Dr. Markus Bundschus
Ludwig-Maximilians-Universität München
Lehr- und Forschungseinheit für Datenbanksysteme
Oettingenstr. 67
80538 München
Germany
| Email: | bundschu@dbs.ifi.lmu.de |
NEWS
- I will update this page soon ...
- I am now working for Roche. The email above is still valid, please feel free to contact me.
- We have released a new version of the Literature-derived Human Gene-Disease Network. [MORE INFORMATION]
I received my diploma degree in bioinformatics from the Ludwig-Maximilians-Universität München (LMU) and the TU München (TUM) in 2007. In June 2007 I started my Ph.D., which is supervised by Prof.Dr. Hans-Peter Kriegel and Dr. Volker Tresp (Siemens AG, Corporate Technology).
During my diploma thesis I had the great opportunity to get supervised by Dr. Kai Yu, who is now leading a research group at NEC laboratories. Currently I am collaborating with Dr. Volker Tresp, Dr. Mathaeus Dejori, Dr. Shipeng Yu, and Holger Arndt, which I appreciate a lot.
The scope of my Ph.D. thesis will be within THESEUS, a research program initiated by the Federal Ministry of Economy and Technology (BMWi), with the goal of developing a new Internet-based infrastructure in order to better use and utilize the knowledge available on the Internet. In particular, I am involved in developing and applying machine learning algorithms for semantic annotation of text corpora. In addition, I am involved in a use case scenario of THESEUS: Medico. Another research program, I am participating in, is LarKC (Large Knowledge Collider).
Research is a very exciting thing, but I am also quite interested in economics. Especially I am interested in how to build bridges between the industry and research, i.e. how to launch new technologies and companies. Even this can be seen as a kind of science. The New York University Center for Advanced Technology, for example, has the ambition to disseminate new developed technologies.
Machine LearningInformation Retrieval
Bioinformatics
Semantic Web
Text Mining
Document Modeling
Type of publication:
JOUR --- Journal paper
CONF --- Conference paper
BC --- Book chapter
WS --- Workshop paper
O --- Other
| 2010 | ||
| Bauer-Mehren A, Bundschus M , Rautschka M, Mayer MA, Sanz F, Furlong LI: Combination of network topology and pathway analysis to reveal functional modules in human disease. Poster presentation at the 9th European Conference on Computational Biology (ECCB 2010), Ghent Belgium. To appear | O | |
| M. Bundschus, A. Bauer-Mehren, V. Tresp and H-P. Kriegel: Digging for Knowledge with Information Extraction: A Case Study on Human Gene-Disease Associations. In Proc. of the 19th ACM International Conference on Information and Knowledge Management (CIKM 2010), Toronto, Canada . To appear | CONF | |
| Y. Huang, V. Tresp, M. Bundschus and A. Rettinger: Multivariate Structured Prediction for Learning on the Semantic Web In Proc. of the 20th International Conference on Inductive Logic Programming (ILP 2010), Florence, Italy. To appear | CONF | |
| D. Magatti, F. Steinke, M. Bundschus and V. Tresp: Combined Structured and Keyword-Based Search in Textually Enriched Entity-Relationship Graphs In 1st Workshop on Automated Knowledge Base Construction (AKBC 2010), Grenoble, France (2010). To appear | WS | 2009 |
| M. Bundschus, V. Tresp and H-P. Kriegel: Topic Models for Semantically Annotated Document Collections In NIPS workshop: Applications for Topic Models: Text and Beyond (NIPS WS 2009), Vancouver, Canada (2009). [PDF] | WS | |
| M. Bundschus, Sh. Yu, V. Tresp, A. Rettinger, M. Dejori and H-P. Kriegel: Hierarchical Bayesian Models for Collaborative Tagging Systems In Proc. IEEE International Conference on Data Mining (ICDM 2009), Miami, USA (2009). [PDF] | CONF | |
| Volker Tresp, Yi Huang, Markus Bundschus and Achim Rettinger: Scalable Relational Learning for Sparse and Incomplete Domains. In International Workshop on Statistical Relational Learning (SRL 2009). [PDF] | WS | |
| Volker Tresp, Yi Huang, Markus Bundschus and Achim Rettinger: Materializing and Querying Learned Knowledge. In ESWC Workshop on Inductive Reasoning and Machine Learning on the Semantic Web (IRMLES 2009). [PDF] | WS | |
| Holger Arndt, Markus Bundschus and Andreas Naegele: Towards a Next-Generation Matrix Library for Java 33rd Annual IEEE International Computer Software and Applications Conference (COMPSAC 2009). | CONF | |
| 2008 | ||
| Fabian Moerchen, Mathaeus Dejori, Dmitriy Fradkin, Julien Etienne, Bernd Wachmann and Markus Bundschus: Anticipating Annotations and Emerging Trends in Biomedical Literature. In Proc. of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (SIGKDD 2008). | CONF | |
| V. Tresp, M. Bundschus, A. Rettinger, Y. Huang: Towards machine learning on the semantic web. Book chapter in Uncertainty Reasoning for the Semantic Web, Lecture Notes in AI, Springer. Extended version: [PDF] | BC | |
| M. Bundschus, M.Dejori, Sh. Yu, V. Tresp and H-P. Kriegel: Statistical modeling of medical indexing processes for biomedical knowledge information discovery from text. In KDD Workshop on Data Mining in Bioinformatics (BIOKDD '08). [Proc. from the BioKDD site] [PDF] [Supplementary Data] | WS | |
| M. Bundschus, M.Dejori, M. Stetter, V. Tresp and H-P. Kriegel: Extraction of semantic biomedical relations from text using conditional random fields. BMC Bioinformatics 2008, 9:207 | JOUR | |
| 2006 | ||
| M. Bundschus: Entity - and relation extraction from biomedical text corpora. Diploma Thesis 2006. [PDF] | THESIS | |
| 2005 | ||
| M. Bundschus, S. Paradies, M. Siebert, F. Birzele, K. Fundel, R. Küffner, R. Zimmer: Disease-relevant gene clusters derived by joint literature and gene expression analysis., Poster at the German Conference on Bioinformatics (GCB) 2005. [PDF] | O |
The Universal Java Matrix Package (UJMP) is a Java library that provides implementations for sparse and dense matrices, as well as a large number of calculations for linear algebra like multiply, add, subtract. But also more advanced methods like mean, correlation, standard deviation, replacement of missing values or mutual information are supported.
Matrices can be imported from and exported to a large number of file formats, also linking to JDBC databases is supported.
I am part of the UJMP team. The head behind UJMP is Holger Arndt. Please have a look at our UJMP to learn more about the features provided with this package!
