Publications for Bioinformatics

  1. Thoma M., Cheng H., Gretton A., Han J., Kriegel H.-P., Smola A., Song L., Yu P. S., Yan X., Borgwardt K.: Near-optimal supervised feature selection among frequent subgraphs, Proc. 9th SIAM Conf. on Data Mining (SDM 2009), Sparks, NV, 2009, pp. 1075-1087.
    Paper (pdf 287K)

  2. Aßfalg J., Gong J., Kriegel H.-P.,Pryakhin A., Wei T., Zimek A.: Supervised Ensembles of Prediction Methods for Subcellular Localization, in: Journal of Bioinformatics and Computational Biology (JBCB), Vol. 7, Issue 2, (April 2009), 2009, pp. 269-285.
    EE (World Scientific), prediction server

  3. Borgwardt K., Yan X., Thoma M., Cheng H., Gretton A., Song L., Smola A., Han J., Yu P. S., Kriegel H.-P.: Combining near-optimal feature selection with gSpan, Proc. 6th Int. Workshop on Mining and Learning with Graphs (MLG'08), Helsinki, Finland, 2008.
    Paper (pdf 144K)

  4. Achtert E., Böhm C., David J., Kröger P., Zimek A.: Robust Clustering in Arbitrarily Oriented Subspace, (Best Paper Honorable Mention Award), Proc. 8th Int. Conf. on Data Mining (SDM'08), Atlanta, GA, 2008, pp. 763-774.
    Paper (pdf 837K)

  5. Aßfalg J., Gong J., Kriegel H.-P., Pryakhin A., Wei T., Zimek A.: Supervised Ensembles of Prediction Methods for Subcellular Localization, Proc. 6th Asia Pacific Bioinformatics Conf. (APBC'08), Kyoto, Japan, 2008, pp. 29-38.
    Paper (pdf 143K)

  6. Achtert E., Böhm C., Kriegel H.-P., Kröger P., Zimek A.: Robust, Complete, and Efficient Correlation Clustering, Proc. 7th SIAM Int. Conf. on Data Mining (SDM'07), Minneapolis, MN, 2007, pp. 413-418.
    Paper (pdf 217K)

  7. Achtert E., Böhm C., Kriegel H.-P., Kröger P., Zimek A.: On Exploring Complex Relationships of Correlation Clusters, Proc. 19th Int. Conf. on Scientific and Statistical Database Management (SSDBM'07), Banff, Canada, 2007.
    Paper (pdf 357K)

  8. Achtert E., Böhm C., Kriegel H.-P., Kröger P., Müller-Gormann I., Zimek A.: Detection and Visualization of Subspace Cluster Hierarchies, Proc. 12th Int. Conf. on Database Systems for Advance Applications (DASFAA'07), Bangkok, Thailand, 2007, pp. 152-163.
    Paper (pdf 239K)

  9. Vishwanathan S. V. N., Borgwardt K. M., Schraudolph N.: Fast Computation of Graph Kernels, Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 1449-1456.
    Paper (pdf 419K)

  10. Gretton A., Borgwardt K. M., Rasch M., Schölkopf B., Smola A.: A Kernel Method for the Two-Sample-Problem, (full oral presentation), Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 513-520.
    Paper (pdf 357K)

  11. Huang J., Smola A., Gretton A., Borgwardt K. M., Schölkopf B.: Correcting Sample Selection Bias by Unlabeled Data, Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 601-608.
    Paper (pdf 386K)

  12. Gretton A., Borgwardt K. M., Rasch M., Schölkopf B., Smola A.: A Kernel Method for the Two-Sample-Problem, (full oral presentation), Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 513-520.
    Paper (pdf 357K)

  13. Huang J., Smola A., Gretton A., Borgwardt K. M., Schölkopf B.: Correcting Sample Selection Bias by Unlabeled Data, Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 601-608.
    Paper (pdf 386K)

  14. Borgwardt K. M., Vishwanathan S. V. N., Schraudolph N., Kriegel H.-P.: Graph Kernels for disease outcome prediction from protein-protein interaction, Proc. Pacific Symposium on Biocomputing (PSB'07), Wailea, Maui, 2007, pp. 4-15.
    Paper (pdf 397K)

  15. Vishwanathan S. V. N., Borgwardt K. M., Schraudolph N.: Fast Computation of Graph Kernels, Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 1449-1456.
    Paper (pdf 419K)

  16. Gretton A., Borgwardt K. M., Rasch M., Schölkopf B., Smola A.: A Kernel Method for the Two-Sample-Problem, (full oral presentation), Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 513-520.
    Paper (pdf 357K)

  17. Huang J., Smola A., Gretton A., Borgwardt K. M., Schölkopf B.: Correcting Sample Selection Bias by Unlabeled Data, Proc. 20th Annual Conf. on Neural Information Processing Systems (NIPS 2006), Vancouver, B.C., Canada, 2007, pp. 601-608.
    Paper (pdf 386K)

  18. Borgwardt K. M., Kriegel H.-P., Wackersreuther P.: Pattern Mining in Frequent Dynamic Subgraphs, Proc. IEEE Int. Conf. on Data Mining (ICDM'06), Hong Kong, 2006, pp. 818-822.
    Paper (pdf 388K)

  19. Aßfalg J., Borgwardt K. M., Kriegel H.-P.: 3DString: A Feature String Kernel for 3D Object Classification on Voxelized Data, Proc. ACM 15th Conf. on Information and Knowledge Management (CIKM'06), Arlington, VA, 2006, pp. 198-207.
    Paper (pdf 111K)

  20. Borgwardt K. M., Gretton A., Rasch M., Kriegel H.-P., Schölkopf B., Smola A. J.: Integrating structured biological data by Kernel Maximum Mean Discrepancy, Proc. 14th Annual Int. Conf. on Intelligent Systems for Molecular Biology (ISMB'06), Fortaleza, Brazil, 2006, in: Bioinformatikcs Vol 22, No. 14, pp. 49-57.
    Abstract (pdf)

  21. Borgwardt K. M., Boettger S., Kriegel H.-P.: VGM: Visual Graph Mining, demo paper, Proc. ACM SIGMOD Int. Conference on Management of Data, Chicago, ILL, 2006, pp. 733-735.

  22. Vishwanathan S.V., Borgwardt K. M., Guttman O., Smola A. J.: Kernel Extrapolation, in: Neurocomputing, Vol. 6, Issues 7-9, March 2006, pp. 721-729.
    Paper (pdf)

  23. Borgwardt K. M., Vishwanathan S. V., Kriegel H.-P.: Class prediction from time series gene expression profiles using dynamical systems kernels, Proc. Pacific Symp. on Biocomputing (PSB), Maui, Hawaii, 2006, pp. 547-558.
    Paper (pdf 148K)

  24. Aßfalg J., Kriegel H.-P., Kröger P., Kunath P., Pryakhin A., Renz M.: Semi-Supervised Threshold Queries on Pharmacogenomics Time Sequences, Proc. 4th Asia Pacific Bioinformatics Conference (APBC'06), Taipei, Taiwan, 2006, pp. 307-316.
    Paper (pdf 298K)

  25. Borgwardt K., Kriegel H.-P.: Shortest-path kernels on graphs, Proc. 5th IEEE Int. Conf. on Data Mining (ICDM'05), Houston, TX, 2005, pp. 74-81.
    Paper (pdf 290K)

  26. Borgwardt K. M., Kriegel H.-P.: Kernel Methods for Protein Function Prediction, short review, Proc. ISMB-satellite "Automated Function Prediction" (AFP 2005), Detroit, MI, 2005.
    Paper (pdf 594K)

  27. Borgwardt K. M., Ong C. S., Schönauer S., Vishwanathan S. V. N., Smola A. J., Kriegel H.-P.: Protein Function Prediction via Graph Kernels , Proc. "Intelligent Systems in Molecular Biology" (ISMB 2005), Detroit, MI, 2005, pp. 47-56.
    Paper pdf

  28. Borgwardt K. M., Guttman O., Vishwanathan S. V. N., Smola A. J.: Joint Regularization, Proc. "European Symp. on Artificial Neural Networks" (ESANN 2005), Brügge, Belgium, 2005.
    Paper (pdf 306K)

  29. Baumgartner C., Gautsch K., Böhm C., Felber S.: Functional cluster analysis of CT perfusion maps: A new tool for diagnosis of acute stroke?, in J. Digit Imaging, Vol. 18, 2005, pp. 219-226.

  30. Baumgartner C., Böhm C., Baumgartner D.: Modelling of classification rules on metabolic patterns including machine learning and expert knowledge, in J. Biomed Inform., Vol. 38, 2005, pp. 89-98.

  31. Baumgartner C., Baumgartner D., Böhm C.: Modelling of classification rules on metabolic patterns including machine learning and expert knowledge, (Abstract + poster), Bioinformatics 2004, Linköping, Sweden, 2004.

  32. Baumgartner C., Böhm C., Baumgartner D., Marini G., Weinberger K., Olgemöller B., Liebl B., Roscher A.A.: Supervised machine learning techniques for the classification of metabolic disorders in newborns, Proc. Bioinformatics 2004, Linköping, Sweden, Vol. 20, No. 17, 2004, pp. 2985-2996.

  33. Kriegel H.-P., Pfeifle M., Schönauer S.: Similarity Search in Biological and Engineering Databases, IEEE Data Engineering Bulletin, Vol. 27, No. 4, 2004, pp. 37-44.
    Paper (pdf 126K)

  34. Böhm C., Kailing K., Kröger P., Zimek A.: Computing Clusters of Correlation Connected Objects, Proc. ACM SIGMOD Int. Conf. on Management of Data, Paris, France, 2004, pp. 455-466.
    Paper (pdf 813K)

  35. Schubert M., Pryakhin A., Kröger P., Kriegel H.-P.: Using Support Vector Machines for Classifying Large Sets of Multi-Represented Objects, Proc. SIAM Int. Conf. on Data Mining (SDM'04), Lake Buena Vista, FL, 2004, pp. 102-114.
    Paper (pdf 347K)

  36. Kröger P., Kriegel H.-P., Kailing K.: Density-Connected Subspace Clustering for High-Dimensional Data, Proc. SIAM Int. Conf. on Data Mining (SDM'04), Lake Buena Vista, FL, 2004, pp. 246-257.
    Paper (pdf 341K)

  37. Baumgartner C., Baumgartner D., Böhm C.: Classification on high dimensional metabolic data: Phenylketonuria as an example, Proc. 2nd Int. Conf. on Biomedical Engineering (BioMED 2004), Innsbruck, Austria, 2004, pp. 357-360.

  38. Kailing K., Kriegel H.-P., Kröger P., Wanka S.: Ranking Interesting Subspaces for Clustering High Dimensional Data, Proc. 7th European Conf. on Principles and Practice of Knowledge Discovery in Databases (PKDD'03), Cavtat-Dubrovnic, Croatia, 2003, in: Lecture Notes in Artificial Intelligence (LNAI), Vol. 2838, 2003, pp. 241-252.
    Paper (pdf 353K)

  39. 1999

    Seidl T., Kriegel H.-P.: Mining Protein Databases, Proc. TdI'99 Tag der Informatik, Institute for Computer Science, 1999.

  40. Ankerst M., Kastenmüller G., Kriegel H.-P., Seidl T.: 3D Shape Histograms for Similarity Search and Classification in Spatial Databases, Proc. 6th Int. Symposium on Large Spatial Databases (SSD'99), Hong Kong, China, in: Lecture Notes in Computer Science, Vol. 1651, Springer, 1999, pp. 207-226.
    Paper (pdf 286K)

  41. Backofen R., Bry F., Clote P., Kriegel H.-P., Seidl T., Schulz K.: Aktuelles Schlagwort / Bioinformatik, in: Informatik Spektrum, Vol. 22, No. 5, 1999, pp. 376-378.
    Abstract, Paper (pdf 54K)

  42. Ankerst M., Kastenmüller G., Kriegel H.-P., Seidl T.: Nearest Neighbor Classification in 3D Protein Databases, Proc. 7th Int. Conf. on Intelligent Systems for Molecular Biology (ISMB'99), Heidelberg, Germany, AAAI Press, 1999, pp. 34-43.
    Paper (pdf 179K)

  43. Kastenmüller G., Kriegel H.-P., Seidl T.: Similarity Search in 3D Protein Databases, Proc. German Conf. on Bioinformatics (GCB'98), Köln, 1998.
    Paper (pdf 198K)

  44. Kriegel H.-P., Seidl T.: Approximation-based Similarity Search for 3D Surface Segments, in: GeoInformatica Journal, Kluwer Academic Publishers, Vol. 2, No. 2, 1998, pp. 113-147.
    Abstract (2K)

  45. Kriegel H.-P., Schmidt T., Seidl T.: Biomolekulare Wechselwirkungen von Proteinen -- Datenbankunterstützung für das Proteindocking (Biomolecular Interactions of Proteins -- Database Support for the Protein Docking Problem (in German)), Final Report, BMBF joint project BIOWEPRO, 1997.
    Paper (pdf 113K)

  46. Kriegel H.-P., Schmidt T., Seidl T.: 3D Similarity Search by Shape Approximation, Proc. 5th Int. Symposium on Large Spatial Databases (SSD'97), Berlin, Germany, 1997, pp. 11-28.
    Paper (postscript 1.1 M)

  47. 1996

    Kriegel H.-P., Schmidt T., Seidl T.: Können Proteine im Computer docken? (Can Proteins dock in the Computer? (in German)), in: Einsichten, University of Munich, ISSN-Nr.: 0941-3642, Vol. 2, 1996, pp. 26-29.
    Paper (postscript 488k)

  48. Ester M., Kriegel H.-P., Wirth S.: Feature Based Classification of Protein Docking Sites: An Algorithm for Large Databases and Experimental Results, Proc. German Conf. on Bioinformatics (GCB'96), Leipzig, Germany, 1996, pp. 193-196.
    Paper (postscript 111k)

  49. 1995

    Schomburg D., Jakob U., Meyer M., Wilson P., Sagerer G., Ackermann F., Herrmann G., Posch S., Soumpasis M., Grimm G., Ihmels B., Strahm M., Kriegel H.-P., Seidl T., Schmidt T., Ester M., Xu X.: 'BIOWEPRO' Wechselwirkungen von Proteinen (BIOWEPRO - Biomolecular Interactions of Proteins (in German)), in: BMBF (Editors): Tagungsband BMBF-Statusseminar Bioinformatik "Molekulare Bioinformatik und Evolutionäre Algorithmen" (Proc. of the German Ministry of Science and Technology on Molecular Bioinformatics and Evolutionary algorithms), Braunschweig, Germany, 1995.

  50. Kriegel H.-P., Schmidt T., Seidl T.: Moleküloberflächen in einer objektorientierten Proteindatenbank (Molecular Surfaces in an object-oriented Protein Database (in German)), 3. GI-Fachtagung `Bioinformatik - Informatik in den Biowissenschaften' (GI-Symposium "Computer Science in Biology"), Braunschweig, Germany, 09.-11.10.95, erweiterte Zusammenfassung (extended abstract).
    Extended Abstract (76k)

  51. Ester M., Kriegel H.-P., Seidl T., Xu X.: Formbasierte Suche nach komplementären 3D-Oberflächen in einer Protein-Datenbank (Form-based Retrieval of Complementary 3D Surfaces in a Protein Database (in German)), Proc. 6. GI-Fachtagung Datenbanksysteme in Büro, Technik und Wissenschaft (BTW'95) (6th Int. Conf. on Databases in Office, Engineering and Science), Dresden, Germany, 1995, in: Informatik Aktuell, Springer, 1995, pp. 373-382.
    Abstract, Paper (postscript 607k)

  52. Seidl T., Kriegel H.-P.: Solvent Accessible Surface Representation in a Database System for Protein Docking, Proc. 3rd Int. Conf. on Intelligent Systems for Molecular Biology (ISMB'95), Cambridge, England, 1995, pp. 350-358.
    Abstract, Paper (postscript 613k)

  53. Seidl T., Kriegel H.-P.: A 3D Molecular Surface Representation Supporting Neighborhood Queries, Proc. 4th Int. Symposium on Large Spatial Databases (SSD'95), Portland, ME, 1995, pp. 240-258.
    Abstract, Paper (postscript 770k)

  54. 1994

    Aldinger K., Ester M., Förstner G., Kriegel H.-P., Seidl T.: Datenbankunterstützung für das Protein-Protein-Docking: ein effizienter und robuster Feature-Index (Database Support for the Protein-Protein-Docking: an Efficient and Robust Feature-Index (in German)), Proc. 2. GI-Fachtagung Informatik in den Biowissenschaften (2nd GI-Symposium "Computer Science Biology", Jena, Germany, 1994, pp. 41-52.
    Abstract, Paper (postscript 150k)

  55. Kriegel H.-P., Schneider R.: Entwurf eines Bioindikations-Datenbanksystems (Design of a Bioindication Database System (in German)), Proc. 5th Int. Symposium Informatik für den Umweltschutz, Vienna, Austria, 1990, in: Informatik-Fachberichte, Vol. 256, Springer, pp. 17-26.