Fabian Buchwald, Dipl.-Bioinf.

E-Mail: buchwald@in.tum.de

Research Interests:

Data Mining, Machine Learning, Predictive Toxicology, Bioinformatics, Cheminformatics

Research:

I studied Bioinformatics at Technische Universität München and Ludwig-Maximilians-Universität München. Until August 2011, I worked on my PhD on predictive toxicology in the scientific staff of Prof. Kramer in the Machine Learning and Data Mining in Bioinformatics group.

I worked in the EU FP7 project OpenTox, that had the goal to develop a predictive toxicology framework, that provides a unified access to toxicological data, (Q)SAR models and toxicological information.

Activities:

(Co-)Reviewing

IEEE International Conference on Data Mining (ICDM-2008, 2009)
ACM Symposium on Applied Computing (SAC-2009) Data Mining Track
European Conference on Machine Learning/European Conference on Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD-2008, 2010)
International Conference on Discovery Science (DS-2008)
SAR and QSAR in Environmental Research (2009)
International Workshop on Mining and Learning with Graphs (MLG-2008, 2009)
BMC Bioinformatics (2010)
SIAM International Conference on Data Mining (SDM-2009, 2010)
ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-2011)

Publications:

Alphonse, E, Girschick, T, Buchwald, F, and Kramer, S (2011).
A Numerical Refinement Operator based on Multi-Instance Learning
In: Inductive Logic Programming - 20th International Conference, ILP 2010, ed. by Paolo Frasconi and Francesca A. Lisi, vol. 6489, pp. 14-21, Springer. LNCS/LNAI.

Buchwald, F, Girschick, T, Seeland, M, and Kramer, S (2011).
Using Local Models to Improve (Q)SAR Predictivity
Molecular Informatics, 30(2-3):205-218.

Buchwald, F, Richter, L, and Kramer, S (2011).
Predicting a small molecule-kinase interaction map: A machine learning approach
Journal of Cheminformatics, 3:22.

Hamp, T, Birzele, F, Buchwald, F, and Kramer, S (2011).
Improving Structure Alignment Based Prediction of SCOP Families Using Vorolign Kernels
Bioinformatics, 27(2):204-210.

Buchwald, F, Girschick, T, Frank, E, and Kramer, S (2010).
Fast Conditional Density Estimation for Quantitative Structure-Activity Relationships
In: Proceedings of the 24th AAAI Conference on Artificial Intelligence, pp. 1268-1273, AAAI Press.

Girschick, T, Buchwald, F, Hardy, B, and Kramer, S (2010).
OpenTox: A Distributed REST Approach to Predictive Toxicology
In: Proceedings of the 3rd Workshop on Third-Generation Data Mining: Towards Service-Oriented Knowledge Discovery (SoKD’10) at the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases 2010, ed. by Melanie Hilario, Nada Lavrač, Vid Podpečan, Joost N. Kok, pp. 61-62.

Hardy, B, Douglas, N, Helma, C, Rautenberg, M, Jeliazkova, N, Jeliazkov, V, Nikolova, I, Benigni, R, Tcheremenskaia, O, Kramer, S, Girschick, T, Buchwald, F, Wicker, J, Karwath, A, Gütlein, M, Maunz, A, Sarimveis, H, Melagraki, G, Afantitis, A, Sopasakis, P, Gallagher, D, Poroikov, V, Filimonov, D, Zakharov, A, Langunin, A, Gloriozova, T, Novikov, S, Skvortsova, N, Druzhilovsky, D, Chawla, S, Gosh, I, Ray, S, Patel, H, and Escher, S (2010).
Collaborative Development of Predictive Toxicology Applications
Journal of Cheminformatics, 2(7).

Rückert, U, Girschick, T, Buchwald, F, and Kramer, S (2010).
Adapted Transfer of Distance Measures for Quantitative Structure-Activity Relationships
In: Proceedings of the 13th International Conference on Discovery Science, ed. by B. Pfahringer, G. Holmes, A. Hoffman, vol. 6332, pp. 341-355, Springer. LNCS/LNAI.

Seeland, M, Girschick, T, Buchwald, F, and Kramer, S (2010).
Online Structural Graph Clustering using Frequent Subgraph Mining
In: Proceedings of the European Conference of Machine Learning and Principles and Practice of Knowledge Discovery in Databases, ed. by J.L. Balcazar, F. Bonchi, A.Gionis, M.Sebag, vol. 3, pp. 213-228.

Zimek, A, Buchwald, F, Frank, E, and Kramer, S (2010).
A Study of Hierarchical and Flat Classification of Proteins
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7:563-571.

Edelstein, M, Buchwald, F, Richter, L, and Kramer, S (2009).
Integrating Background Knowledge from Internet Databases into Predictive Toxicology Models
SAR QSAR Environmental Research, 21(1):21-35.

Selected Talks and Tutorials:

Talks:

Integrating Background Knowledge from Internet Databases into Predictive Toxicology Models, at the 5th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Istanbul, Turkey, July 4, 2009
Using Local Models to Improve (Q)SAR Predictivity, at the 18th European Symposium on Quantitative Structure-Activity Relationships, Rhodes, Greece, Sept. 20, 2010

Posters:

Girschick, T, Buchwald, F, Kramer, S (2010), Combining Local and Global Chemical Distance Measures for Quantitative Structure-Activity Relationships, 18th European Symposium on Quantitative Structure-Activity Relationships, Rhodes, Greece
Seeland, M, Girschick, T, Buchwald, F, Kramer, S (2010), Clustering Structure Databases Using Frequent Substructure Mining, 18th European Symposium on Quantitative Structure-Activity Relationships, Rhodes, Greece

Teaching:

Programmierpraktikum Bioinformatik (2006, 2007, 2008)
Proseminar (SS2009)
Hauptseminar Bioinformatik (WS08/09, WS09/10, WS10/11)
Tutor Machine Learning and Data Mining in Bioinformatics (WS09/10)

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