bibtex][ link to publisher]
In: Dubitzky W., Wolkenhauer O., Cho K.-H., Yokota H. (Eds)
Encyclopedia of Systems Biology, (to appear), Springer, New York, USA